Contacts of the strand formed by residues 13 - 19 (chain B) in PDB entry 2W83
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 GLU 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B MET* 1.3 77.0 - - - +
14B MET* 1.3 62.6 + - - +
57B VAL* 5.0 0.7 - - - -
58B LYS* 3.6 24.2 - - + +
82B GLN* 3.6 15.5 + - - +
429C CYS* 4.4 21.4 - - - +
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Residues in contact with MET 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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12B MET 4.2 0.2 + - - -
13B GLU* 1.3 76.7 - - - +
15B ARG* 1.3 63.2 + - - +
16B ILE* 3.5 20.4 + - + +
57B VAL* 4.3 13.5 - - + -
58B LYS 3.2 6.8 + - - +
59B PHE* 3.5 35.5 - - + -
60B ASN* 2.9 26.6 + - - -
82B GLN* 3.3 22.0 - - + +
83B GLY* 5.2 1.6 - - - -
116B ILE* 6.1 2.2 - - - -
169B LEU* 3.7 30.1 - - - +
170B THR* 4.9 3.6 - - - +
172B ASN 5.5 4.9 - - - +
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Residues in contact with ARG 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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14B MET* 1.3 70.1 - - - +
16B ILE* 1.3 61.8 + - - +
17B LEU* 4.9 3.8 - - - +
60B ASN* 3.8 5.6 - - + +
62B TRP* 3.4 44.5 - - + +
77B TYR* 3.0 22.4 + - - +
79B THR 2.9 22.9 + - - -
80B GLY* 3.5 23.6 - - - +
81B THR* 2.9 28.2 + - - -
82B GLN* 2.8 40.8 + - - +
83B GLY 3.2 7.1 + - - +
421C ILE* 3.5 17.2 - - - +
425C ASP* 2.9 30.7 + - - +
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Residues in contact with ILE 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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14B MET* 3.9 30.3 - - + +
15B ARG* 1.3 74.6 - - - +
17B LEU* 1.3 65.1 + - - +
59B PHE* 3.8 27.8 - - + -
60B ASN 2.8 14.2 + - - +
61B VAL* 4.0 15.9 - - + -
62B TRP* 2.8 36.6 + - - +
81B THR* 4.9 0.2 - - - -
83B GLY* 3.3 26.9 - - - +
85B ILE* 3.6 33.2 - - + -
169B LEU* 4.2 13.7 - - + -
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Residues in contact with LEU 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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15B ARG* 4.9 0.9 - - - +
16B ILE* 1.3 73.9 - - - +
18B MET* 1.3 59.6 + - - +
19B LEU* 3.8 24.2 - - + -
62B TRP* 3.7 22.9 - - + +
64B VAL* 3.8 22.4 - - + -
74B TRP 4.5 2.0 - - - +
77B TYR* 3.8 25.1 - - + +
78B TYR* 3.5 31.9 - - + -
81B THR* 3.7 24.0 - - + +
83B GLY 3.0 6.5 + - - -
84B LEU* 3.4 8.1 - - - +
85B ILE 2.8 24.2 + - - -
112B MET* 4.1 6.3 - - + -
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Residues in contact with MET 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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16B ILE 4.0 0.4 - - - -
17B LEU* 1.3 72.2 - - - +
19B LEU* 1.3 63.1 + - - +
26B LYS* 3.2 40.0 - - + +
29B ILE* 4.1 14.1 - - + -
30B LEU* 3.9 18.8 - - + +
33B LEU* 6.3 0.2 - - + -
61B VAL* 3.8 26.9 - - + -
62B TRP 2.7 22.2 + - - +
63B ASP* 3.9 9.3 - - + -
64B VAL 3.5 16.8 + - - -
85B ILE* 3.2 23.8 - - + +
87B VAL* 3.8 31.0 - - + -
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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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17B LEU* 3.8 33.6 + - + -
18B MET* 1.3 82.8 - - - +
20B GLY* 1.3 59.4 + - - +
26B LYS* 3.4 12.3 - - - +
64B VAL* 3.8 15.0 - - + +
74B TRP* 3.7 47.1 - - + +
78B TYR* 4.1 4.5 - - + -
84B LEU* 4.2 9.6 - - + -
85B ILE 2.8 8.4 + - - +
86B PHE* 3.3 7.1 - - + -
87B VAL* 2.9 25.1 + - - +
106B ILE* 3.6 36.1 - - + -
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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