Contacts of the helix formed by residues 3 - 17 (chain A) in PDB entry 3V6A
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 THR 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 1.3 85.3 - - + +
4A VAL* 1.3 66.4 + - - +
5A GLU* 4.1 8.9 - - - +
6A GLU* 3.3 27.2 + - - +
7A LEU* 3.0 25.1 + - - +
41A GLU* 4.1 8.5 - - - +
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Residues in contact with VAL 4 (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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3A THR* 1.3 73.5 - - - +
5A GLU* 1.3 62.7 + - + +
7A LEU* 3.3 4.5 + - - +
8A TYR* 2.9 49.0 + - + -
40A LYS* 3.9 32.1 - - + +
41A GLU* 3.8 23.7 + - + +
44A LEU* 4.0 17.4 - - + +
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Residues in contact with GLU 5 (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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3A THR* 3.2 7.0 - - - +
4A VAL* 1.3 84.5 - - + +
6A GLU* 1.3 59.0 + - + +
8A TYR* 3.5 8.6 + - - +
9A ARG* 3.0 36.6 + - + +
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Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 4.6 11.4 - - - +
3A THR* 3.2 23.3 + - - +
5A GLU* 1.3 80.6 - - + +
7A LEU* 1.3 60.1 + - + +
9A ARG* 3.4 30.0 + - - +
10A ASN* 2.9 46.0 + - - +
30A VAL* 4.0 21.9 - - + +
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Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PRO* 5.3 2.7 - - + -
3A THR 3.0 24.5 + - - +
4A VAL 3.3 4.5 + - - +
6A GLU* 1.3 77.9 - - - +
8A TYR* 1.3 56.6 + - - +
10A ASN* 3.4 2.7 + - - +
11A TYR* 2.9 29.8 + - - +
30A VAL* 3.8 13.7 - - + +
31A ILE* 3.8 40.2 - - + +
34A GLY* 4.2 10.1 - - - -
41A GLU* 3.8 41.3 - - + +
44A LEU* 4.1 18.4 - - + -
45A ALA* 5.1 2.7 - - + +
48A PHE* 4.0 11.5 - - + -
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Residues in contact with TYR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 2.9 38.9 + - + +
5A GLU* 3.8 7.0 - - - +
7A LEU* 1.3 75.8 - - - +
9A ARG* 1.3 58.8 + - - +
11A TYR* 3.2 9.6 + + + +
12A GLY* 2.9 26.7 + - - -
44A LEU* 3.7 38.4 - - + +
48A PHE* 4.2 12.8 - + - -
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Residues in contact with ARG 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU* 3.0 27.4 + - - +
6A GLU* 3.4 36.8 + - - +
7A LEU 3.2 0.4 - - - -
8A TYR* 1.3 77.0 - - - +
10A ASN* 1.3 73.7 + - - +
12A GLY* 3.4 3.2 + - - -
13A ILE* 3.1 41.6 + - + +
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Residues in contact with ASN 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 GLU* 2.9 29.9 + - - +
7A LEU 3.9 2.5 - - - +
9A ARG* 1.3 84.3 + - - +
11A TYR* 1.3 62.5 + - - +
13A ILE* 3.3 23.3 + - - +
14A LEU* 3.1 27.4 + - - +
27A ALA* 3.5 25.1 - - + +
30A VAL* 2.6 46.0 - - + +
31A ILE* 4.2 7.4 - - + -
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Residues in contact with TYR 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 LEU 2.9 15.6 + - - +
8A TYR* 3.3 13.0 - + - +
10A ASN* 1.3 74.3 - - - +
12A GLY* 1.3 63.9 + - - +
14A LEU* 3.2 3.8 + - - +
15A ALA* 2.9 36.4 + - + +
31A ILE* 4.1 8.2 - - - +
48A PHE* 3.4 48.2 - + + -
51A LYS* 3.2 42.7 + - + +
52A PHE* 3.6 16.5 - + - -
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Residues in contact with GLY 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 TYR 2.9 14.0 + - - -
9A ARG* 3.7 4.0 - - - -
10A ASN 3.3 0.2 - - - -
11A TYR* 1.3 82.8 - - - +
13A ILE* 1.3 55.5 + - - +
15A ALA* 3.2 3.1 + - - -
16A ASP* 2.9 46.7 + - - +
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Residues in contact with ILE 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 ARG* 3.1 32.2 + - + +
10A ASN* 3.4 30.1 - - - +
11A TYR 3.2 0.2 - - - -
12A GLY* 1.3 75.9 - - - +
14A LEU* 1.3 62.4 + - - +
16A ASP* 4.1 2.9 - - - +
17A ALA* 3.2 24.1 + - - +
24A HIS* 3.9 32.3 - - + +
26A ASP* 5.7 0.2 - - - +
27A ALA* 4.3 10.3 - - + -
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Residues in contact with LEU 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 ASN 3.1 12.7 + - - +
11A TYR 3.7 3.4 - - - +
13A ILE* 1.3 78.9 - - - +
15A ALA* 1.3 63.7 + - - +
17A ALA* 3.8 3.9 + - - -
21A VAL* 3.1 33.6 - - + +
24A HIS* 3.6 38.8 - - + +
27A ALA* 3.8 5.6 - - + -
28A TYR* 3.9 20.2 - - + +
31A ILE* 3.5 30.5 - - + -
52A PHE* 3.6 34.5 - - + -
56A PHE* 3.9 14.6 - - + -
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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
----------------------------------------------------------
11A TYR* 2.9 34.0 + - + +
12A GLY* 3.8 4.9 - - - +
14A LEU* 1.3 78.0 - - - +
16A ASP* 1.3 66.1 + - - +
18A THR* 3.3 20.3 + - - +
51A LYS* 5.5 2.9 - - - -
52A PHE* 4.0 12.3 - - + -
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Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY* 2.9 27.2 + - - +
13A ILE* 4.4 3.1 - - - +
15A ALA* 1.3 75.3 - - - +
17A ALA* 1.3 65.1 + - - +
18A THR* 3.1 14.9 + - - +
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Residues in contact with ALA 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 ILE 3.2 19.6 + - - +
14A LEU 3.9 6.1 - - - +
15A ALA 3.3 0.6 - - - -
16A ASP* 1.3 72.5 - - - +
18A THR* 1.3 74.9 + - - +
19A GLU* 2.9 2.9 + - - +
20A GLN* 2.9 19.7 + - + +
21A VAL* 3.9 13.2 - - - +
24A HIS* 3.7 29.4 - - + +
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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