Contacts of the strand formed by residues 174 - 178 (chain B) in PDB entry 5GQQ
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 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TRP* 5.2 3.1 - - - -
91B SER 3.8 0.2 - - - +
92B TYR* 3.4 6.3 - - - -
93B VAL* 3.0 64.2 + - + +
148B ALA* 5.6 1.6 + - - -
151B ASN* 4.6 16.9 + - + +
152B GLN* 5.4 3.3 + - - +
155B LEU* 3.5 39.7 - - + -
173B VAL* 1.3 78.5 - - - +
175B TYR* 1.3 78.1 + - - +
176B THR* 3.6 22.7 - - + +
192B VAL* 4.9 0.9 - - + -
193B TRP 3.4 15.3 - - - +
194B LEU* 4.2 3.6 - - + +
195B ILE* 5.1 2.9 - - - -
57D TRP* 3.7 25.1 - - + -
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Residues in contact with TYR 175 (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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90B THR* 4.2 14.6 - - - -
91B SER 3.0 15.5 - - - -
92B TYR* 3.4 37.5 - + + -
130B GLU* 4.5 3.8 + - - -
132B ARG* 3.8 38.0 + - - +
135B MET* 3.8 26.7 - - + -
137B VAL* 4.9 0.2 - - + -
174B TYR* 1.3 83.7 - - - +
176B THR* 1.3 66.0 + - - +
192B VAL* 3.4 4.3 - - - -
193B TRP* 2.9 59.7 + + + -
195B ILE* 3.8 26.7 - - + -
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Residues in contact with THR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TRP* 3.4 19.6 - - + +
62B ILE* 5.2 0.9 - - - +
89B VAL 5.1 0.7 + - - -
90B THR* 3.1 9.0 - - - +
91B SER* 2.9 50.2 + - - +
93B VAL* 4.9 0.2 - - + -
146B SER* 5.8 2.2 - - - -
151B ASN* 3.8 24.9 - - - +
174B TYR* 3.6 22.9 - - + -
175B TYR* 1.3 80.1 - - - +
177B ALA* 1.3 62.6 + - - +
191B GLU 3.3 11.9 - - - -
192B VAL* 4.3 2.5 - - + +
193B TRP* 5.4 0.9 - - - -
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PRO* 3.8 18.6 - - + -
89B VAL 3.4 4.7 - - - -
90B THR* 4.5 1.3 - - + -
146B SER* 5.0 1.9 + - - -
176B THR* 1.3 77.8 - - - +
178B GLY* 1.3 59.5 + - - +
179B TYR* 4.1 4.0 - - + -
190B ASN* 3.5 5.9 - - - +
191B GLU* 2.9 45.3 + - + +
193B TRP* 3.8 30.3 - - + +
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Residues in contact with GLY 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PRO* 3.2 2.8 - - - +
89B VAL 2.8 37.5 + - - -
146B SER* 5.3 1.8 - - - -
176B THR* 4.4 0.6 + - - -
177B ALA* 1.3 73.1 - - - +
179B TYR* 1.3 60.9 + - - -
181B SER* 3.6 17.8 - - - +
185B LEU* 3.4 5.5 - - - +
190B ASN* 3.2 13.5 - - - -
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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