Contacts of the helix formed by residues 4 - 26 (chain A) in PDB entry 3VOR
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 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 3.4 8.6 + - - -
3A ASP* 1.3 74.4 - - - +
5A ARG* 1.3 62.1 + - - +
6A THR* 3.7 7.4 + - - -
7A VAL* 3.2 35.4 + - - +
8A SER* 3.1 24.5 + - - -
105A GLN* 5.0 3.1 + - - -
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Residues in contact with ARG 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 1.3 71.2 + - - +
6A THR* 1.3 71.4 + - + +
8A SER* 4.9 2.5 - - - -
9A GLU* 3.2 62.8 + - + +
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Residues in contact with THR 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 3.7 6.9 + - - -
5A ARG* 1.3 87.6 - - + +
7A VAL* 1.3 61.8 + - - +
9A GLU* 4.3 6.5 - - - +
10A LEU* 3.1 23.6 + - - +
71A GLY* 3.6 27.0 + - - +
72A ILE* 3.1 33.8 + - - +
105A GLN* 4.1 6.6 + - - -
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 3.2 27.2 + - - +
6A THR* 1.3 76.1 + - - +
8A SER* 1.3 59.4 + - - +
10A LEU* 3.0 5.4 + - - +
11A VAL* 2.9 27.4 + - - +
72A ILE* 3.5 22.2 - - + -
105A GLN* 3.6 26.0 - - + +
108A SER* 3.6 24.9 - - - +
109A ILE* 3.8 19.5 - - + -
112A GLN* 3.9 10.8 - - - +
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Residues in contact with SER 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 3.1 17.4 + - - -
5A ARG* 4.2 3.6 - - - -
7A VAL* 1.3 78.6 - - - +
9A GLU* 1.3 60.8 + - - +
11A VAL* 3.3 9.3 + - - +
12A THR* 3.0 32.1 + - - -
112A GLN* 4.9 7.3 + - - +
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Residues in contact with GLU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 3.2 54.1 + - + +
6A THR* 4.3 5.5 - - - +
8A SER* 1.3 81.0 + - - +
10A LEU* 1.3 60.1 + - - +
12A THR* 3.4 6.8 + - - +
13A ASN* 2.9 39.0 + - - +
71A GLY* 6.1 1.4 - - - -
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR 3.1 17.0 + - - +
7A VAL 3.0 5.6 + - - +
9A GLU* 1.3 76.3 - - - +
11A VAL* 1.3 67.4 + - - +
13A ASN* 3.1 7.8 + - + +
14A THR* 3.0 25.9 + - + +
69A ARG 4.2 2.0 - - - +
70A ASN* 3.7 43.3 - - + +
71A GLY 5.4 0.9 - - - +
72A ILE* 4.1 9.4 - - + -
77A ILE* 3.8 27.6 - - + -
98A LEU* 4.1 23.3 - - + -
101A LEU* 4.4 3.4 - - + -
109A ILE* 3.9 24.5 - - + -
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Residues in contact with VAL 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL 2.9 15.8 + - - +
8A SER 3.3 7.8 + - - +
10A LEU* 1.3 77.1 - - - +
12A THR* 1.3 66.6 + - - +
14A THR* 2.7 27.2 + - - -
15A ASN* 3.5 14.4 + - - +
109A ILE* 4.1 20.6 - - + -
112A GLN* 3.7 45.8 - - + +
113A VAL* 3.7 24.2 - - + -
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Residues in contact with THR 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 3.0 19.9 + - - -
9A GLU* 3.8 7.0 - - - -
10A LEU 3.3 0.2 - - - -
11A VAL* 1.3 77.3 - - - +
13A ASN* 1.3 66.2 + - - +
15A ASN* 3.0 16.4 + - + +
16A THR* 3.0 31.4 + - - +
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Residues in contact with ASN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 2.9 24.8 + - - +
10A LEU* 3.1 10.4 + - - +
12A THR* 1.3 79.9 - - - +
14A THR* 1.3 63.2 + - - +
16A THR* 4.3 6.3 + - - -
17A ILE* 2.8 30.8 + - - +
66A ASP* 3.2 17.9 + - - +
67A GLU* 3.2 34.2 + - - +
69A ARG 2.9 25.7 + - - -
77A ILE* 4.3 9.9 - - + -
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Residues in contact with THR 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.0 22.1 + - + +
11A VAL* 2.7 19.6 + - - +
13A ASN* 1.3 75.7 - - - +
15A ASN* 1.3 61.7 + - - +
18A ARG* 3.1 27.5 + - - +
77A ILE* 5.7 0.7 - - + -
96A MET* 3.6 29.9 - - + +
98A LEU* 4.0 37.5 - - + -
109A ILE* 5.8 0.4 - - + -
113A VAL* 4.0 14.7 - - + +
117A TRP* 4.0 5.6 + - - -
179A LEU* 4.2 9.9 - - + +
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Residues in contact with ASN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.7 20.5 + - - +
12A THR* 3.0 15.3 + - + +
14A THR* 1.3 81.5 + - - +
16A THR* 1.3 66.3 + - - +
18A ARG* 3.2 26.4 + - - +
19A VAL* 3.0 30.1 + - + +
113A VAL* 5.3 4.3 - - - +
116A ASN* 5.7 2.6 + - - +
117A TRP* 4.9 1.9 + - - -
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Residues in contact with THR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 3.0 26.7 + - - +
13A ASN* 3.7 8.2 + - - -
15A ASN* 1.3 76.9 - - - +
17A ILE* 1.3 62.1 + - - +
19A VAL* 3.4 7.4 + - - +
20A ALA* 3.1 21.8 + - - +
62A LYS 5.4 2.9 - - - +
63A LEU* 3.9 12.8 - - + -
67A GLU* 3.8 34.5 + - + +
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Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN 2.8 20.7 + - - +
14A THR 3.9 3.1 - - - +
16A THR* 1.3 73.3 - - - +
18A ARG* 1.3 59.9 + - - +
20A ALA* 3.1 6.7 + - - +
21A MET* 2.8 37.9 + - + +
54A VAL* 4.7 4.7 - - + -
57A LEU* 4.5 3.8 - - + -
63A LEU* 4.0 15.9 - - + -
67A GLU 3.6 22.9 - - - +
68A ALA* 4.4 4.5 - - - -
77A ILE* 3.6 30.5 - - + -
79A ILE* 3.6 25.6 - - + -
94A PHE* 5.5 1.1 - - + -
96A MET* 3.8 20.6 - - + -
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR 3.1 19.3 + - - +
15A ASN* 3.2 21.7 + - - +
17A ILE* 1.3 77.1 - - - +
19A VAL* 1.3 67.6 + - - +
21A MET* 3.4 1.6 + - - +
22A LYS* 3.1 43.3 + - + +
94A PHE* 4.0 19.1 - - + -
116A ASN* 3.2 37.6 + - - +
117A TRP* 3.3 51.5 - - + +
181A SER* 4.6 8.8 + - - -
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Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 3.0 15.2 + - + +
16A THR* 3.7 10.3 - - - +
18A ARG* 1.3 80.4 - - + +
20A ALA* 1.3 59.9 + - - +
22A LYS* 3.4 6.4 + - - +
23A ASP* 3.0 29.5 + - + +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR 3.1 16.8 + - - +
17A ILE* 3.1 5.1 + - - +
19A VAL* 1.3 76.9 - - - +
21A MET* 1.3 59.0 + - - +
23A ASP* 3.3 6.4 + - - +
24A ALA* 2.9 32.2 + - - +
57A LEU* 3.7 22.1 - - + +
62A LYS* 3.7 31.2 - - + +
63A LEU* 4.7 3.4 - - + -
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Residues in contact with MET 21 (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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17A ILE* 2.8 36.0 + - + +
18A ARG 3.7 4.7 - - - +
20A ALA* 1.3 72.2 - - - +
22A LYS* 1.3 63.5 + - - +
25A TYR* 3.0 61.6 + - + +
26A GLN 4.0 0.2 + - - -
31A TYR* 4.0 9.1 - - + -
32A PRO* 4.2 8.7 - - + -
53A ALA* 4.3 3.1 - - - -
57A LEU* 3.8 16.2 - - + -
79A ILE* 3.7 24.9 - - + -
94A PHE* 3.7 50.5 - - + -
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Residues in contact with LYS 22 (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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18A ARG* 3.1 33.2 + - + +
19A VAL* 3.7 6.5 - - - +
21A MET* 1.3 77.2 - - - +
23A ASP* 1.3 63.2 + - - +
26A GLN* 3.0 63.7 + - - +
27A ARG 4.8 0.3 + - - -
31A TYR* 3.7 12.3 - - - +
94A PHE* 4.7 7.4 - - + -
181A SER* 4.3 4.7 + - - -
182A ARG* 2.7 31.3 + - - +
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL* 3.0 21.0 + - + +
20A ALA* 3.3 7.6 + - - +
22A LYS* 1.3 77.7 - - - +
24A ALA* 1.3 62.9 + - - +
26A GLN 4.8 0.5 + - - -
27A ARG* 5.5 2.9 + - - +
62A LYS* 3.0 34.6 + - + +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 2.9 17.5 + - - +
23A ASP* 1.3 80.0 - - - +
25A TYR* 1.3 74.7 + - + +
27A ARG* 5.1 6.4 - - - +
28A ASP* 3.8 5.9 - - - +
57A LEU* 3.7 21.1 - - + -
60A LEU* 3.8 21.5 - - + +
62A LYS* 4.1 11.2 - - + +
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Residues in contact with TYR 25 (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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21A MET* 3.0 49.0 + - + +
24A ALA* 1.3 97.7 - - + +
26A GLN* 1.3 67.9 + - - +
27A ARG 3.1 2.9 - - - -
28A ASP* 2.9 33.2 + - - +
29A GLY 3.6 1.0 + - - -
30A LYS 3.4 11.7 + - - +
31A TYR* 3.7 15.5 - - + -
32A PRO* 3.7 31.9 - - + +
53A ALA* 4.3 4.4 + - + -
56A GLN* 2.5 45.1 + - - +
57A LEU* 4.0 6.1 - - + +
60A LEU* 5.2 4.9 - - + -
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET 4.0 0.8 + - - -
22A LYS* 3.0 63.3 + - - +
24A ALA 3.9 0.2 - - - -
25A TYR* 1.3 77.3 - - - +
27A ARG* 1.3 56.7 + - - +
29A GLY* 3.0 20.4 + - - +
31A TYR* 4.1 14.8 + - - +
182A ARG 4.6 2.4 - - - +
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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
------------------------------------------------------------
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