Contacts of the helix formed by residues 8 - 27 (chain V) in PDB entry 2V8S
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 8 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51E THR 4.6 0.5 + - - -
52E PHE* 2.9 21.3 + - - -
54E TYR* 3.4 30.0 - - - -
94E SER* 3.8 2.3 + - - -
96E ARG* 4.6 7.2 + - - -
7V SER* 1.3 70.9 - - - +
9V GLU* 1.3 59.1 + - - +
10V HIS 3.3 2.5 - - - -
11V PHE* 3.3 8.1 + - - +
12V GLU* 2.7 56.5 + - - +
73V PHE* 4.7 9.4 - - - -
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Residues in contact with GLU 9 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E PHE* 3.7 36.9 - - + +
53E MET* 5.7 0.7 - - - +
2V ALA* 4.8 13.6 - - - +
7V SER* 3.1 16.2 + - - +
8V SER* 1.3 79.9 + - - +
10V HIS* 1.3 59.9 + - - +
12V GLU* 3.2 2.6 + - - +
13V LYS* 2.9 53.2 + - - +
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Residues in contact with HIS 10 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3V SER 6.5 0.2 - - - -
4V SER* 4.9 3.8 - - - +
7V SER 4.6 3.5 + - - +
8V SER 3.3 0.4 - - - -
9V GLU* 1.3 75.4 - - - +
11V PHE* 1.3 67.5 + - - +
13V LYS* 3.1 30.5 + - + +
14V LEU* 3.1 37.2 + - + +
61V GLU* 5.1 4.8 + - - -
65V GLU* 3.5 38.4 - - + +
1095V GOL 5.6 2.7 - - - -
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Residues in contact with PHE 11 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E TYR* 4.6 6.3 - - - +
95E GLU* 4.6 2.0 - - - -
7V SER 5.3 1.0 + - - +
8V SER* 3.3 15.6 + - - +
10V HIS* 1.3 78.8 - - - +
12V GLU* 1.3 57.6 + - + +
14V LEU* 3.3 6.5 + - - +
15V HIS* 2.7 55.7 + - + +
62V MET* 3.7 49.8 - - + -
65V GLU* 3.7 21.8 + - + +
66V LEU* 3.7 24.9 - - + -
73V PHE* 4.0 22.4 - + - -
77V MET* 3.4 33.2 - - + -
81V LEU* 4.4 2.2 - - + -
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Residues in contact with GLU 12 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E PHE* 3.3 19.1 - - + -
94E SER* 2.4 26.5 + - - -
95E GLU* 2.9 46.8 + - - +
96E ARG* 4.1 4.0 - - + +
149E ARG* 3.9 4.9 + - - +
8V SER* 2.7 47.9 + - - +
9V GLU* 3.5 6.1 - - - +
10V HIS 3.2 0.2 - - - -
11V PHE* 1.3 75.5 - - + +
13V LYS* 1.3 66.7 + - - +
15V HIS* 3.6 7.5 - - - +
16V GLU* 3.1 23.8 + - - +
73V PHE* 5.9 1.3 - - + -
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Residues in contact with LYS 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E LYS* 3.8 37.0 - - - +
9V GLU* 2.9 41.9 + - - +
10V HIS* 3.2 28.5 - - + +
12V GLU* 1.3 77.0 - - - +
14V LEU* 1.3 63.7 + - + +
15V HIS 3.3 0.2 + - - -
16V GLU* 3.4 9.7 + - + +
17V ILE* 3.3 34.1 + - + +
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Residues in contact with LEU 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V HIS* 3.1 41.7 + - + +
11V PHE* 3.6 4.5 - - - +
13V LYS* 1.3 76.7 - - + +
15V HIS* 1.3 64.0 + - - +
17V ILE* 3.7 12.7 + - + -
18V PHE* 2.9 25.1 + - - +
58V THR* 3.5 19.1 - - + +
61V GLU* 3.6 51.8 - - + +
62V MET* 3.4 19.3 - - + +
65V GLU* 4.2 7.0 - - + -
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Residues in contact with HIS 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E GLU* 3.0 27.0 + - - +
11V PHE* 2.7 31.6 + + + +
12V GLU* 3.1 3.7 + - - +
14V LEU* 1.3 75.6 - - - +
16V GLU* 1.3 58.2 + - - +
18V PHE* 3.4 2.5 + + - +
19V ARG* 3.0 40.7 + - + +
62V MET* 3.5 26.7 - - + -
77V MET* 4.0 15.9 - - + +
80V LYS* 3.9 17.7 - - - -
84V TYR* 2.4 34.5 + + - -
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Residues in contact with GLU 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E GLU* 4.1 9.6 - - + +
146E ARG* 2.5 61.2 + - + +
150E LYS* 4.0 24.5 + - - +
153E LYS* 5.2 7.3 + - - -
12V GLU 3.1 13.8 + - - +
13V LYS* 3.8 12.4 - - - +
15V HIS* 1.3 74.6 - - - +
17V ILE* 1.3 79.8 + - - +
19V ARG* 3.5 15.2 + - - +
20V GLY 3.2 8.0 + - - -
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Residues in contact with ILE 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E ARG* 4.7 1.6 - - - +
13V LYS* 3.3 27.5 + - + +
14V LEU* 3.7 19.7 - - + +
16V GLU* 1.3 82.9 - - - +
18V PHE* 1.3 67.6 + - - +
20V GLY* 3.0 13.4 + - - -
21V LEU* 3.0 25.0 + - + +
54V GLU* 6.2 1.1 - - + -
58V THR* 4.1 20.4 - - + +
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Residues in contact with PHE 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V LEU 2.9 22.0 + - - +
15V HIS 3.6 4.5 - - - +
16V GLU 3.3 0.4 - - - -
17V ILE* 1.3 77.1 - - - +
19V ARG* 1.3 60.7 + - - +
21V LEU* 3.3 6.1 + - - +
22V LEU* 2.9 40.6 + - + -
55V ALA* 3.4 44.4 - - + -
58V THR* 4.0 4.9 - - + -
59V LEU* 3.6 25.4 - - + -
62V MET* 3.6 13.2 - - - -
84V TYR* 3.5 55.4 - + + -
88V LEU* 4.2 11.4 - - + -
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Residues in contact with ARG 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E GLU* 2.7 39.9 + - - +
142E ASP* 2.8 45.4 + - - +
145E LEU* 6.0 0.4 - - - +
146E ARG* 4.8 15.4 - - - +
149E ARG* 6.2 1.4 - - - +
15V HIS* 3.0 37.6 + - + +
16V GLU* 3.5 10.8 + - - +
17V ILE 3.4 0.2 - - - -
18V PHE* 1.3 72.5 - - + +
20V GLY* 1.3 56.0 + - - +
22V LEU* 3.8 7.0 - - + +
23V GLU* 2.7 35.6 + - - +
80V LYS* 5.4 2.0 - - - +
84V TYR* 3.3 32.5 - - + +
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Residues in contact with GLY 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E ARG* 4.0 24.3 - - - +
16V GLU 3.2 10.1 + - - -
17V ILE* 3.0 8.7 + - - -
19V ARG* 1.3 73.2 - - - +
21V LEU* 1.3 63.2 + - - +
23V GLU* 3.5 7.5 + - - +
24V ASP* 3.3 27.7 + - - +
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Residues in contact with LEU 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17V ILE* 3.0 24.1 + - + +
18V PHE* 3.6 8.1 - - - +
20V GLY* 1.3 72.9 - - - +
22V LEU* 1.3 65.0 + - - +
24V ASP* 3.0 18.3 + - - +
25V LEU* 3.0 18.8 + - + +
51V LYS* 3.8 24.0 - - + +
54V GLU* 3.1 37.5 - - + +
55V ALA* 3.5 42.0 - - + +
58V THR* 4.2 7.2 - - - +
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Residues in contact with LEU 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18V PHE* 2.9 27.6 + - + +
19V ARG* 3.8 7.6 - - + +
21V LEU* 1.3 75.9 - - - +
23V GLU* 1.3 56.8 + - - +
25V LEU* 4.2 4.9 - - - +
26V GLN* 2.8 52.8 + - + +
55V ALA* 5.3 0.4 - - - +
84V TYR* 3.8 33.0 - - + +
87V ASP* 4.1 24.5 - - + +
88V LEU* 3.7 28.3 - - + -
91V LEU* 3.8 18.2 - - + -
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Residues in contact with GLU 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E ASP 6.3 0.2 - - - -
143E ASP* 2.4 34.5 - - - +
146E ARG* 4.2 20.6 + - - -
19V ARG 2.7 20.3 + - - +
20V GLY* 3.6 7.1 - - - +
22V LEU* 1.3 74.2 - - - +
24V ASP* 1.3 62.5 + - - +
26V GLN* 3.7 12.2 + - - +
27V GLY* 3.3 18.2 + - - -
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Residues in contact with ASP 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20V GLY 3.3 15.5 + - - +
21V LEU* 3.0 9.7 + - - +
23V GLU* 1.3 74.7 - - - +
25V LEU* 1.3 68.0 + - - +
26V GLN 3.3 0.2 + - - -
27V GLY* 3.3 11.5 + - - -
28V VAL* 3.4 16.8 + - - +
51V LYS* 2.6 40.3 + - + +
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Residues in contact with LEU 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V LEU 3.0 21.7 + - - +
22V LEU* 3.9 3.1 - - - +
24V ASP* 1.3 71.8 - - - +
26V GLN* 1.3 64.2 + - - +
28V VAL* 3.0 19.0 + - + +
48V PHE* 3.5 36.2 - - + +
51V LYS* 3.7 14.8 - - + +
52V GLN* 3.5 40.8 - - + +
55V ALA* 4.0 12.6 - - + -
88V LEU* 3.7 28.0 - - + -
91V LEU* 3.4 25.1 - - + +
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Residues in contact with GLN 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V LEU* 2.8 39.9 + - + +
23V GLU* 3.7 15.1 + - - +
24V ASP 3.2 0.2 - - - -
25V LEU* 1.3 72.4 - - - +
27V GLY* 1.3 56.7 + - - +
28V VAL 3.1 5.4 + - - -
29V PRO* 3.2 14.6 - - - +
30V GLU* 5.2 0.5 + - - +
87V ASP* 4.2 16.6 + - - -
90V LYS* 4.6 9.4 - - - +
91V LEU* 3.6 25.1 - - + +
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Residues in contact with GLY 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23V GLU 3.3 11.4 + - - -
24V ASP 3.3 6.6 + - - -
26V GLN* 1.3 75.8 - - - +
28V VAL* 1.3 62.9 + - - +
29V PRO* 3.6 0.9 - - - -
30V GLU* 4.0 10.0 + - - +
31V ARG* 3.6 20.4 + - - +
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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