Contacts of the strand formed by residues 162 - 165 (chain B) in PDB entry 3Q3G
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 THR 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PRO* 5.4 6.3 - - + -
161B VAL* 1.3 79.5 - - - +
163B VAL* 1.3 61.2 + - - +
164B THR* 4.2 7.5 - - - +
207B ASN 3.4 1.7 - - - +
208B VAL* 3.4 5.2 - - - +
209B ALA* 2.9 48.8 + - + +
211B PRO* 5.3 9.4 - - + -
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B CYS* 4.7 2.0 - - - -
153B VAL* 4.1 3.8 - - + -
161B VAL* 4.1 6.7 + - + -
162B THR* 1.3 78.1 - - - +
164B THR* 1.3 73.8 - - - +
165B TRP* 4.2 7.6 - - - +
174B VAL* 5.4 2.4 - - - +
176B THR* 4.1 23.7 + - + +
188B LEU* 3.8 30.1 - - + -
190B SER* 3.7 23.8 - - - +
206B CYS* 4.4 7.2 - - + -
207B ASN 3.4 4.9 - - - +
208B VAL* 4.1 22.4 - - + -
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Residues in contact with THR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B THR* 5.5 6.3 - - - +
163B VAL* 1.3 78.9 - - - +
165B TRP* 1.3 65.8 + - - +
167B SER* 3.9 6.5 - - - -
168B GLY* 3.9 17.7 - - - +
174B VAL* 6.2 0.2 - - - -
206B CYS* 3.4 6.4 - - - +
207B ASN* 2.8 58.7 + - - +
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Residues in contact with TRP 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLY* 3.5 26.0 - - - -
151B CYS* 3.4 24.9 - - + -
163B VAL* 4.2 3.1 - - + +
164B THR* 1.3 78.4 - - - +
166B ASN* 1.3 67.5 + - - +
167B SER 3.2 0.4 - - - -
168B GLY 3.2 8.5 + - - +
170B LEU* 3.2 42.5 + - + +
174B VAL* 3.6 28.3 - - + +
190B SER* 2.9 36.3 + - - -
191B SER 4.1 2.4 + - - -
192B VAL* 3.6 33.7 - - + -
204B VAL* 3.7 9.9 - - + -
205B THR 3.4 18.8 - - - -
206B CYS* 3.6 14.4 - - + -
221B ILE* 3.7 21.8 - - + -
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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
------------------------------------------------------------
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