Contacts of the helix formed by residues 10 - 24 (chain C) in PDB entry 4WMJ
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 10 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 3.7 8.3 - - + +
6C ASN 3.3 2.8 + - - -
7C LEU* 2.9 15.8 + - + +
9C GLN* 1.3 77.1 - - - +
11C PRO* 1.3 70.1 - - - +
12C ALA* 2.9 27.7 + - - +
13C TYR* 3.1 12.7 + - + +
14C GLN* 2.9 23.1 + - - +
75C LEU* 3.9 2.3 - - - +
78C SER* 2.8 29.2 + - - +
79C ARG* 3.4 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 5.0 3.6 - - + -
9C GLN 3.6 6.5 - - - +
10C ASP* 1.3 92.7 - - - +
12C ALA* 1.4 56.6 + - - +
14C GLN* 3.4 16.3 + - - +
15C LYS* 3.1 27.4 + - - +
78C SER* 4.5 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASP* 2.9 11.5 + - - +
11C PRO* 1.4 76.4 - - - +
13C TYR* 1.3 66.2 + - - +
15C LYS* 3.3 7.2 + - - +
16C LEU* 3.0 26.4 + - - +
71C LEU* 4.8 2.5 - - - +
74C ASN* 3.7 31.9 - - + +
75C LEU* 3.7 17.7 - - - +
78C SER* 3.8 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 3.2 58.6 - - + +
8C LYS* 2.9 52.8 + - + -
10C ASP* 3.1 12.0 + - + +
12C ALA* 1.3 77.4 - - - +
14C GLN* 1.3 59.9 + - - +
16C LEU* 3.1 12.1 + - + +
17C GLN* 2.9 39.2 + - + +
75C LEU* 3.9 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LYS 3.5 14.1 + - - +
9C GLN* 3.6 31.5 + - - +
10C ASP 2.9 14.1 + - - +
11C PRO* 3.6 23.1 - - + +
12C ALA 3.2 0.2 - - - -
13C TYR* 1.3 74.6 - - - +
15C LYS* 1.3 65.6 + - - +
17C GLN* 3.2 8.7 + - - +
18C GLU* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PRO 3.1 16.2 + - - +
12C ALA* 3.8 7.2 - - - +
13C TYR 3.3 0.2 - - - -
14C GLN* 1.3 78.4 - - - +
16C LEU* 1.3 60.7 + - - +
18C GLU* 3.3 22.0 + - - +
19C TYR* 3.0 24.3 + - - +
71C LEU* 3.5 31.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
12C ALA 3.0 18.2 + - - +
13C TYR* 3.1 12.8 + - + +
15C LYS* 1.3 76.4 - - - +
17C GLN* 1.4 57.1 + - - +
19C TYR* 3.3 4.8 + - + +
20C TYR* 2.9 31.5 + - - +
68C THR* 4.5 9.0 - - + +
71C LEU* 3.5 37.0 - - + +
72C LEU* 3.8 28.5 - - + -
75C LEU* 3.8 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LYS* 4.6 7.4 + - - +
13C TYR* 2.9 32.9 + - + +
14C GLN* 3.2 12.3 + - - +
16C LEU* 1.4 76.5 - - - +
18C GLU* 1.3 58.8 + - - +
20C TYR* 3.3 17.3 + - - +
21C ASP* 2.8 67.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLN 3.0 15.3 + - - +
15C LYS* 3.7 27.3 + - - +
17C GLN* 1.3 78.2 - - - +
19C TYR* 1.3 61.6 + - - +
21C ASP* 3.3 7.7 + - - +
22C ASN* 3.0 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LYS 3.0 17.2 + - - +
16C LEU* 3.7 6.7 - - + +
18C GLU* 1.3 77.7 - - - +
20C TYR* 1.3 60.0 + - + +
22C ASN* 3.2 3.1 + - - +
23C ASN* 2.8 63.0 + - + +
27C ILE* 3.7 23.1 - - + +
65C ASP* 3.0 20.2 + - - -
67C THR* 3.5 29.6 - - + -
68C THR* 2.7 40.6 + - + -
71C LEU* 3.5 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU 2.9 17.9 + - - +
17C GLN* 3.5 16.2 - - - +
19C TYR* 1.3 80.9 - - + +
21C ASP* 1.3 80.2 + - - +
23C ASN 4.4 0.2 - - - +
24C ALA* 2.9 58.9 + - + +
27C ILE* 6.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLN* 2.8 55.9 + - - +
18C GLU* 3.3 7.3 + - - +
20C TYR* 1.3 82.3 - - - +
22C ASN* 1.3 65.5 + - - +
23C ASN 3.7 0.2 + - - -
24C ALA* 5.7 0.2 - - - +
25C ASP* 4.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 3.0 37.1 + - - +
19C TYR* 4.9 1.2 - - - +
21C ASP* 1.3 82.2 - - - +
23C ASN* 1.3 71.3 + - - +
24C ALA 4.1 0.2 - - - -
25C ASP* 4.1 3.1 - - - -
26C LYS* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 2.8 55.5 + - + +
20C TYR* 3.1 0.6 + - - -
22C ASN* 1.3 89.1 + - - +
24C ALA* 1.3 56.5 + - - +
25C ASP* 3.1 4.3 - - - -
26C LYS* 2.8 39.3 + - - +
27C ILE* 3.1 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 2.9 63.9 + - + +
23C ASN* 1.3 72.2 - - - +
25C ASP* 1.3 61.8 + - + +
26C LYS 3.6 0.3 + - - -
27C ILE* 4.2 16.4 + - - +
63C ARG* 5.4 7.4 + - - -
----------------------------------------------------------
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