Contacts of the helix formed by residues 12 - 25 (chain C) in PDB entry 5UWS
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 ASP 12 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 4.3 2.4 - - - +
10C ASP 3.3 6.9 + - - +
11C LEU* 1.3 75.8 - - - +
13C ILE* 1.3 70.1 + - - +
14C ALA* 3.4 16.0 + - - +
15C LEU* 3.0 39.8 + - + +
16C LEU 3.1 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.3 26.3 + - + +
12C ASP* 1.3 72.7 + - - +
14C ALA* 1.3 60.5 + - - +
16C LEU* 2.8 23.1 + - + +
17C ASP* 2.9 27.8 + - - +
53C GLN* 4.3 13.9 - - + +
54C ILE* 4.2 31.0 - - + +
57C PHE* 3.8 20.9 - - + +
58C SER* 3.7 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP* 3.2 13.7 + - - +
13C ILE* 1.3 79.8 - - - +
15C LEU* 1.3 61.9 + - - +
17C ASP* 3.4 7.9 + - - +
18C GLN* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C SER* 4.4 15.0 - - - +
1C MET* 4.5 9.4 - - - +
3C GLY* 3.7 16.2 - - - +
4C ILE* 3.7 32.8 - - + +
12C ASP* 3.0 32.6 + - + +
14C ALA* 1.3 78.5 - - - +
16C LEU* 1.3 63.1 + - - +
18C GLN* 3.4 25.2 + - - +
19C VAL* 3.2 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 3.9 28.6 - - + +
11C LEU* 4.2 13.2 - - + -
12C ASP 3.1 9.5 + - - +
13C ILE* 2.8 14.1 + - + +
15C LEU* 1.3 77.3 - - - +
17C ASP* 1.3 59.6 + - - +
19C VAL* 3.0 6.1 + - - +
20C VAL* 2.9 40.1 + - + +
38C LEU* 4.3 8.1 - - + -
41C PHE* 4.5 15.5 - - + -
54C ILE* 3.5 46.7 - - + -
63C SER* 4.2 15.7 - - - +
66C ILE* 6.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ILE* 2.9 25.8 + - - +
14C ALA* 3.4 8.1 + - - +
15C LEU 3.4 0.2 - - - -
16C LEU* 1.3 77.5 - - - +
18C GLN* 1.3 57.1 + - - +
21C SER* 2.9 35.4 + - - +
58C SER* 3.2 26.4 + - - -
59C THR* 3.7 21.8 + - - +
60C ASN* 3.7 15.7 + - + +
63C SER* 3.3 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0C SER* 5.7 2.6 + - - -
1C MET* 3.7 28.5 - - - +
14C ALA 3.2 12.3 + - - +
15C LEU* 3.4 31.4 - - - +
16C LEU 3.1 0.6 - - - -
17C ASP* 1.3 74.1 - - - +
19C VAL* 1.3 56.9 + - - +
21C SER* 3.3 4.9 + - - -
22C THR* 2.7 45.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
1C MET* 3.8 46.7 - - + +
4C ILE* 4.2 10.8 - - + -
15C LEU* 3.2 16.1 + - + +
16C LEU 3.0 7.7 + - - +
18C GLN* 1.3 75.0 - - - +
20C VAL* 1.3 63.6 + - - +
22C THR 3.2 1.0 + - - -
23C PHE* 3.0 22.3 + - - +
34C ALA* 3.6 22.5 - - + +
37C ILE* 4.1 10.5 - - + -
38C LEU* 3.5 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 2.9 22.1 + - + +
19C VAL* 1.3 76.1 - - - +
21C SER* 1.3 62.3 + - - +
23C PHE* 3.1 2.8 + - - +
24C TYR* 3.0 38.5 + - + -
38C LEU* 3.9 26.5 - - + -
60C ASN* 3.5 14.4 - - - +
62C GLN* 3.3 34.5 - - + +
63C SER* 3.2 27.1 - - - +
66C ILE* 4.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASP* 2.9 20.4 + - - +
18C GLN* 3.8 4.0 - - - -
20C VAL* 1.3 76.0 - - - +
22C THR* 1.3 58.2 + - - +
24C TYR* 5.2 0.2 - - - -
25C GLN* 2.9 44.1 + - - +
26C GLY 3.4 3.6 + - - -
60C ASN* 3.4 13.8 + - - +
62C GLN* 5.8 0.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 4.2 12.1 - - - -
18C GLN* 2.7 40.3 + - - +
19C VAL 3.6 5.4 - - - -
21C SER* 1.3 72.8 - - - +
23C PHE* 1.3 58.0 + - - +
26C GLY* 3.1 26.7 - - - +
30C GLN* 3.4 46.7 - - + +
31C GLN* 3.6 7.8 - - - -
34C ALA* 4.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.2 4.7 - - + -
47A VAL* 5.7 1.8 - - + -
64A TRP* 3.3 36.5 - + - -
75A LEU* 3.6 16.6 - - + -
79A TYR* 3.6 20.4 - + - -
19C VAL 3.0 12.1 + - - +
20C VAL 3.1 6.5 + - - +
22C THR* 1.3 76.5 - - - +
24C TYR* 1.3 89.2 + + - +
31C GLN* 2.6 46.7 + - + +
34C ALA* 3.9 7.8 - - + +
35C GLN* 3.3 38.6 - - + -
38C LEU* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 4.5 5.2 - - - -
64A TRP* 4.2 23.2 - + - -
75A LEU* 4.6 1.0 - - - +
78A GLY* 2.8 35.8 + - - -
81A ILE* 3.5 34.8 - - + +
82A GLN* 5.1 2.7 - - - +
20C VAL* 3.0 38.3 + - + +
23C PHE* 1.3 103.9 - + - +
25C GLN* 1.3 82.4 + - - +
26C GLY 4.4 0.9 - - - +
31C GLN* 4.2 2.4 + - - -
62C GLN* 3.7 26.2 - - + +
66C ILE* 4.1 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLN* 2.9 31.7 + - - +
21C SER* 2.9 22.4 + - - +
24C TYR* 1.3 92.1 + - - +
26C GLY* 1.3 66.8 + - - +
62C GLN* 4.2 10.3 + - - +
----------------------------------------------------------
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