Contacts of the helix formed by residues 10 - 22 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 1.3 74.1 - - - +
11D VAL* 1.3 65.6 + - - +
12D ALA* 3.3 10.9 + - - +
13D GLU* 2.7 51.9 + - - +
14D ILE* 3.0 21.7 + - - +
118D SER* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASN* 1.3 75.4 - - - +
12D ALA* 1.3 63.9 + - - +
14D ILE* 3.2 9.5 + - + +
15D VAL* 3.0 24.1 + - + +
33D LYS* 3.8 42.0 - - + +
36D LEU* 4.1 18.8 - - + +
37D TYR* 3.6 32.5 - - + -
114D ALA 5.8 0.9 - - - +
118D SER* 4.7 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASN* 3.3 10.4 + - - +
11D VAL* 1.3 80.6 - - - +
13D GLU* 1.3 63.3 + - + +
15D VAL* 3.3 11.6 + - - +
16D ILE* 3.4 19.8 + - + +
33D LYS* 3.7 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ARG 4.4 2.3 - - - +
9D TYR* 3.4 28.2 - - + -
10D ASN* 2.7 59.2 + - - +
12D ALA* 1.3 76.6 - - + +
14D ILE* 1.3 66.9 + - - +
16D ILE* 3.1 10.4 + - - +
17D HIS* 3.0 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 3.2 38.1 - - + +
10D ASN 3.0 14.6 + - - +
11D VAL* 3.4 11.9 - - + +
13D GLU* 1.3 74.7 - - - +
15D VAL* 1.3 63.3 + - - +
17D HIS* 3.3 1.0 + - - -
18D ILE* 2.9 44.3 + - + +
36D LEU* 4.4 7.2 - - + -
118D SER* 3.6 39.0 - - - +
121D LEU* 3.7 21.5 - - + -
122D SER* 3.8 5.4 - - - +
125D ILE* 3.8 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D VAL* 3.0 17.1 + - + +
12D ALA* 3.6 8.3 - - - +
13D GLU 3.2 0.4 - - - -
14D ILE* 1.3 75.3 - - - +
16D ILE* 1.3 58.5 + - + +
18D ILE* 3.1 3.1 + - - +
19D ARG* 2.8 61.9 + - - +
31D LEU* 3.5 31.5 - - + +
32D THR* 4.0 5.8 - - - +
33D LYS* 3.9 28.9 - - + +
36D LEU* 4.4 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ALA* 3.4 14.2 + - + +
13D GLU* 3.1 12.0 + - - +
15D VAL* 1.3 80.7 - - + +
17D HIS* 1.3 66.5 + - + +
19D ARG* 3.7 22.9 - - - +
20D ASN* 3.0 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D TYR* 3.2 36.8 - + - -
13D GLU* 3.0 27.5 + - + +
15D VAL 3.3 0.4 - - - -
16D ILE* 1.3 82.9 - - + +
18D ILE* 1.3 63.3 + - - +
20D ASN* 4.5 8.4 + - - +
21D LYS* 2.8 36.6 + - - +
125D ILE* 3.5 30.0 - - + +
129D HIS* 3.0 35.6 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 2.9 41.0 + - + +
15D VAL 3.7 3.8 - - - +
17D HIS* 1.3 73.8 - - - +
19D ARG* 1.3 60.3 + - - +
22D ILE* 2.8 45.2 + - + +
23D LEU* 2.8 44.1 + - + +
31D LEU* 4.1 9.9 - - + -
36D LEU* 4.5 5.6 - - + -
48D ILE* 4.3 17.3 - - + -
121D LEU* 3.9 24.0 - - + -
125D ILE* 3.7 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D VAL* 2.8 37.0 + - + +
16D ILE* 3.7 22.0 - - + +
18D ILE* 1.3 77.6 - - - +
20D ASN* 1.3 66.4 + - - +
23D LEU* 2.9 27.6 - - - +
28D GLY* 3.0 32.0 + - - +
29D LYS* 4.4 10.8 + - - +
31D LEU* 2.9 25.1 + - + -
32D THR* 4.9 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE* 3.0 31.3 + - - +
17D HIS* 3.9 10.8 + - - +
19D ARG* 1.3 83.0 - - - +
21D LYS* 1.3 78.9 + - + +
23D LEU 4.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D HIS* 2.8 23.2 + - + +
20D ASN* 1.3 89.3 + - + +
22D ILE* 1.3 62.2 + - + +
23D LEU 5.2 0.2 - - - -
55D ILE* 3.5 16.6 - - - +
125D ILE* 5.9 3.1 - - + -
128D ILE* 3.9 24.6 - - + +
129D HIS* 4.1 29.4 - - + +
132D GLU* 3.0 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D ILE* 2.8 37.2 + - + +
19D ARG 4.1 0.2 + - - -
20D ASN 3.8 0.6 - - - -
21D LYS* 1.3 83.7 - - + +
23D LEU* 1.3 63.9 + - + +
24D THR* 5.0 0.4 + - - -
48D ILE* 3.8 24.7 - - + +
51D ARG* 3.0 49.2 + - + +
52D ALA* 3.9 10.8 - - + +
55D ILE* 3.9 6.9 - - + +
121D LEU* 6.0 0.7 - - + -
124D ILE* 4.0 17.9 - - + -
125D ILE* 4.5 8.7 - - + -
128D ILE* 3.7 27.4 - - + -
----------------------------------------------------------
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