Contacts of the helix formed by residues 12 - 25 (chain A) in PDB entry 2VT5
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A VAL* 5.5 3.4 - - + -
11A ASN* 1.3 79.2 + - - +
13A LEU* 1.3 59.4 + - - +
14A THR* 3.8 5.6 + - - -
15A ARG* 3.2 27.9 + - + +
16A PHE* 2.9 30.5 + - - +
184A PHE* 4.0 4.3 - - - -
192A GLU* 3.5 26.6 + - - +
193A PHE 3.1 9.0 - - - -
194A ILE* 4.0 18.2 - - + -
39C THR* 4.5 14.5 + - + +
84C MET* 5.0 8.7 - - + -
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Residues in contact with LEU 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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12A THR* 1.3 73.4 - - - +
14A THR* 1.3 56.2 - - - +
16A PHE* 3.2 0.9 + - - +
17A VAL* 2.9 48.7 + - + +
34A LEU* 4.8 8.3 - - + +
35A ASN* 5.8 2.2 - - - +
38A CYS* 3.7 34.8 - - + -
173A LEU* 4.0 23.8 - - + -
175A LEU* 3.9 9.9 - - + -
184A PHE* 3.6 34.7 - - + -
193A PHE* 2.9 30.0 + - + +
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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
----------------------------------------------------------
12A THR* 3.4 6.0 + - - -
13A LEU* 1.3 78.7 - - - +
15A ARG* 1.3 61.6 + - - +
17A VAL* 4.2 1.2 - - - +
18A MET* 3.1 28.9 + - - +
31A THR* 4.9 3.5 - - + +
35A ASN* 3.7 38.3 + - - +
38A CYS* 5.4 7.3 - - - -
192A GLU* 5.2 5.1 + - - -
14C THR* 4.1 7.4 + - + +
35C ASN* 3.3 34.1 - - + +
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Residues in contact with ARG 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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9A ASP* 5.7 0.2 - - - +
10A VAL* 2.7 35.1 + - - +
11A ASN* 3.2 22.1 - - - +
12A THR* 3.2 19.9 + - - +
14A THR* 1.3 77.3 - - - +
16A PHE* 1.3 58.2 + - - +
18A MET* 3.6 1.2 - - - +
19A GLU* 3.0 34.3 + - + +
32C GLN* 3.5 29.0 + - - +
36C SER* 2.5 30.3 + - - -
84C MET* 3.2 20.9 + - - +
87C SER* 2.7 50.2 + - - -
88C SER* 4.3 3.2 - - - +
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Residues in contact with PHE 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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11A ASN* 3.6 23.3 + - - +
12A THR 2.9 19.4 + - - +
13A LEU 3.6 3.6 - - - +
15A ARG* 1.3 78.1 - - - +
17A VAL* 1.3 68.8 + - + +
19A GLU* 3.6 4.9 + - - +
20A GLU* 3.2 34.8 + - + +
175A LEU* 5.2 2.7 - - + -
177A MET* 3.9 22.2 - - + -
179A CYS* 3.9 11.9 - - - -
182A ASN* 3.1 38.1 - - + -
184A PHE* 3.8 22.7 - + + -
195A LEU* 4.2 12.8 - - + -
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Residues in contact with VAL 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 LEU* 2.9 39.6 + - + +
14A THR* 4.3 3.1 - - - +
16A PHE* 1.3 78.6 - - + +
18A MET* 1.3 60.6 + - - +
20A GLU* 3.3 7.0 + - - +
21A GLY* 2.9 25.3 + - - -
31A THR* 3.3 27.5 + - + +
34A LEU* 3.7 29.4 - - + -
35A ASN* 5.3 1.8 - - - +
175A LEU* 3.8 18.8 - - + -
177A MET* 4.7 4.9 - - + -
1337A ROK 3.6 12.8 - - + -
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Residues in contact with MET 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 THR* 3.1 21.0 + - - +
15A ARG 3.6 4.5 - - - +
17A VAL* 1.3 78.3 - - - +
19A GLU* 1.3 56.1 + - - +
21A GLY* 3.1 3.6 + - - -
22A ARG* 3.0 34.9 + - - +
31A THR* 3.9 15.1 + - + +
1337A ROK 3.5 33.6 - - + -
18C MET* 4.4 10.3 - - - +
28C GLY* 3.4 31.9 - - - +
31C THR* 3.7 25.8 - - + -
32C GLN* 3.7 26.2 - - + +
35C ASN* 4.7 4.7 - - - -
1337C ROK 4.3 1.3 - - + -
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Residues in contact with GLU 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 ARG* 3.0 20.0 + - + +
16A PHE* 3.8 5.8 - - - +
18A MET* 1.3 73.1 - - - +
20A GLU* 1.3 66.8 + - + +
22A ARG* 3.3 20.5 + - - +
23A LYS* 3.2 54.3 + - - +
32C GLN* 4.7 7.0 + - - +
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Residues in contact with GLU 20 (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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16A PHE* 3.2 28.6 + - + +
17A VAL 3.6 8.1 - - - +
19A GLU* 1.3 79.6 - - + +
21A GLY* 1.3 62.2 - - - +
23A LYS* 3.5 32.2 + - - +
24A ALA* 3.3 21.5 + - - +
177A MET* 3.9 19.1 - - + +
179A CYS* 3.7 27.9 - - - +
1337A ROK 3.8 19.2 + - - +
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Residues in contact with GLY 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 VAL 2.9 10.5 + - - -
18A MET 3.1 3.1 + - - -
20A GLU* 1.3 77.8 - - - +
22A ARG* 1.3 56.2 + - - +
24A ALA* 3.2 2.6 + - - +
25A ARG 2.9 23.0 + - - -
26A GLY 3.0 11.8 + - - -
1337A ROK 3.4 44.6 - - - -
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Residues in contact with ARG 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 MET* 3.0 23.5 + - - +
19A GLU* 3.3 22.0 + - - +
21A GLY* 1.3 71.8 - - - +
23A LYS* 1.3 65.9 + - - +
25A ARG* 3.1 20.5 + - - +
1337A ROK 3.6 19.1 - - + -
27C THR* 3.6 30.1 + - - +
28C GLY 3.8 1.2 - - - -
29C GLU* 3.7 45.2 + - - +
32C GLN* 3.7 20.3 - - - +
88C SER 5.6 1.6 + - - -
89C PHE* 6.4 0.2 - - - +
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Residues in contact with LYS 23 (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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19A GLU* 3.2 40.9 + - - +
20A GLU* 3.6 34.6 + - - +
22A ARG* 1.3 77.3 - - - +
24A ALA* 1.3 57.9 + - + +
25A ARG* 3.8 5.7 + - - +
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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
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20A GLU 3.3 12.7 + - - +
21A GLY 3.2 4.8 + - - +
22A ARG 3.1 0.6 - - - -
23A LYS* 1.3 77.3 - - + +
25A ARG* 1.3 72.0 + - - +
26A GLY* 3.5 0.9 + - - -
1337A ROK 4.0 20.4 - - + +
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Residues in contact with ARG 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 GLY 2.9 4.5 + - - -
22A ARG* 3.1 16.2 + - - +
23A LYS 4.9 4.6 + - - +
24A ALA* 1.3 81.8 - - - +
26A GLY* 1.3 64.9 + - - +
27A THR* 4.0 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
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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