Contacts of the helix formed by residues 7 - 21 (chain B) in PDB entry 4OL0
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 7 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LYS* 5.6 0.9 - - - +
6B PRO* 1.3 77.2 - - + +
8B LEU* 1.3 64.7 + - - +
9B GLN* 4.1 4.3 + - - +
10B LEU* 3.3 33.4 + - + +
11B VAL* 3.3 12.7 + - - +
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Residues in contact with LEU 8 (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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5B LYS* 5.3 4.5 - - - +
6B PRO 4.9 3.8 - - - +
7B THR* 1.3 75.0 - - - +
9B GLN* 1.3 56.7 + - - +
11B VAL* 2.9 11.6 + - + +
12B TYR* 2.8 40.6 + - + -
46B ILE* 4.5 16.6 - - + -
49B GLN* 3.6 46.2 - - + +
50B LEU* 4.4 16.6 - - + -
53B ILE* 4.1 25.4 - - + -
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Residues in contact with GLN 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 3.4 4.7 + - - +
8B LEU* 1.3 78.2 - - - +
10B LEU* 1.3 57.8 + - - +
12B TYR* 3.5 21.2 - - + +
13B GLN* 2.8 40.2 + - + +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 4.7 7.6 - - + -
7B THR* 3.3 27.6 + - + +
8B LEU 3.1 0.4 - - - -
9B GLN* 1.3 75.9 - - - +
11B VAL* 1.3 59.2 + - - +
13B GLN* 3.1 22.2 + - + +
14B ALA* 2.8 26.9 + - + +
33B TRP* 3.8 33.0 - - + +
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PRO* 4.4 4.9 - - + +
7B THR 3.5 15.3 - - - +
8B LEU* 3.2 10.8 - - + +
10B LEU* 1.3 77.8 - - - +
12B TYR* 1.3 56.3 + - - +
14B ALA* 3.0 3.5 + - - +
15B VAL* 2.8 36.0 + - + +
33B TRP* 3.7 11.0 - - + -
34B LEU* 4.2 11.2 - - + -
37B LEU* 3.5 33.0 - - + -
46B ILE* 4.2 15.5 - - + -
50B LEU* 3.9 27.1 - - + -
62B PHE* 4.4 4.7 - - + -
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Residues in contact with TYR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 2.8 29.5 + - + -
9B GLN* 3.5 27.6 - - + +
11B VAL* 1.3 73.8 - - - +
13B GLN* 1.3 60.5 + - - +
15B VAL* 3.8 6.1 - - + +
16B GLN* 2.9 32.8 + - - +
50B LEU* 3.4 36.5 + - + +
53B ILE* 3.6 35.3 - - + +
55B GLN* 3.1 32.9 - - - +
59B SER* 3.8 25.5 + - - -
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Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 2.8 30.6 + - + +
10B LEU* 3.1 28.4 + - + +
12B TYR* 1.3 70.9 - - - +
14B ALA* 1.3 57.7 + - - +
16B GLN* 3.5 13.3 + - - +
17B ALA* 2.8 32.7 + - - +
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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
----------------------------------------------------------
10B LEU* 2.8 11.8 + - + +
11B VAL 3.3 8.1 - - - +
13B GLN* 1.3 76.7 - - - +
15B VAL* 1.3 56.6 + - - +
17B ALA* 3.4 4.7 + - - -
18B LEU* 2.8 30.3 + - - +
30B ALA* 3.3 13.9 - - + +
33B TRP* 3.4 34.8 - - + -
34B LEU* 3.5 13.2 - - + +
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Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 2.8 28.7 + - + +
12B TYR* 3.8 9.4 - - + +
14B ALA* 1.3 68.6 - - - +
16B GLN* 1.3 69.4 + - - +
18B LEU* 3.1 3.6 + - - +
19B TYR* 2.9 49.7 + - + -
34B LEU* 4.0 15.5 - - + -
50B LEU* 5.3 2.2 - - + -
58B GLU* 4.4 13.9 - - + +
59B SER* 4.4 14.6 - - - +
62B PHE* 3.9 29.2 - - + -
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Residues in contact with GLN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR 2.9 17.9 + - - +
13B GLN* 3.7 13.9 - - - +
15B VAL* 1.3 77.4 - - - +
17B ALA* 1.3 56.3 + - - +
19B TYR* 3.6 0.6 - - - -
20B HIS* 2.7 58.9 + - + +
58B GLU* 5.3 1.8 - - - -
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Residues in contact with ALA 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 GLN 2.8 22.4 + - - +
14B ALA* 3.6 5.6 - - - +
16B GLN* 1.3 75.8 + - - +
18B LEU* 1.3 64.5 - - - +
21B ASP* 3.0 41.8 + - + +
26B GLY 4.9 2.7 - - - +
27B LYS* 3.9 4.5 - - - +
30B ALA* 4.0 12.3 - - + -
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Residues in contact with LEU 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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45A VAL* 5.3 0.9 - - + -
64A TRP* 3.5 24.2 - - + -
75A LEU* 3.7 16.8 - - + -
78A GLY 4.6 2.7 - - - +
79A TYR* 4.5 4.7 - - + -
14B ALA 2.8 21.7 + - - +
15B VAL* 3.1 4.0 + - - +
17B ALA* 1.3 73.7 - - - +
19B TYR* 1.3 89.4 + - + +
27B LYS* 2.9 46.7 + - + +
30B ALA* 3.6 9.8 - - + +
31B SER* 3.9 17.0 - - - -
34B LEU* 3.6 20.2 - - + -
62B PHE* 5.2 1.1 - - + -
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Residues in contact with TYR 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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12A LYS* 4.6 7.2 - - - +
64A TRP* 4.4 13.4 - + - -
78A GLY* 2.6 34.3 + - - -
81A ILE* 3.5 25.5 - - + +
82A GLN* 3.7 20.2 + - - +
15B VAL* 2.9 38.4 + - + +
18B LEU* 1.3 98.5 - - + +
20B HIS* 1.3 69.3 + - - +
27B LYS* 3.5 9.0 + - - +
58B GLU* 3.4 45.5 - - + +
61B TYR* 3.9 10.8 - + - -
62B PHE* 4.4 10.7 - - + +
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Residues in contact with HIS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLN* 4.3 10.5 + - - -
16B GLN* 2.7 35.2 + - + +
19B TYR* 1.3 79.2 + - - +
21B ASP* 1.3 63.2 + - - +
22B PRO* 3.2 12.5 - - - +
27B LYS* 3.9 2.0 - - - +
58B GLU* 3.0 40.4 + - - -
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLN 3.8 1.2 + - - -
17B ALA* 3.0 32.9 + - + +
20B HIS* 1.3 75.0 - - - +
22B PRO* 1.3 71.8 - - - +
23B ASP* 3.0 31.2 + - - +
26B GLY* 3.8 16.2 - - - -
27B LYS* 3.0 27.3 + - + +
29B ARG* 5.0 3.1 + - - -
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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