Contacts of the helix formed by residues 2 - 25 (chain C) in PDB entry 5FN4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 2 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A GLU* 3.5 30.2 + - - -
3C ALA* 1.3 62.8 + - - +
4C ALA* 3.2 2.5 - - - +
5C VAL* 3.2 14.9 + - - +
6C PHE* 2.9 28.1 + - - +
141C ALA 3.8 4.6 - - - +
142C LEU 3.5 22.1 - - - +
143C GLY 4.0 15.0 - - - -
144C PRO* 4.5 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 3 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C GLY* 1.3 74.9 - - - +
4C ALA* 1.3 57.7 + - - +
6C PHE* 3.2 9.3 + - - +
7C PHE* 2.9 36.8 + - + +
142C LEU* 3.8 13.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 4 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A GLU* 4.2 29.4 - - + +
670A LEU* 5.0 2.0 - - - +
673A LEU* 3.8 33.5 - - + +
2C GLY 4.2 0.6 - - - +
3C ALA* 1.3 78.5 - - - +
5C VAL* 1.3 58.5 + - - +
7C PHE* 3.2 5.9 + - - +
8C GLY* 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 5 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A GLU* 3.6 39.9 + - + +
672A THR* 4.1 13.5 - - + +
2C GLY* 3.2 13.9 + - - +
4C ALA* 1.3 80.7 - - - +
6C PHE* 1.3 55.8 + - - +
8C GLY* 3.2 1.6 + - - -
9C CYS* 2.9 51.9 + - - -
141C ALA* 4.2 19.1 - - + +
146C VAL* 5.6 9.6 - - + -
157C PHE* 4.6 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 6 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C GLY 2.9 12.9 + - - +
3C ALA* 3.4 7.2 - - - +
5C VAL* 1.3 78.5 - - - +
7C PHE* 1.3 84.8 + + - +
9C CYS* 4.0 3.3 - - - +
10C THR* 2.9 60.9 + - + +
138C LEU* 3.7 35.7 - - + -
139C ALA* 5.7 0.2 - - - -
141C ALA* 4.9 4.3 - - - -
142C LEU* 3.9 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 7 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A LEU* 4.6 13.5 - - + -
677A PHE* 4.2 13.2 - + - -
3C ALA* 2.9 18.1 + - + +
4C ALA* 3.5 11.0 - - - +
6C PHE* 1.3 102.2 - + - +
8C GLY* 1.3 60.9 + - - +
10C THR* 3.2 6.1 - - + +
11C PHE* 3.0 59.9 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 8 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A THR* 3.7 26.9 - - - -
673A LEU* 3.8 7.5 - - - +
676A GLY* 3.4 13.6 - - - -
4C ALA 2.9 13.3 + - - -
5C VAL 3.2 3.8 + - - -
7C PHE* 1.3 78.9 - - - +
9C CYS* 1.3 56.6 + - - +
11C PHE 3.2 1.4 + - - -
12C VAL* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A THR* 4.3 2.4 - - - +
5C VAL* 2.9 45.0 + - - +
6C PHE* 4.0 3.8 - - - +
8C GLY* 1.3 71.8 - - - +
10C THR* 1.3 58.9 + - - +
12C VAL* 3.2 3.1 + - - -
13C ALA* 2.9 26.0 + - - +
138C LEU* 4.7 13.2 - - + -
141C ALA* 5.0 3.1 - - + -
157C PHE* 3.8 25.6 - - + +
158C LEU* 4.0 20.9 - - - -
161C ALA* 3.1 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 2.9 44.3 + - + +
7C PHE* 3.2 15.0 - - + +
9C CYS* 1.3 77.2 - - - +
11C PHE* 1.3 74.7 + - + +
13C ALA* 3.2 2.6 + - - +
14C PHE* 2.9 41.2 + - - +
138C LEU* 3.3 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A GLY 3.4 20.4 - - - +
677A PHE* 3.5 46.2 - + - -
679A ILE* 3.9 5.1 - - - +
680A LEU* 4.1 31.2 - - + -
7C PHE* 3.0 43.0 + + - +
8C GLY 3.8 0.2 - - - +
10C THR* 1.3 91.8 - - + +
12C VAL* 1.3 58.6 - - - +
15C GLY* 2.6 35.3 + - - +
16C PRO* 3.6 2.1 - - - +
18C PHE* 6.5 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A VAL* 4.3 5.8 - - + -
676A GLY* 3.7 11.0 - - - +
679A ILE* 3.6 25.1 - - + +
8C GLY 2.9 15.7 + - - +
9C CYS* 3.5 8.1 - - - +
11C PHE* 1.3 77.4 - - - +
13C ALA* 1.3 59.7 + - - +
16C PRO* 3.6 9.4 - - - +
158C LEU* 4.3 11.2 - - + +
161C ALA* 3.6 5.6 - - + -
162C PHE* 3.2 62.1 - - + +
165C ALA* 3.0 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C CYS 2.9 13.0 + - - +
10C THR* 3.2 10.5 + - - +
12C VAL* 1.3 81.2 - - - +
14C PHE* 1.3 80.2 + - + +
16C PRO* 4.1 3.1 - - - +
17C ALA* 4.6 1.2 - - - +
134C VAL* 4.4 6.3 - - + -
138C LEU* 4.9 1.3 - - + -
161C ALA* 3.6 17.3 - - + +
164C THR* 4.0 15.9 - - + -
165C ALA* 3.5 8.1 - - - +
168C ILE* 3.1 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C THR* 2.9 25.9 + - - +
13C ALA* 1.3 76.9 - - + +
15C GLY* 1.3 58.2 + - - +
16C PRO* 3.3 3.6 - - - -
17C ALA* 2.7 11.3 + - + +
18C PHE* 2.5 44.3 + - + +
127C ILE* 4.6 6.1 - - + -
131C VAL* 3.5 32.5 - - + -
134C VAL* 3.4 21.1 - - + -
135C ILE* 4.1 14.1 - - + -
138C LEU* 3.8 20.6 - - + -
164C THR* 4.0 9.9 - - + -
168C ILE* 3.6 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LEU* 3.8 23.2 - - - +
683A SER* 3.5 11.1 + - - -
10C THR 3.8 1.0 + - - -
11C PHE* 2.6 30.2 + - - +
14C PHE* 1.3 69.5 - - - +
16C PRO* 1.4 60.5 - - - +
18C PHE* 3.2 5.5 + - - +
19C ALA* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A ILE* 3.9 28.3 - - + +
683A SER* 3.3 17.9 - - - -
11C PHE 3.6 7.6 - - - +
12C VAL 3.6 13.7 - - - +
13C ALA 4.1 2.5 - - - +
14C PHE 3.4 3.6 - - - -
15C GLY* 1.4 88.7 - - - +
17C ALA* 1.3 55.3 + - - +
19C ALA* 3.2 2.8 + - - +
20C LEU* 2.9 39.1 + - + +
165C ALA* 4.8 9.0 - - + +
168C ILE* 6.2 0.2 - - + -
169C LEU* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA 4.6 0.4 + - - +
14C PHE* 2.7 23.5 + - + +
16C PRO* 1.3 76.5 - - - +
18C PHE* 1.3 56.3 - - - +
20C LEU* 3.2 10.8 + - - +
21C PHE* 2.9 29.2 + - - +
123C LEU* 4.6 0.2 - - - -
127C ILE* 3.6 25.4 - - + +
168C ILE* 3.5 34.9 - - + +
169C LEU* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LEU* 5.2 8.3 - - + -
11C PHE* 6.5 0.4 - + - -
14C PHE* 2.5 31.7 + - + +
15C GLY* 3.4 7.0 - - - +
17C ALA* 1.3 73.5 - - - +
19C ALA* 1.3 57.2 + - - +
21C PHE* 3.2 22.0 + + + +
22C LEU* 2.9 59.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LEU* 5.3 1.5 - - + +
683A SER* 3.3 45.3 - - - +
684A LEU* 3.9 20.6 - - + +
687A THR* 4.2 3.1 - - - +
15C GLY 2.9 6.0 + - - +
16C PRO 3.4 6.5 - - - +
18C PHE* 1.3 76.5 - - - +
20C LEU* 1.3 58.6 + - - +
22C LEU* 3.2 6.0 + - - +
23C ILE* 2.9 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A SER* 5.7 0.4 - - - -
687A THR* 3.1 35.4 - - + +
16C PRO* 2.9 27.8 + - + +
17C ALA* 3.2 6.9 + - - +
19C ALA* 1.3 77.5 - - - +
21C PHE* 1.3 53.5 - - - +
24C THR* 2.6 44.1 + - - -
119C TYR* 3.5 21.8 - - + +
123C LEU* 3.7 33.7 - - + -
169C LEU* 4.8 15.9 - - + -
172C THR* 4.8 8.7 - - + +
173C PHE* 5.8 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ALA 2.9 12.9 + - - +
18C PHE* 3.3 25.6 - + + +
20C LEU* 1.3 76.4 - - - +
22C LEU* 1.3 70.7 + - + +
25C VAL* 2.7 59.0 + - + +
26C ALA* 3.0 27.8 + - + -
32C VAL* 5.6 6.5 - - + -
35C LEU* 4.3 22.4 - - + -
123C LEU* 4.0 3.3 - - + +
127C ILE* 5.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A LEU* 4.6 14.8 - - + -
18C PHE* 2.9 49.1 + - + +
19C ALA* 3.2 10.1 + - - +
21C PHE* 1.3 89.5 - - + +
23C ILE* 1.3 67.0 + - + +
26C ALA* 4.3 18.1 + - + +
27C GLY 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A LEU* 3.8 15.3 - - + +
687A THR* 3.6 24.7 - - + +
688A TYR* 3.2 51.4 - - + +
691A ASN* 3.3 44.7 + - + +
19C ALA 2.9 15.5 + - - +
22C LEU* 1.3 86.5 - - + +
24C THR* 1.3 63.5 + - - +
27C GLY 5.6 1.0 + - - -
31C ARG* 4.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A THR* 4.6 2.3 - - - +
691A ASN* 5.8 0.4 - - - -
20C LEU* 2.6 30.1 + - - -
23C ILE* 1.3 81.6 - - - +
25C VAL* 1.3 68.7 + - + +
27C GLY* 4.6 3.3 + - - -
28C ASP 4.9 0.7 + - - -
31C ARG* 2.9 41.9 + - - +
119C TYR* 3.3 46.1 + - + -
120C VAL* 4.7 8.5 - - + -
123C LEU* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE* 2.7 42.8 + - + +
24C THR* 1.3 78.6 - - + +
26C ALA* 1.3 60.5 + - - +
27C GLY 2.9 8.4 + - - -
28C ASP 3.3 20.4 + - - +
31C ARG* 3.9 9.0 - - - +
32C VAL* 3.5 34.3 - - + +
35C LEU* 3.7 28.3 - - + -
120C VAL* 5.1 8.3 - - + -
123C LEU* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il