Contacts of the helix formed by residues 3 - 16 (chain D) in PDB entry 2AXV
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 LYS 3 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D PHE* 1.3 71.5 - - + +
4D ILE* 1.3 61.4 + - - +
6D SER* 2.9 21.6 + - - +
7D VAL* 3.1 20.6 - - + +
10D GLN* 6.1 0.4 - - - +
38D ASP* 2.8 20.6 - - - +
64D ARG 3.2 24.1 + - - -
65D ALA* 3.4 18.9 + - - +
66D GLY* 4.8 3.6 - - - +
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Residues in contact with ILE 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 3.8 37.5 - - + -
2D PHE* 3.3 14.9 + - - +
3D LYS* 1.3 73.6 - - - +
5D GLY* 1.3 59.8 + - - +
7D VAL* 3.0 4.7 + - - +
8D LEU* 2.9 35.8 + - + +
38D ASP* 3.2 1.8 + - - -
42D ILE* 3.9 18.6 - - + -
47D LEU* 3.7 26.9 - - + -
61D ILE* 4.4 8.5 - - + -
62D LEU* 4.0 16.4 - - + -
65D ALA* 3.6 22.9 - - + -
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Residues in contact with GLY 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LYS 3.3 1.2 - - - -
4D ILE* 1.3 79.8 - - - +
6D SER* 1.3 56.7 + - - +
8D LEU* 3.2 13.2 + - - +
9D LYS* 2.9 25.6 + - - +
35D VAL* 3.4 19.9 + - - +
36D GLU* 3.3 15.7 - - - +
38D ASP* 3.2 14.3 + - - -
42D ILE* 5.7 1.0 - - - +
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Residues in contact with SER 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LYS* 2.9 27.6 + - - +
5D GLY* 1.3 73.1 - - - +
7D VAL* 1.3 58.8 + - - +
9D LYS* 3.3 10.6 + - - +
10D GLN* 2.9 28.9 + - - +
36D GLU 4.1 4.7 - - - -
38D ASP* 2.9 18.6 + - - -
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Residues in contact with VAL 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LYS* 3.1 27.6 - - + +
4D ILE* 3.0 6.4 + - - +
6D SER* 1.3 75.9 - - - +
8D LEU* 1.3 64.9 + - - +
10D GLN* 3.4 17.5 + - - +
11D ILE* 3.0 49.1 + - + +
61D ILE* 4.0 13.0 - - + -
64D ARG* 3.8 28.3 - - + +
65D ALA* 3.5 26.0 - - + +
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Residues in contact with LEU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 2.9 33.6 + - + +
5D GLY* 3.4 13.5 - - - +
7D VAL* 1.3 76.8 - - - +
9D LYS* 1.3 55.9 + - - +
11D ILE* 3.8 4.3 - - - +
12D ARG* 2.8 32.0 + - - +
22D LEU* 5.4 1.3 - - + -
32D TYR* 4.6 13.2 - - + +
35D VAL* 4.5 7.9 - - + -
36D GLU* 4.4 4.0 - - + +
42D ILE* 4.1 22.0 - - + -
47D LEU* 4.1 12.8 - - + -
50D PHE* 4.0 22.7 - - + -
54D LEU* 3.8 27.4 - - + +
61D ILE* 4.6 9.0 - - + -
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Residues in contact with LYS 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D GLY 2.9 11.7 + - - +
6D SER* 3.4 13.0 - - - +
8D LEU* 1.3 76.1 - - - +
10D GLN* 1.3 57.5 + - - +
12D ARG* 3.0 4.4 + - - +
13D GLN* 2.9 63.3 + - - +
19D GLN* 6.2 0.2 - - - +
36D GLU* 3.5 42.7 + - + +
37D ALA* 6.0 1.4 - - - +
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Residues in contact with GLN 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C THR* 4.0 28.0 + - - +
149C PHE* 5.4 5.7 - - - -
3D LYS* 6.1 0.4 - - - +
6D SER 2.9 16.4 + - - +
7D VAL* 3.6 23.7 + - - +
9D LYS* 1.3 74.2 - - - +
11D ILE* 1.3 62.4 + - - +
13D GLN* 3.5 6.8 + - - +
14D GLU* 2.9 30.4 + - + +
64D ARG* 5.4 8.6 + - - +
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Residues in contact with ILE 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C PHE* 3.7 25.6 - - + -
7D VAL* 3.0 40.6 + - + +
8D LEU* 3.8 4.3 - - - +
10D GLN* 1.3 75.1 - - - +
12D ARG* 1.3 68.1 + - - +
14D GLU* 3.3 6.8 + - - +
15D LEU* 3.1 42.9 + - + +
54D LEU* 3.6 18.4 - - + -
56D VAL* 3.8 20.4 - - + -
61D ILE* 3.8 28.5 - - + -
64D ARG* 5.0 2.9 - - - -
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Residues in contact with ARG 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU 2.8 19.0 + - - +
9D LYS* 3.3 7.3 - - - +
11D ILE* 1.3 79.0 - - - +
13D GLN* 1.3 94.8 + - - +
15D LEU* 3.1 2.4 + - - +
16D ASN 3.0 17.2 + - - -
17D TYR* 3.1 40.2 + - + +
18D HIS* 3.8 16.0 - - - +
19D GLN* 3.2 37.4 - - - +
22D LEU* 3.8 14.1 - - + -
32D TYR* 3.8 9.9 - - - +
36D GLU* 2.9 48.2 + - - -
54D LEU* 3.7 9.9 - - + -
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Residues in contact with GLN 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LYS* 2.9 44.1 + - - +
10D GLN* 4.0 5.3 - - - +
12D ARG* 1.3 107.0 + - - +
14D GLU* 1.3 68.9 + - - +
16D ASN* 3.0 24.3 + - - +
17D TYR 4.7 2.9 - - - +
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Residues in contact with GLU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LYS 5.0 5.0 - - - +
145C ARG* 3.1 38.1 + - - +
146C THR* 2.8 40.6 + - - +
147C THR* 3.2 28.7 + - - +
149C PHE* 3.8 9.0 - - + -
10D GLN* 2.9 20.1 + - + +
11D ILE* 3.5 9.6 - - - +
12D ARG 3.2 0.2 - - - -
13D GLN* 1.3 79.0 - - - +
15D LEU* 1.3 63.5 + - + +
16D ASN* 3.3 12.5 + - - -
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LEU* 3.6 22.0 - - + -
145C ARG* 3.7 33.7 - - - +
149C PHE* 3.9 3.8 - - + -
11D ILE* 3.1 35.8 + - + +
12D ARG 3.1 1.0 + - - -
13D GLN 3.1 0.4 - - - -
14D GLU* 1.3 88.7 - - + +
16D ASN* 1.3 73.2 + - - +
17D TYR* 3.3 27.4 + - + -
54D LEU* 3.7 22.0 - - + +
56D VAL* 4.3 6.7 - - + -
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Residues in contact with ASN 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C LYS* 5.2 9.1 + - - +
145C ARG* 5.9 1.0 - - - +
12D ARG 3.0 0.6 + - - -
13D GLN* 3.0 16.5 + - - +
14D GLU 3.5 13.5 + - - -
15D LEU* 1.3 81.7 + - - +
17D TYR* 1.3 65.7 + - - +
18D HIS* 5.0 8.7 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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