Contacts of the strand formed by residues 168 - 173 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN* 1.3 72.3 - - - +
169A ILE* 1.3 59.0 + - - +
170A THR* 4.1 0.9 - - - -
210A ARG* 2.8 27.7 + - - -
248A VAL 3.9 0.3 - - - +
249A LEU* 3.7 3.6 - - - +
250A LYS* 3.0 43.5 + - - +
586A TYR* 4.1 4.2 + - - -
617A GLU* 2.5 25.4 + - - -
621A LYS* 5.1 2.0 - - - +
634A ALA* 4.1 5.5 - - - +
674A GLU* 3.9 7.5 + - - -
676A GLU* 5.9 1.3 - - - -
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Residues in contact with ILE 169 (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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152A ILE* 4.1 20.9 - - + -
154A THR* 3.9 21.3 - - - +
162A PRO* 4.4 19.3 - - + +
165A THR* 4.2 16.2 - - + +
167A GLN 3.2 11.1 + - - +
168A SER* 1.3 74.2 - - - +
170A THR* 1.3 62.0 + - - +
171A VAL* 4.3 7.4 + - + +
247A GLU* 4.4 5.6 - - + -
248A VAL 3.4 32.8 - - - +
249A LEU* 4.1 14.6 - - + +
621A LYS* 4.2 13.3 - - - +
676A GLU* 4.7 3.3 - - - +
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Residues in contact with THR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A SER 4.1 0.4 - - - -
169A ILE* 1.3 71.3 + - - +
171A VAL* 1.3 65.2 + - - +
172A VAL* 5.4 0.2 - - + -
192A THR* 4.0 12.1 - - + -
193A PRO* 3.6 31.6 - - + -
247A GLU 3.8 0.2 - - - -
248A VAL* 2.8 40.8 + - - +
250A LYS* 3.0 27.2 + - - +
676A GLU* 2.4 28.8 + - - +
688A GLN* 3.6 12.6 - - - +
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Residues in contact with VAL 171 (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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147A TYR 4.1 6.8 - - - +
149A PRO* 3.8 36.3 - - + +
152A ILE* 4.3 11.4 - - + -
169A ILE* 4.3 8.2 + - + -
170A THR* 1.3 76.9 - - - +
172A VAL* 1.3 77.4 + - - +
173A THR* 3.8 17.4 + - + -
245A ARG* 4.2 14.6 - - - -
246A VAL 3.5 7.6 - - - +
247A GLU* 3.5 24.9 - - + +
688A GLN* 3.0 22.9 + - - +
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL* 1.3 74.8 - - - +
173A THR* 1.3 63.9 + - - +
176A ASN* 4.0 18.2 - - + +
177A MET* 3.7 26.2 - - + +
182A LEU* 4.5 7.4 - - + -
188A VAL* 3.7 24.2 - - + +
191A HIS* 4.5 4.0 - - + +
192A THR* 3.6 34.8 - - + +
245A ARG* 3.6 3.1 - - - +
246A VAL* 2.9 34.6 + - + +
248A VAL* 5.6 2.0 - - + +
688A GLN* 4.2 11.7 - - - +
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Residues in contact with THR 173 (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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141A THR* 4.0 20.0 - - + -
144A SER* 5.8 0.2 - - - +
146A SER 2.8 23.8 + - - +
147A TYR* 3.1 31.1 - - - +
148A THR 3.8 18.8 - - - +
171A VAL* 3.8 19.2 + - + +
172A VAL* 1.3 76.4 - - - +
174A ARG* 1.3 68.0 + - - +
175A GLN 4.3 0.4 - - - -
176A ASN* 3.0 28.5 + - - +
177A MET* 3.2 7.5 + - - +
244A ASP 4.2 0.2 - - - -
245A ARG* 4.3 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