Contacts of the helix formed by residues 2 - 17 (chain B) in PDB entry 1O0W
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 ASN 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0B HIS* 3.5 14.2 + - + +
1B MET* 1.3 75.7 - - - +
3B GLU* 1.3 58.9 + - - +
4B SER* 3.1 12.1 + - - -
5B GLU* 2.9 36.6 + - - +
6B ARG* 2.8 27.9 + - - +
35B TYR* 4.4 2.8 + - - -
39B GLN* 5.0 1.4 + - - -
44B ARG* 3.2 33.0 - - - +
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Residues in contact with GLU 3 (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 ASN* 1.3 75.6 - - - +
4B SER* 1.3 57.6 + - - +
6B ARG* 3.4 6.8 + - - +
7B LYS* 3.0 39.6 + - - +
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Residues in contact with SER 4 (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 ASN* 3.1 17.6 + - - -
3B GLU* 1.3 76.7 - - - +
5B GLU* 1.3 68.0 + - - +
7B LYS* 3.6 7.9 + - - +
8B ILE* 3.2 29.1 + - - +
35B TYR* 4.8 3.1 + - - -
108B PHE* 4.8 1.5 - - - -
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Residues in contact with GLU 5 (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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-1B HIS* 3.2 8.7 + - - -
1B MET* 3.5 7.4 - - + -
2B ASN* 2.9 29.6 + - - +
4B SER* 1.3 75.8 - - - +
6B ARG* 1.3 65.9 + - - +
8B ILE* 3.3 2.8 + - - +
9B VAL* 3.1 29.9 + - - +
27B PHE* 3.7 29.2 - - + -
35B TYR* 2.7 36.9 + - - +
44B ARG* 2.7 39.8 + - - -
47B VAL* 4.6 0.3 - - - +
108B PHE* 3.7 13.1 - - + -
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Residues in contact with ARG 6 (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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1B MET* 3.6 48.7 + - - +
2B ASN 2.8 16.2 + - - +
3B GLU* 3.6 9.0 - - - +
5B GLU* 1.3 78.4 - - - +
7B LYS* 1.3 57.8 + - + +
9B VAL* 3.4 3.8 + - - +
10B GLU* 2.9 52.0 + - - +
23B GLU* 2.9 25.1 + - - -
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Residues in contact with LYS 7 (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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3B GLU* 3.0 26.3 + - - +
4B SER* 4.0 7.4 - - - +
5B GLU 3.3 0.4 - - - -
6B ARG* 1.3 77.7 - - + +
8B ILE* 1.3 54.0 + - + +
10B GLU* 3.8 14.9 - - - +
11B GLU* 2.7 49.8 + - + +
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Residues in contact with ILE 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B SER* 3.2 16.9 + - - +
5B GLU 3.7 0.7 - - - +
7B LYS* 1.3 77.5 - - + +
9B VAL* 1.3 54.6 + - - +
11B GLU* 3.2 18.8 + - - +
12B PHE* 2.8 33.6 + - - +
30B LEU* 4.6 2.7 - - + -
105B LYS 4.4 14.1 - - - +
106B PHE* 3.4 40.4 - - + +
107B LEU 5.6 1.8 - - - +
108B PHE* 3.5 30.3 - - + -
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Residues in contact with VAL 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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1B MET* 4.0 18.8 - - - -
5B GLU 3.1 17.5 + - - +
6B ARG* 3.7 4.3 - - - +
8B ILE* 1.3 75.7 - - - +
10B GLU* 1.3 63.3 + - + +
12B PHE* 3.4 6.9 + - - +
13B GLN* 3.2 46.1 + - - +
23B GLU* 4.0 26.0 - - + +
26B LEU* 3.9 14.5 - - + +
27B PHE* 4.3 26.7 - - + +
30B LEU* 5.0 2.0 - - + -
108B PHE* 4.6 5.6 - - + -
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Residues in contact with GLU 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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6B ARG* 2.9 45.9 + - + +
7B LYS* 3.8 17.3 - - - +
9B VAL* 1.3 76.1 - - + +
11B GLU* 1.3 65.3 + - + +
13B GLN* 3.3 10.9 + - - +
14B LYS* 3.0 51.1 + - - +
23B GLU* 5.4 5.4 - - - +
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Residues in contact with GLU 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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7B LYS* 2.7 38.0 + - + +
8B ILE* 3.5 23.0 - - - +
10B GLU* 1.3 73.8 - - + +
12B PHE* 1.3 60.6 + - - +
14B LYS* 4.5 4.5 - - - -
15B GLU* 2.8 52.2 + - - +
105B LYS* 5.9 1.2 - - - +
106B PHE* 3.8 12.9 - - + -
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Residues in contact with PHE 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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8B ILE 2.8 20.0 + - - +
9B VAL* 3.7 5.8 - - - +
10B GLU 3.3 0.2 - - - -
11B GLU* 1.3 72.6 - - - +
13B GLN* 1.3 58.8 + - - +
16B THR* 2.8 65.9 + - + +
18B ILE* 4.0 18.2 - - + -
20B PHE* 4.5 4.0 - + - -
26B LEU* 3.4 35.4 - - + -
30B LEU* 4.3 4.7 - - + -
101B MET* 4.2 7.0 - - + -
103B LEU* 4.1 20.4 - - + -
106B PHE* 3.4 43.2 - + + -
132B LEU* 3.8 28.3 - - + -
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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
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9B VAL* 3.2 29.5 + - - +
10B GLU* 3.7 8.9 - - - +
11B GLU 3.2 0.6 - - - -
12B PHE* 1.3 77.2 - - - +
14B LYS* 1.3 59.2 + - + +
16B THR* 4.1 0.2 - - - -
17B GLY* 2.8 31.9 + - - -
18B ILE 3.3 20.9 - - - +
19B ASN* 3.5 25.6 + - - +
20B PHE* 2.7 35.6 + - - +
23B GLU* 2.8 27.6 + - - +
26B LEU* 3.6 15.5 - - + -
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Residues in contact with LYS 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 GLU* 3.0 41.9 + - - +
11B GLU* 3.8 5.4 - - - +
13B GLN* 1.3 80.8 - - + +
15B GLU* 1.3 69.3 + - - +
17B GLY* 3.6 5.7 + - - -
19B ASN* 5.6 2.0 - - - +
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Residues in contact with GLU 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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11B GLU* 2.8 50.9 + - - +
12B PHE 3.9 2.0 - - - +
14B LYS* 1.3 81.3 - - - +
16B THR* 1.3 62.6 + - + +
17B GLY 3.7 0.2 + - - -
102B ASN* 6.3 0.9 - - - +
105B LYS* 3.6 24.9 + - - +
106B PHE* 3.9 21.8 - - + -
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Residues in contact with THR 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 PHE* 2.8 56.6 + - + +
15B GLU* 1.3 78.6 - - + +
17B GLY* 1.3 62.2 + - - +
18B ILE* 3.1 28.9 + - - +
101B MET* 4.1 24.7 - - + +
106B PHE* 4.8 3.1 - - + -
148B LEU* 5.6 1.6 - - - +
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Residues in contact with GLY 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 15.7 + - - -
14B LYS 3.6 4.4 + - - -
15B GLU 3.4 2.6 - - - -
16B THR* 1.3 76.8 - - - +
18B ILE* 1.3 59.2 + - - +
19B ASN* 3.3 16.9 + - - +
144B LYS* 5.3 5.2 + - - -
148B LEU* 6.2 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