Contacts of the strand formed by residues 161 - 165 (chain B) in PDB entry 3AG2
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 HIS 161 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLY* 3.6 12.6 - - - -
102B HIS 3.2 27.5 - - - -
103B GLN* 3.8 4.9 - - + -
106B TRP* 3.6 15.3 - - + -
156B SER* 3.5 10.8 - - - -
158B ASP* 2.8 22.3 + - - -
159B VAL* 3.2 25.3 + - + +
160B LEU* 1.3 71.6 - - - +
162B SER* 1.3 66.4 + - - +
173B ASP* 3.7 2.9 - - - +
174B ALA* 2.8 30.2 + - + +
196B CYS* 3.6 11.4 - - - -
198B GLU* 3.6 10.0 - - - +
200B CYS* 3.3 38.6 - - + +
207B MET* 3.4 12.6 - - + +
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B TRP* 3.5 5.5 - - - -
161B HIS* 1.3 81.2 - - - +
163B TRP* 1.3 62.0 + - - +
164B ALA 3.6 1.6 + - - -
171B LYS* 3.4 19.1 - - - +
172B THR 3.4 9.6 + - - -
173B ASP* 2.8 26.3 + - - -
174B ALA 4.0 1.1 - - - +
196B CYS* 3.4 14.8 - - - -
197B SER* 3.0 44.4 + - - -
198B GLU* 3.6 1.8 - - - +
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Residues in contact with TRP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B THR* 3.7 13.7 - - + -
106B TRP* 3.6 33.8 - + + -
108B TYR* 3.0 29.8 + + - -
142B VAL* 5.1 0.7 - - + -
152B MET* 4.1 30.1 - - + -
154B VAL* 3.9 22.2 - - + +
162B SER* 1.3 70.7 + - - +
164B ALA* 1.3 59.4 + - - +
165B VAL* 4.1 8.5 - - + -
170B LEU* 3.8 26.4 - - + +
171B LYS* 3.3 2.1 + - - -
172B THR* 2.9 38.8 + - - +
182B THR* 5.1 4.3 - - + -
184B LEU* 4.0 13.2 - - + -
209B ILE* 3.6 20.9 - - + +
211B LEU* 3.7 31.9 - - + -
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Residues in contact with ALA 164 (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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162B SER 3.6 2.6 + - - -
163B TRP* 1.3 74.8 - - - +
165B VAL* 1.3 69.8 + - - +
166B PRO* 4.0 9.4 - - + -
170B LEU* 3.2 11.4 - - - +
171B LYS* 3.9 17.3 - - + -
194B GLY* 3.1 19.4 - - - -
195B GLN 3.7 6.1 - - - +
197B SER* 3.5 25.6 - - - +
209B ILE* 3.4 13.0 - - - +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TRP* 4.1 16.2 - - + -
164B ALA* 1.3 80.1 - - - +
166B PRO* 1.3 67.0 - - - +
167B SER* 4.2 7.4 - - - +
168B LEU* 3.1 19.3 + - + +
170B LEU* 2.9 29.8 + - + +
192B TYR* 4.1 24.9 - - + -
193B TYR 3.7 15.5 - - - +
194B GLY 4.9 1.1 - - - +
209B ILE* 4.0 18.4 - - + -
211B LEU* 3.9 24.9 - - + -
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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