Contacts of the strand formed by residues 168 - 173 (chain B) in PDB entry 2W77
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 SER 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B GLN* 1.3 72.7 - - - +
169B ILE* 1.3 59.5 + - - +
210B ARG* 3.0 31.9 + - - -
249B LEU* 3.3 11.3 - - - +
250B LYS* 3.1 37.9 + - - -
586B TYR* 4.2 4.2 + - - -
617B GLU* 3.0 23.6 + - - -
621B LYS* 5.2 1.8 - - - +
634B ALA* 4.5 6.2 - - - +
674B GLU* 4.0 6.7 + - - +
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Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PRO* 6.3 0.7 - - + -
152B ILE* 3.6 33.0 - - + -
154B THR* 4.1 20.4 - - + +
155B ALA* 6.3 0.9 - - + -
162B PRO* 4.6 11.4 - - + -
165B THR* 4.9 7.9 - - + -
167B GLN 3.4 9.6 + - - +
168B SER* 1.3 76.3 - - - +
170B THR* 1.3 67.2 + - - +
171B VAL* 4.4 7.7 + - + +
247B GLU* 4.6 2.5 - - + -
248B VAL 3.4 22.4 - - - +
249B LEU* 3.6 25.6 - - + -
250B LYS* 5.8 0.2 - - - +
621B LYS* 4.3 12.0 - - - +
676B GLU* 4.0 6.1 - - - +
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Residues in contact with THR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 1.3 74.1 - - - +
171B VAL* 1.3 67.2 + - - +
192B THR* 3.9 19.3 - - + -
193B PRO* 3.7 25.1 - - + +
246B VAL 3.9 0.2 - - - +
248B VAL* 2.7 46.9 + - - +
250B LYS* 2.9 28.3 + - - -
676B GLU* 2.7 26.4 + - - +
688B GLN* 3.8 9.2 - - - +
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Residues in contact with VAL 171 (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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147B TYR 4.6 1.7 - - - +
149B PRO* 3.7 35.8 - - + +
152B ILE* 4.6 4.7 - - + -
169B ILE* 4.5 11.9 - - + +
170B THR* 1.3 84.2 - - - +
172B VAL* 1.3 77.4 + - - +
173B THR* 3.6 12.5 + - + +
245B ARG* 4.0 26.0 - - + -
246B VAL 3.5 10.1 - - - +
247B GLU* 4.3 15.5 - - + -
688B GLN* 3.1 23.7 + - - +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 1.3 78.2 - - - +
173B THR* 1.3 65.4 + - - +
176B ASN* 3.9 26.9 - - + +
177B MET* 4.1 18.1 - - + +
182B LEU* 4.2 10.8 - - + -
188B VAL* 3.7 21.8 - - + +
189B MET* 5.7 0.4 - - + -
191B HIS 4.5 9.9 - - - +
192B THR* 3.7 29.8 - - + +
245B ARG* 3.4 3.3 - - - -
246B VAL* 3.1 30.8 + - + +
248B VAL* 6.2 0.9 - - + -
688B GLN* 4.3 6.5 - - - +
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Residues in contact with THR 173 (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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141B THR* 3.8 21.3 - - + -
146B SER 2.7 22.8 + - - +
147B TYR* 3.4 34.8 - - - +
148B THR 3.5 16.2 - - - +
149B PRO* 4.3 1.8 - - + -
171B VAL* 3.6 9.3 + - + +
172B VAL* 1.3 75.9 - - - +
174B ARG* 1.3 64.6 + - - +
175B GLN 3.7 0.4 + - - -
176B ASN* 3.1 24.3 + - - +
177B MET* 3.1 12.8 + - - +
244B ASP 4.1 0.2 - - - -
245B ARG* 4.2 2.9 - - - -
688B GLN* 4.9 0.4 - - - +
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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