Contacts of the helix formed by residues 9 - 25 (chain C) in PDB entry 6CAJ
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 SER 9 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY* 1.3 72.1 - - - +
10C GLU* 1.3 61.4 + - - +
12C SER* 3.9 2.2 - - - -
13C GLU* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY 4.5 0.8 - - - +
9C SER* 1.3 75.8 - - - +
11C LEU* 1.3 65.9 + - + +
13C GLU* 3.3 26.2 - - - +
14C ARG* 2.9 39.2 + - + +
44C GLN* 4.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY* 3.5 27.3 + - - +
9C SER 3.3 0.6 - - - -
10C GLU* 1.3 83.9 - - + +
12C SER* 1.3 57.8 + - - +
14C ARG* 3.8 3.9 - - - +
15C ILE* 2.9 40.9 + - + +
41C LEU* 5.5 2.6 - - + +
44C GLN* 3.4 48.7 - - + +
45C ILE* 4.1 5.8 - - + +
48C ASP* 3.5 27.4 - - + +
49C HIS* 3.7 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B THR* 3.9 12.0 + - - -
8C GLY* 3.1 18.1 + - - -
9C SER* 4.2 2.5 - - - -
11C LEU* 1.3 78.4 - - - +
13C GLU* 1.3 58.1 + - - +
15C ILE* 3.8 11.6 - - - +
16C GLU* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B THR* 4.5 11.7 - - - +
117B LEU* 5.4 8.0 - - + +
9C SER* 2.9 24.2 + - - +
10C GLU* 3.3 29.3 - - - +
12C SER* 1.3 77.0 - - - +
14C ARG* 1.3 56.9 + - - +
16C GLU* 3.4 3.1 + - - +
17C SER* 2.9 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 2.9 26.5 + - - +
11C LEU* 4.0 3.8 - - - +
13C GLU* 1.3 73.5 - - - +
15C ILE* 1.3 61.0 + - - +
17C SER* 3.7 7.8 - - - -
18C PHE* 2.9 35.1 + - + +
37C GLU* 4.2 27.5 + - - +
40C GLY* 4.8 4.2 - - - -
41C LEU* 3.5 43.2 - - + +
44C GLN* 3.2 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 2.9 32.0 + - + +
12C SER* 3.8 9.9 - - - +
14C ARG* 1.3 76.2 - - - +
16C GLU* 1.3 57.7 + - - +
18C PHE* 3.3 4.3 + - - +
19C VAL* 2.9 30.2 + - + +
41C LEU* 3.8 24.7 - - + -
45C ILE* 3.8 31.0 - - + -
49C HIS* 5.7 1.3 - - + +
64C GLU* 4.1 20.9 - - + +
67C ARG* 3.5 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LYS* 4.7 11.9 + - - +
113B ARG* 5.7 2.8 + - - -
115B THR* 3.7 39.2 + - - +
116B SER* 5.6 1.6 - - - -
117B LEU 6.1 0.2 - - - +
329B ASP* 4.3 13.0 - - - +
12C SER 2.9 18.9 + - - +
13C GLU* 3.8 3.8 - - - +
15C ILE* 1.3 76.7 - - - +
17C SER* 1.3 58.1 + - - +
19C VAL* 3.4 7.5 + - - +
20C GLU* 2.9 39.6 + - + +
23C LYS* 5.6 1.4 + - - -
67C ARG* 3.2 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLU* 2.9 19.0 + - - -
14C ARG* 3.7 9.2 - - - -
15C ILE 3.3 0.2 - - - -
16C GLU* 1.3 77.3 - - - +
18C PHE* 1.3 52.2 + - - +
20C GLU* 3.2 18.0 + - - +
21C THR* 2.5 41.7 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
14C ARG* 2.9 23.4 + - + +
15C ILE* 3.7 7.0 - - - +
17C SER* 1.3 75.5 - - - +
19C VAL* 1.3 58.1 + - + +
21C THR* 3.6 5.9 - - + -
22C LEU* 3.0 62.4 + - + +
27C GLY 4.9 3.4 - - - -
34C MET* 4.5 7.0 - - + -
37C GLU* 4.0 34.8 - - + -
38C THR* 4.1 11.9 - - - -
41C LEU* 3.8 17.3 - - + -
68C MET* 3.6 34.3 - - + -
78C VAL* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 2.9 22.6 + - + +
16C GLU* 3.8 7.4 - - - +
17C SER 3.3 0.2 - - - -
18C PHE* 1.3 78.6 - - + +
20C GLU* 1.3 59.3 + - - +
22C LEU* 3.3 4.5 + - - +
23C LYS* 2.9 52.9 + - - +
67C ARG* 3.5 46.9 - - + +
68C MET* 4.2 23.8 - - + -
71C ALA* 3.9 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LYS* 6.1 3.1 - - - +
117B LEU* 5.5 8.4 - - - +
16C GLU* 2.9 30.9 + - + +
17C SER* 3.2 24.0 + - - +
19C VAL* 1.3 77.1 - - - +
21C THR* 1.3 66.1 + - - +
23C LYS* 4.1 11.7 - - + -
24C ARG* 2.9 75.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C SER* 2.5 27.0 + - - -
18C PHE* 3.6 9.6 - - + -
19C VAL 3.3 0.2 - - - -
20C GLU* 1.3 89.6 + - - +
22C LEU* 1.3 59.1 + - - +
24C ARG* 4.5 2.4 - - - +
25C GLY 2.9 27.5 + - - +
27C GLY* 3.5 34.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
18C PHE* 3.0 56.9 + - + +
19C VAL* 3.3 4.5 + - - +
21C THR* 1.3 74.8 - - - +
23C LYS* 1.3 64.1 + - - +
25C GLY 3.8 8.6 - - - +
27C GLY 3.9 16.4 - - - +
34C MET* 4.7 11.2 - - + -
68C MET* 4.2 15.5 - - + +
71C ALA* 4.2 8.7 - - + -
72C GLN* 3.3 35.9 + - + +
75C GLU* 4.6 9.0 - - + -
78C VAL* 3.8 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LYS* 5.1 4.4 - - - +
320B PRO* 4.6 5.0 - - - +
325B ALA* 4.5 22.3 - - + +
326B ASN* 3.5 16.4 + - - +
327B PHE* 4.7 10.2 + - - +
329B ASP* 2.6 38.0 + - - -
16C GLU* 5.6 1.6 + - - -
19C VAL* 2.9 40.9 + - + +
20C GLU* 3.2 11.6 + - + +
22C LEU* 1.3 79.3 - - - +
24C ARG* 1.3 65.8 + - + +
67C ARG* 5.6 1.1 - - - +
70C ALA 5.4 1.1 - - - -
71C ALA* 3.8 30.0 - - + +
72C GLN* 4.5 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 4.3 12.9 + - - +
84B THR* 2.7 53.4 + - - +
85B ALA* 3.5 27.5 + - + +
87B GLY* 6.1 0.2 - - - -
117B LEU* 5.9 5.3 - - - +
319B TYR* 4.9 7.3 + - - -
320B PRO* 3.3 34.1 - - + +
20C GLU* 2.9 49.6 + - + +
21C THR* 4.5 2.7 - - - +
22C LEU 4.7 0.2 - - - -
23C LYS* 1.3 82.2 - - + +
25C GLY* 1.3 59.5 + - - +
72C GLN* 5.4 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B TYR* 5.8 1.8 - - - -
21C THR 2.9 17.8 + - - +
22C LEU* 3.8 12.2 - - - +
24C ARG* 1.3 81.9 - - - +
26C GLY* 1.3 61.1 + - - -
27C GLY 3.4 1.9 + - - -
72C GLN* 5.0 5.9 + - - +
287C LYS* 6.3 0.4 - - - -
----------------------------------------------------------
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