Contacts of the helix formed by residues 3 - 19 (chain A) in PDB entry 5VXA
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 SER 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A GLY* 1.3 76.5 - - - -
4A GLU* 1.3 67.7 + - - +
5A ALA* 3.9 3.5 - - - +
6A ALA* 3.2 23.8 + - - +
7A GLN* 3.0 22.8 + - - +
4B GLU* 3.3 16.8 + - - -
44B THR* 5.2 0.2 - - - +
49B ILE 5.2 0.5 + - - -
50B THR* 4.0 30.6 - - - +
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Residues in contact with GLU 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 1.3 72.0 - - - +
5A ALA* 1.3 64.7 + - - +
7A GLN* 3.2 13.8 + - - +
8A LEU* 2.9 22.4 + - - +
50A THR* 3.8 19.7 - - - +
52A ILE* 3.5 23.8 - - + +
3B SER* 4.5 5.5 - - - -
4B GLU* 3.5 22.8 + - + +
5B ALA* 3.4 30.9 + - + +
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Residues in contact with ALA 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A SER* 3.9 3.1 - - - +
4A GLU* 1.3 76.3 - - - +
6A ALA* 1.3 58.2 + - - +
8A LEU* 3.1 3.1 + - - -
9A LEU* 2.9 28.9 + - - +
4B GLU* 3.1 29.1 + - + +
8B LEU* 3.3 31.7 - - + +
50B THR 5.2 0.2 - - - +
52B ILE* 4.7 0.9 - - + -
55B LEU* 3.7 25.6 - - + -
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A GLY* 4.7 5.8 - - - +
3A SER* 3.2 26.1 + - - +
5A ALA* 1.3 78.4 - - - +
7A GLN* 1.3 57.2 + - + +
9A LEU* 3.3 1.7 + - - +
10A GLU* 2.9 35.5 + - + +
44B THR* 3.7 35.6 + - + +
45B HIS* 6.1 0.7 - - - -
49B ILE 5.6 0.7 - - - +
50B THR* 6.2 0.7 - - + -
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Residues in contact with GLN 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLY 3.6 26.2 - - - +
3A SER 3.0 23.0 + - - +
4A GLU* 3.5 12.7 + - - +
6A ALA* 1.3 75.2 - - - +
8A LEU* 1.3 62.1 + - - +
10A GLU* 3.4 7.8 + - - +
11A ALA 3.3 12.5 + - - -
52A ILE* 3.7 30.6 - - + +
56A GLN* 3.0 36.1 + - - +
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Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLU 2.9 10.6 + - - +
5A ALA 3.1 6.9 + - - +
7A GLN* 1.3 77.3 - - - +
9A LEU* 1.3 58.8 + - - +
11A ALA* 3.1 3.2 + - - -
12A ALA* 2.8 29.8 + - - +
52A ILE* 3.6 22.9 - - + -
55A LEU* 3.8 22.7 - - + -
56A GLN* 4.3 6.3 - - + +
59A LEU* 3.6 22.8 - - + +
5B ALA* 3.6 45.1 - - + +
8B LEU* 4.0 13.5 - - + -
9B LEU* 4.0 19.3 - - + -
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA 2.9 16.2 + - - +
6A ALA 3.9 4.0 - - - +
8A LEU* 1.3 72.2 - - - +
10A GLU* 1.3 60.9 + - - +
12A ALA* 4.2 11.4 - - + -
13A ASP* 2.9 33.8 + - - +
8B LEU* 3.6 25.8 - - + -
12B ALA* 6.1 1.6 - - + -
37B ILE* 4.4 9.2 - - + +
40B ALA* 3.8 33.4 - - + +
41B ARG* 3.9 9.3 - - + +
44B THR* 3.6 36.8 - - + +
55B LEU* 4.6 3.8 - - + -
59B LEU* 4.3 17.0 - - + -
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 2.9 21.0 + - + +
7A GLN* 3.5 11.7 - - - +
8A LEU 3.2 0.2 - - - -
9A LEU* 1.3 75.5 - - - +
11A ALA* 1.3 57.5 + - - +
13A ASP* 4.0 1.2 - - - +
14A PHE* 3.0 30.1 + - - +
17A ARG* 5.7 0.2 + - - -
56A GLN* 5.0 0.7 - - - +
78A PHE* 3.8 16.3 - - + -
203A EDO 3.5 19.6 + - - +
41B ARG* 2.7 51.6 + - - +
44B THR* 4.9 1.0 + - - -
45B HIS* 3.5 18.7 + - - +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLN 3.3 1.6 + - - -
8A LEU 3.1 8.1 + - - +
10A GLU* 1.3 79.2 - - - +
12A ALA* 1.3 59.5 + - - +
14A PHE* 3.7 1.0 - - - +
15A ALA* 2.9 31.4 + - - +
56A GLN* 3.8 29.8 - - + -
59A LEU* 3.8 16.3 - - + +
60A LEU* 3.8 14.2 - - + +
78A PHE* 3.7 17.6 - - + -
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU 2.8 20.9 + - - +
9A LEU* 4.0 12.3 - - + +
11A ALA* 1.3 73.2 - - - +
13A ASP* 1.3 58.4 + - - +
15A ALA* 3.4 3.0 + - - +
16A ALA* 2.8 30.3 + - - +
33A ILE* 4.4 3.7 - - - +
37A ILE* 5.5 3.8 - - + -
59A LEU* 3.7 23.0 - - + +
9B LEU* 6.2 1.3 - - + -
12B ALA* 6.0 5.4 - - + -
37B ILE* 4.1 21.2 - - + +
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU 2.9 19.0 + - - +
10A GLU 4.1 1.8 - - - +
12A ALA* 1.3 72.9 - - - +
14A PHE* 1.3 65.0 + - - +
16A ALA* 3.4 3.0 + - - +
17A ARG* 3.1 59.7 + - - +
34B ASN 5.0 1.4 - - - +
37B ILE* 3.7 14.0 - - + +
38B GLY* 3.6 24.9 + - - -
41B ARG* 3.8 32.1 + - + +
125B TYR* 5.6 0.9 - - - -
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Residues in contact with PHE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU 3.0 20.4 + - - +
11A ALA 3.7 3.4 - - - +
13A ASP* 1.3 78.0 + - - +
15A ALA* 1.3 62.1 + - - +
17A ARG* 3.3 25.4 + - - +
18A LYS* 3.0 59.1 + - + +
60A LEU* 3.5 22.7 - - + -
63A THR* 4.5 4.9 - - + -
69A THR* 3.9 18.8 - - + -
73A GLU* 3.8 26.2 - - + -
74A VAL* 5.1 3.1 - - + -
77A HIS* 4.1 27.1 - + - -
78A PHE* 3.8 21.5 - + + -
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 2.9 17.8 + - - +
12A ALA* 3.9 2.7 - - - +
14A PHE* 1.3 77.3 - - - +
16A ALA* 1.3 63.0 + - - +
18A LYS 3.2 0.3 + - - -
19A HIS* 2.9 36.8 + - + +
33A ILE* 3.7 16.4 - - + -
59A LEU* 3.4 27.1 - - + +
60A LEU* 4.4 1.3 - - + -
63A THR* 4.1 17.3 - - + -
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA 2.8 20.2 + - - +
13A ASP* 3.6 9.2 - - - +
14A PHE 3.3 0.2 - - - -
15A ALA* 1.3 76.1 - - - +
17A ARG* 1.3 62.8 + - + +
19A HIS* 3.5 1.4 + - - +
20A ARG* 3.1 18.2 + - - -
33A ILE* 3.5 21.8 - - + +
34B ASN* 3.3 34.5 + - + +
37B ILE* 4.3 14.4 - - + -
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Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASP* 3.1 45.8 + - - +
14A PHE* 3.7 29.2 + - - +
15A ALA 3.2 0.2 - - - -
16A ALA* 1.3 78.0 - - + +
18A LYS* 1.3 68.4 + - + +
20A ARG* 2.7 47.2 + - - +
203A EDO 5.8 1.2 + - - -
34B ASN* 4.4 4.9 - - - +
41B ARG* 5.0 11.7 - - - +
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PHE* 3.0 53.2 + - + +
15A ALA 3.8 3.6 - - - +
17A ARG* 1.3 86.1 - - + +
19A HIS* 1.3 59.9 + - + +
20A ARG* 3.3 6.1 + - - +
21A GLN 5.0 0.7 + - - -
22A GLN* 4.4 2.1 - - - +
63A THR* 4.3 10.3 - - + -
67A THR* 3.3 24.7 - - + +
68A ASP* 3.8 19.0 + - - +
69A THR* 3.3 26.8 + - - +
73A GLU* 3.2 27.7 + - - -
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Residues in contact with HIS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 2.9 36.8 + - + +
16A ALA 3.7 2.7 - - - +
18A LYS* 1.3 74.1 - - - +
20A ARG* 1.3 64.3 + - - +
21A GLN 3.2 2.7 - - - -
22A GLN* 2.7 49.7 + - - +
32A TYR* 3.4 31.2 + + + +
33A ILE* 4.2 21.7 + - + +
36A PRO* 4.1 12.4 - - + +
59A LEU 5.0 0.4 + - - -
62A ASP* 3.6 29.7 + - + +
63A THR* 3.8 22.5 + - + +
66A LYS* 4.4 1.6 - - + -
67A THR* 4.0 5.0 - - + +
31B PRO* 5.3 0.7 - - - +
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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
------------------------------------------------------------
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