Contacts of the helix formed by residues 10 - 22 (chain C) in PDB entry 2VE7
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 ASN 10 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ARG 3.8 1.2 + - - -
9C TYR* 1.3 74.8 - - - +
11C VAL* 1.3 64.1 + - - +
12C ALA* 3.1 14.4 + - - +
13C GLU* 2.8 58.9 + - - +
14C ILE* 2.9 10.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR 4.0 1.0 + - - -
10C ASN* 1.3 71.5 - - - +
12C ALA* 1.3 63.6 + - - +
14C ILE* 3.0 22.6 + - + +
15C VAL* 3.0 14.9 + - + +
33C LYS* 3.7 42.0 - - + +
36C LEU* 4.1 15.7 - - + +
37C TYR* 3.9 30.3 - - + -
118C SER* 5.0 13.6 + - - +
----------------------------------------------------------
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 ASN* 3.0 11.8 + - - +
11C VAL* 1.3 80.1 - - - +
13C GLU* 1.3 62.8 + - + +
15C VAL* 3.4 10.8 + - - +
16C ILE* 3.6 17.4 + - - +
33C LYS* 3.7 34.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
8C ARG 4.7 0.3 - - - +
9C TYR* 3.3 28.5 - - + -
10C ASN* 2.8 53.6 + - - +
12C ALA* 1.3 70.8 - - + +
14C ILE* 1.3 64.1 - - - +
16C ILE* 3.3 8.4 + - - +
17C HIS* 3.0 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR* 3.5 37.0 - - + +
10C ASN 2.9 12.3 + - - +
11C VAL* 3.0 11.6 + - + +
13C GLU* 1.3 76.9 - - - +
15C VAL* 1.3 63.7 + - - +
17C HIS* 4.8 0.2 - - - -
18C ILE* 3.0 44.6 + - + +
36C LEU* 5.0 7.9 - - + -
118C SER* 3.6 36.3 - - - +
121C LEU* 3.9 19.1 - - + -
122C SER* 3.9 5.4 - - - +
125C ILE* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 3.0 14.6 + - + +
12C ALA 3.7 7.6 - - - +
13C GLU 3.2 0.2 - - - -
14C ILE* 1.3 76.2 - - - +
16C ILE* 1.3 55.6 + - + +
18C ILE* 3.4 2.4 + - - +
19C ARG* 2.8 66.0 + - - +
31C LEU* 3.7 26.4 - - + +
32C THR* 4.0 7.6 - - - +
33C LYS* 3.9 28.7 - - + +
36C LEU* 4.4 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA 3.6 13.4 + - - +
13C GLU* 3.3 11.7 + - - +
15C VAL* 1.3 81.0 - - + +
17C HIS* 1.3 68.9 + - + +
19C ARG* 3.3 24.5 + - + +
20C ASN* 2.9 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR* 3.4 33.7 - + - -
13C GLU* 3.0 34.5 + - + +
14C ILE 4.8 0.2 - - - -
16C ILE* 1.3 84.2 - - + +
18C ILE* 1.3 57.8 + - - +
20C ASN* 3.3 8.1 + - - -
21C LYS* 2.8 37.6 + - + +
125C ILE* 3.6 30.5 - - + -
129C HIS* 3.2 33.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 3.0 38.8 + - + +
15C VAL 3.7 2.7 - - - +
17C HIS* 1.3 72.7 - - - +
19C ARG* 1.3 61.8 + - - +
22C ILE* 2.7 46.7 + - + -
23C LEU* 2.8 35.2 + - + +
31C LEU* 3.6 22.9 - - + -
36C LEU* 5.1 1.3 - - + -
48C ILE* 3.7 29.6 - - + -
121C LEU* 3.9 13.2 - - + -
125C ILE* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL* 2.8 40.2 + - + +
16C ILE* 3.6 25.9 - - + +
18C ILE* 1.3 73.3 - - - +
20C ASN* 1.3 67.0 + - - +
23C LEU 2.9 21.8 - - - +
28C GLY* 2.7 37.8 + - - +
29C LYS* 4.1 11.8 + - - +
31C LEU* 2.8 28.1 + - + -
32C THR* 5.0 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 2.9 32.9 + - - +
17C HIS* 3.6 11.0 + - - +
18C ILE 3.3 0.2 - - - -
19C ARG* 1.3 81.9 - - - +
21C LYS* 1.3 77.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C HIS* 2.8 23.1 + - + +
20C ASN* 1.3 90.8 + - + +
22C ILE* 1.3 63.1 + - + +
23C LEU 5.3 0.2 - - - -
51C ARG* 5.4 0.2 + - - -
55C ILE* 3.2 19.6 - - - +
125C ILE* 5.8 2.9 - - + -
128C ILE* 3.9 26.3 - - + +
129C HIS* 4.3 22.4 - - + +
132C GLU* 2.8 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE* 2.7 35.9 + - + +
20C ASN 3.9 0.6 - - - -
21C LYS* 1.3 84.2 - - + +
23C LEU* 1.3 63.9 + - + +
24C THR* 5.4 0.4 - - - -
48C ILE* 3.8 27.8 - - + +
51C ARG* 2.7 57.2 + - + +
52C ALA* 4.1 6.3 - - + +
55C ILE* 3.9 4.5 - - + -
121C LEU* 6.2 0.7 - - + -
124C ILE* 4.0 16.2 - - + -
125C ILE* 4.8 8.5 - - + -
128C ILE* 3.8 28.3 - - + -
----------------------------------------------------------
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