Contacts of the helix formed by residues 9 - 17 (chain A) in PDB entry 1WXR
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 TYR 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.7 32.1 - - + -
7A LEU 3.3 3.3 + - - +
8A GLY* 1.3 71.4 - - - -
10A GLN* 1.3 63.7 + - - +
12A PHE* 3.0 23.3 + + - +
13A ARG* 3.6 20.0 + - + +
146A GLN* 3.5 17.5 + - - +
147A TYR 4.8 3.5 + - - -
148A ILE* 3.9 17.5 - - + -
158A MET* 5.2 2.5 - - + -
164A TRP* 2.9 36.1 + + - -
166A THR* 3.4 18.7 - - + +
615A ASN* 5.3 1.6 - - - -
619A VAL* 5.5 1.6 - - + -
623A LEU* 3.5 33.4 - - + -
628A ASP* 3.0 20.7 + - - +
630A SER* 3.4 2.2 + - - -
631A VAL* 4.1 14.4 - - + -
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Residues in contact with GLN 10 (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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8A GLY 4.9 0.4 - - - -
9A TYR* 1.3 78.4 - - - +
11A LEU* 1.3 63.3 + - + +
13A ARG* 3.1 12.3 + - - +
14A ASP* 3.0 52.4 + - - +
612A HIS* 5.3 0.4 - - - +
613A ALA* 2.9 30.8 + - - +
614A TYR* 5.1 0.7 - - - -
615A ASN* 5.1 0.9 - - - +
630A SER* 3.3 30.3 + - - +
631A VAL* 3.5 8.2 - - - +
632A LEU* 3.1 40.3 + - + +
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Residues in contact with LEU 11 (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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7A LEU* 4.5 3.6 - - + -
8A GLY* 3.0 33.9 + - - +
10A GLN* 1.3 79.5 - - + +
12A PHE* 1.3 61.5 + - + +
14A ASP 3.4 0.2 + - - -
15A PHE* 3.0 28.4 + - - +
21A MET* 5.3 8.3 - - + -
22A PHE* 3.5 31.6 - - + -
31A ILE* 4.5 21.3 - - + -
32A TYR 4.4 15.0 - - - +
198A MET* 3.6 16.8 - - + +
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Residues in contact with PHE 12 (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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3A VAL* 3.5 47.3 - - + -
4A ASN* 4.7 3.6 - - - -
7A LEU* 3.9 35.7 - - + -
8A GLY 3.9 13.2 - - - -
9A TYR* 3.0 19.8 + + - +
11A LEU* 1.3 73.9 - - + +
13A ARG* 1.3 60.0 + - - +
15A PHE* 3.9 1.1 - - - -
16A ALA* 3.2 21.8 + - - +
166A THR* 3.7 19.1 - - + -
167A GLY 3.2 36.0 + - - +
198A MET* 3.6 36.6 - - + -
199A PRO 3.9 4.3 - - - -
200A ILE* 4.6 0.2 - - + -
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Residues in contact with ARG 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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9A TYR* 3.7 26.7 - - + +
10A GLN* 3.1 16.8 + - - +
12A PHE* 1.3 78.2 - - - +
14A ASP* 1.3 63.2 + - - +
16A ALA* 4.0 0.5 - - - +
17A GLU* 3.0 60.5 + - - +
164A TRP* 3.3 34.6 - - - +
165A LEU* 2.7 36.4 + - - +
166A THR* 4.4 1.8 - - + -
613A ALA* 3.6 19.7 - - + +
614A TYR 2.8 27.9 + - - +
615A ASN* 2.8 25.4 + - - +
631A VAL* 5.9 0.7 - - + -
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Residues in contact with ASP 14 (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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10A GLN* 3.0 30.3 + - - +
11A LEU* 6.1 0.2 - - + -
13A ARG* 1.3 75.8 - - - +
15A PHE* 1.3 64.8 + - - +
18A ASN* 3.1 3.5 + - - -
19A LYS* 2.8 45.1 + - - +
20A GLY* 4.2 0.7 - - - -
22A PHE* 3.6 16.7 - - + +
612A HIS* 2.6 32.9 + - - -
613A ALA* 2.8 32.3 + - - +
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Residues in contact with PHE 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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11A LEU 3.0 18.4 + - - +
12A PHE 3.7 5.4 - - - +
14A ASP* 1.3 74.9 - - - +
16A ALA* 1.3 64.6 + - - +
18A ASN* 3.1 15.4 + - - -
22A PHE* 3.4 30.8 - + + +
42A LEU* 4.6 7.0 - - + -
47A MET* 4.2 9.5 - - + +
50A PHE* 3.5 27.0 - + - -
139A TYR* 3.5 44.6 - + - -
140A ARG 3.6 10.5 - - - -
167A GLY* 3.3 16.8 - - - -
168A GLY* 3.3 27.6 - - - -
169A THR* 5.0 2.5 - - + -
198A MET* 3.9 19.7 - - + -
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Residues in contact with ALA 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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12A PHE 3.2 16.6 + - - +
13A ARG 4.0 2.9 - - - +
15A PHE* 1.3 85.0 - - - +
17A GLU* 1.3 61.1 + - - +
18A ASN 3.3 0.7 + - - -
50A PHE* 3.8 9.5 - - - +
141A LEU* 3.3 29.8 - - + +
165A LEU* 4.0 16.1 - - + +
166A THR* 3.6 14.8 - - - +
167A GLY* 3.4 17.9 - - - +
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Residues in contact with GLU 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 ARG* 3.0 47.0 + - - +
14A ASP 4.3 0.7 - - - +
15A PHE 3.1 1.0 - - - -
16A ALA* 1.3 79.5 - - - +
18A ASN* 1.3 70.2 + - - +
19A LYS* 2.8 50.9 + - + +
164A TRP* 5.4 0.3 - - - +
165A LEU* 4.4 20.8 + - + +
613A ALA* 3.4 17.5 - - + +
614A TYR 4.8 0.2 + - - -
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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