Contacts of the strand formed by residues 6 - 11 (chain B) in PDB entry 1WYI
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 PHE 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ARG 3.2 5.2 + - - -
5B LYS* 1.3 73.3 - - - +
7B PHE* 1.3 56.7 + - - +
8B VAL* 4.9 3.8 - - + -
36B ASP* 3.2 24.8 + - - +
37B THR* 3.5 24.2 - - + +
38B GLU* 2.4 35.0 + - - +
221B ALA* 3.8 21.1 - - + -
226B VAL 4.1 4.3 - - - -
227B ASP* 3.6 15.5 - - - -
228B GLY* 3.3 21.3 - - - -
229B PHE* 3.3 35.4 - + - -
243B ILE 4.0 4.9 - - - -
244B ILE 3.7 15.9 - - - -
246B ALA* 4.1 7.0 - - + -
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Residues in contact with PHE 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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6B PHE* 1.3 75.4 - - - +
8B VAL* 1.3 58.4 + - - +
9B GLY* 4.3 10.1 - - - -
38B GLU* 3.2 35.2 - - - -
40B VAL* 3.4 34.1 - - + -
90B TRP* 4.6 8.3 - + - -
124B ILE* 3.6 34.1 - - + -
161B VAL* 3.8 19.7 - - + -
205B ARG* 3.9 17.9 - - + +
207B ILE* 3.2 41.8 - - + +
227B ASP 3.0 11.0 + - - +
228B GLY* 3.1 23.2 - - - -
229B PHE 3.2 1.9 + - - +
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Residues in contact with VAL 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 4.9 4.3 - - + -
7B PHE* 1.3 74.4 - - - +
9B GLY* 1.3 58.4 + - - +
37B THR* 3.7 18.4 - - + -
38B GLU 2.8 11.0 + - - +
39B VAL* 3.1 26.7 - - + +
40B VAL 2.8 25.1 + - - +
229B PHE* 3.9 6.5 - - + +
231B VAL* 4.2 11.2 - - + -
240B PHE* 3.5 26.2 - - + -
243B ILE* 4.3 7.6 - - + +
244B ILE* 3.7 31.2 - - + +
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Residues in contact with GLY 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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7B PHE* 3.8 14.0 + - - -
8B VAL* 1.3 74.4 - - - +
10B GLY* 1.3 59.3 + - - -
11B ASN 4.0 0.7 - - - -
40B VAL* 3.3 9.4 - - - -
124B ILE* 5.4 1.1 - - - -
229B PHE 2.9 13.6 + - - -
230B LEU* 3.3 14.3 - - - -
231B VAL* 2.8 32.6 + - - +
240B PHE* 4.1 2.2 - - - -
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Residues in contact with GLY 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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9B GLY* 1.3 71.4 - - - -
11B ASN* 1.3 61.3 + - - -
12B TRP* 3.4 12.0 + - - -
40B VAL 2.7 14.9 + - - -
41B CYS* 3.7 0.7 - - - -
42B ALA* 2.8 29.7 + - - -
230B LEU* 5.1 0.9 - - - -
235B SER* 3.4 21.1 - - - -
240B PHE* 3.7 12.4 - - - -
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Residues in contact with ASN 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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75A THR* 3.2 10.3 + - - +
9B GLY 4.0 1.0 - - - -
10B GLY* 1.3 70.7 - - - +
12B TRP* 1.3 58.6 + - - +
13B LYS* 2.8 27.1 + - - +
42B ALA* 4.2 9.5 - - + +
64B GLN* 3.2 21.7 + - - +
92B VAL* 5.5 4.2 - - + +
95B HIS* 2.8 40.3 + - - -
230B LEU* 4.2 18.6 - - + +
231B VAL 2.7 17.2 + - - +
232B GLY* 3.2 11.3 - - - +
235B SER* 3.2 9.6 + - - -
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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