Contacts of the strand formed by residues 163 - 171 (chain B) in PDB entry 4A12
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 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B HIS* 3.1 29.8 + + + -
159B GLN* 3.4 2.3 - - - -
160B THR* 2.8 46.1 + - - +
162B LYS* 1.4 96.0 - - + +
164B TYR* 1.3 58.8 + - - +
165B TYR* 4.1 17.8 + - + -
183B LYS* 3.6 41.3 - - + -
184B MSE 3.3 4.3 - - - +
185B PHE* 3.7 24.8 - + + +
186B TYR* 3.4 8.0 - - - -
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Residues in contact with TYR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASN* 3.4 43.1 + - + +
126B ILE* 3.8 42.2 - - + -
128B GLN* 4.0 10.5 + - + -
156B VAL* 3.7 25.4 - - + -
158B ASN 3.7 2.2 - - - -
159B GLN* 3.0 36.0 + - + -
163B HIS* 1.3 70.7 - - - +
165B TYR* 1.3 61.8 - - - +
166B VAL* 3.8 1.5 + - + -
182B PHE 3.5 2.3 - - - +
183B LYS* 3.8 1.2 - - - -
184B MSE 2.7 38.5 + - + +
186B TYR* 3.4 46.4 - + + -
188B LYS* 5.7 0.2 + - - -
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Residues in contact with TYR 165 (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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156B VAL* 3.5 3.5 - - - -
157B VAL* 2.7 40.8 + - + -
158B ASN* 2.7 49.6 + - + +
159B GLN 4.4 0.7 - - - -
160B THR* 3.7 29.0 + - + +
163B HIS* 4.1 18.0 + - + +
164B TYR* 1.3 72.0 - - - +
166B VAL* 1.3 55.8 + - - +
182B PHE 3.4 6.5 - - - +
183B LYS* 3.6 47.6 + - + -
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B CYS* 3.8 19.3 - - - -
125B LEU* 3.8 7.9 - - + -
126B ILE* 3.8 28.9 - - + -
154B ALA* 3.8 28.9 - - + -
155B ARG 3.4 11.2 - - - +
156B VAL* 4.4 11.9 - - + -
157B VAL* 4.7 1.1 - - - -
164B TYR 4.3 3.1 - - - +
165B TYR* 1.3 76.9 - - - +
167B GLU* 1.3 65.9 + - - +
168B VAL* 5.0 0.2 - - - -
180B GLY 3.7 0.9 - - - +
181B ASN* 3.4 4.0 - - - +
182B PHE* 2.7 42.4 + - + +
184B MSE 4.1 10.8 - - + -
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Residues in contact with GLU 167 (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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153B GLU 3.7 1.7 - - - +
154B ALA* 3.4 1.4 - - - -
155B ARG* 2.9 38.5 + - + +
157B VAL* 3.7 35.4 - - + +
166B VAL* 1.3 72.3 - - - +
168B VAL* 1.3 62.3 + - - +
169B LYS* 3.5 25.9 + - - +
180B GLY 3.5 2.9 - - - +
181B ASN* 3.3 26.0 - - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ALA* 3.9 24.7 - - + +
121B LEU* 4.7 2.2 - - + -
122B CYS* 3.7 30.1 - - - -
152B ALA* 4.5 6.5 - - + -
153B GLU 3.4 12.1 - - - +
154B ALA* 3.8 11.2 - - + -
166B VAL* 4.3 1.1 - - + -
167B GLU* 1.3 76.6 - - - +
169B LYS* 1.3 66.5 + - - +
170B SER* 4.1 15.0 - - - +
178B PHE* 4.5 3.1 - - + -
179B LYS* 3.4 5.8 - - - +
180B GLY* 2.6 38.6 + - - +
182B PHE* 3.8 18.8 - - + -
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Residues in contact with LYS 169 (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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153B GLU* 2.9 42.2 + - + +
155B ARG* 4.5 15.5 - - - +
167B GLU* 3.5 31.2 + - - +
168B VAL* 1.3 77.3 - - - +
170B SER* 1.3 60.5 + - - +
171B TYR* 3.4 32.8 - - + +
176B LEU* 3.8 12.8 - - + -
178B PHE 3.6 3.8 - - - -
179B LYS* 3.8 29.8 - - + +
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Residues in contact with SER 170 (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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114B LEU* 4.8 3.1 + - - +
117B GLN* 4.4 2.3 + - - -
118B ALA* 5.3 0.9 - - - +
150B VAL* 3.6 22.2 - - - +
151B ARG 3.4 4.3 - - - -
152B ALA* 3.3 20.9 - - - +
168B VAL* 4.1 3.3 - - - +
169B LYS* 1.3 73.0 - - - +
171B TYR* 1.3 61.0 + - - +
176B LEU* 3.6 5.2 - - - +
177B VAL* 3.0 25.1 + - - -
178B PHE* 2.9 41.5 + - - +
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Residues in contact with TYR 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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149B THR 3.7 0.7 - - - +
150B VAL* 3.5 4.9 - - - -
151B ARG* 2.8 77.4 + - - +
153B GLU* 3.3 24.5 + - + -
169B LYS* 3.4 42.6 - - + +
170B SER* 1.3 72.5 - - - +
172B VAL* 1.3 63.2 + - - +
173B LYS 4.2 0.6 + - - -
174B HIS* 4.3 7.2 - - + -
175B THR 3.3 16.6 - - - +
176B LEU* 3.5 39.5 - - + +
177B VAL* 4.1 0.9 - - - -
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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