Contacts of the helix formed by residues 8 - 19 (chain B) in PDB entry 2O5C
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 LYS 8 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ALA* 3.3 1.5 - - - +
7B GLU* 1.3 90.3 - - + +
9B PRO* 1.4 77.6 - - + +
10B SER* 3.4 16.6 - - - +
11B LEU* 3.3 10.8 + - + +
12B ALA* 3.0 21.1 + - - +
40B TRP* 3.6 6.4 - - - +
41B CYS 3.6 5.8 - - - +
103B ASP* 5.6 0.2 - - - +
317B GLN* 5.0 2.4 - - - +
321B GLU* 2.7 33.7 + - + +
6D C 3.1 44.9 + - - +
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Residues in contact with PRO 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS* 1.4 90.3 - - + +
10B SER* 1.3 56.6 + - - +
12B ALA* 3.2 3.0 + - + +
13B ARG* 2.9 52.1 + - - +
40B TRP* 3.5 47.2 - - + +
41B CYS 4.2 2.9 - - - +
42B ILE* 5.4 4.9 - - + -
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Residues in contact with SER 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS* 3.4 9.8 - - - +
9B PRO* 1.3 75.4 - - - +
11B LEU* 1.3 66.9 + - - +
13B ARG* 3.4 27.0 + - - +
14B ALA* 3.3 21.3 + - - +
137B LEU* 4.5 6.6 - - - +
321B GLU* 3.1 46.7 + - - +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ALA* 3.9 5.2 - - + -
7B GLU* 3.6 21.8 - - + +
8B LYS* 3.3 18.7 + - + +
10B SER* 1.3 80.7 + - - +
12B ALA* 1.3 63.3 + - - +
14B ALA* 3.2 6.7 + - + +
15B ILE* 3.1 26.9 + - + +
101B ALA 3.1 27.6 - - - +
102B GLY 5.0 1.3 - - - -
103B ASP* 4.6 8.1 - - - +
134B ILE* 3.7 34.5 - - + +
137B LEU* 3.7 30.1 - - + -
320B TYR* 4.7 3.4 - - + +
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ALA* 3.9 11.1 - - + +
8B LYS 3.0 12.3 + - - +
9B PRO 3.2 9.2 + - - +
11B LEU* 1.3 75.9 - - - +
13B ARG* 1.3 56.2 + - - +
15B ILE* 3.4 1.9 + - - -
16B ALA* 2.9 28.1 + - - +
30B ILE* 4.4 2.9 - - + -
38B VAL* 3.6 26.7 - - + +
39B THR 4.1 0.9 - - - +
40B TRP* 3.5 32.1 - - + -
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Residues in contact with ARG 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 2.9 33.5 + - + +
10B SER* 3.4 37.0 - - - +
11B LEU 3.3 0.2 - - - -
12B ALA* 1.3 75.3 - - - +
14B ALA* 1.3 55.1 + - - +
16B ALA* 3.0 9.0 + - - +
17B ASP* 2.8 42.1 + - - +
30B ILE* 4.3 13.7 - - + -
40B TRP* 6.3 0.2 - - + -
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B SER 3.3 9.2 + - - +
11B LEU* 3.2 11.1 + - + +
13B ARG* 1.3 77.9 - - - +
15B ILE* 1.3 61.4 + - + +
17B ASP* 3.8 15.4 - - - +
18B VAL* 3.9 6.1 + - - +
137B LEU* 3.7 38.8 - - + +
139B PRO* 5.7 0.7 - - - +
142B VAL* 3.8 17.8 - - + +
324B LYS* 3.9 15.0 - - - +
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PHE* 3.8 35.7 - - + -
6B ALA* 4.1 15.5 - - + -
11B LEU* 3.1 15.9 + - + +
12B ALA 3.7 6.3 - - - +
13B ARG 3.2 0.2 - - - -
14B ALA* 1.3 75.7 - - + +
16B ALA* 1.3 65.7 + - - +
18B VAL* 3.1 15.8 + - - +
19B LEU* 3.5 15.5 + - + +
38B VAL* 4.1 14.4 - - + -
101B ALA* 3.9 22.9 - - + -
132B CYS* 5.5 1.6 - - - -
134B ILE* 3.7 30.3 - - + -
142B VAL* 4.1 8.5 - - + -
146B ILE* 4.3 7.6 - - + -
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA 2.9 14.3 + - - +
13B ARG* 3.0 9.2 + - - +
15B ILE* 1.3 76.5 - - - +
17B ASP* 1.3 61.2 + - - +
19B LEU* 3.2 9.4 + - - +
23B HIS* 3.0 30.1 + - + -
30B ILE* 3.9 35.9 - - + -
32B CYS* 4.0 10.8 - - - -
38B VAL* 4.1 7.8 - - + +
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Residues in contact with ASP 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 2.8 31.1 + - - +
14B ALA* 3.8 12.0 - - - +
15B ILE 3.2 0.2 - - - -
16B ALA* 1.3 79.6 - - - +
18B VAL* 1.3 63.5 + - + +
19B LEU 3.4 2.1 + - - +
23B HIS* 3.7 18.8 + - - -
139B PRO* 5.8 7.8 - - + +
324B LYS* 4.7 9.0 + - - -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA 3.9 4.9 + - - +
15B ILE 3.1 8.5 + - - +
17B ASP* 1.3 79.1 - - + +
19B LEU* 1.3 62.2 + - + +
20B PRO* 4.6 1.0 - - - +
139B PRO* 3.3 40.6 - - + +
142B VAL* 4.1 10.3 - - + -
143B GLU* 3.4 39.3 - - + +
146B ILE* 3.8 24.9 - - + -
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ARG* 4.8 4.0 - - - +
4B PHE* 3.9 23.6 - - + -
15B ILE* 3.5 14.6 - - + +
16B ALA 3.2 9.0 + - - +
17B ASP 3.8 1.4 - - - +
18B VAL* 1.3 82.3 - - + +
20B PRO* 1.4 71.6 - - + +
21B LYS* 3.6 0.7 + - - +
23B HIS* 2.5 29.1 + - - -
32B CYS* 4.0 11.2 - - + -
36B GLN* 3.9 27.6 - - + +
38B VAL* 3.6 31.0 - - + -
146B ILE* 4.3 17.9 - - + -
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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