Contacts of the strand formed by residues 160 - 165 (chain B) in PDB entry 2ZQK
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 VAL 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B GLN* 2.6 21.7 + - - -
155B GLU* 2.7 36.5 + - + +
158B SER* 3.6 19.5 - - - +
159B GLY* 1.3 83.6 - - - +
161B SER* 1.3 59.9 + - - +
174B GLY* 3.9 19.7 - - - +
175B VAL 2.8 25.6 - - - +
177B VAL* 3.3 3.8 - - - -
27D LYS* 3.7 24.5 - - + -
43D LYS* 4.5 11.4 - - + +
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Residues in contact with SER 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B TYR* 3.2 28.7 - - - -
148B TRP* 3.5 23.7 - - - -
149B ILE 3.3 14.0 + - - -
151B GLN* 3.5 2.7 + - - -
155B GLU* 3.2 12.7 + - - -
160B VAL* 1.3 79.8 - - - +
162B SER* 1.3 69.3 + - - +
174B GLY 4.0 2.8 + - - -
175B VAL* 2.9 37.4 + - - +
177B VAL* 4.4 0.2 - - - -
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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
----------------------------------------------------------
120B GLN* 5.9 3.8 - - - -
148B TRP* 3.7 0.9 - - - -
149B ILE* 3.1 44.3 + - - -
155B GLU* 3.0 24.5 + - - -
161B SER* 1.3 75.1 + - - +
163B THR* 1.3 72.4 + - - +
171B PRO 6.4 0.2 - - - -
172B LEU 3.8 7.4 - - - -
173B PRO* 4.1 15.6 - - - +
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Residues in contact with THR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B THR* 3.4 27.8 - - + +
147B ALA 3.2 11.9 - - - +
148B TRP* 4.1 17.3 - - + -
149B ILE* 3.8 4.4 - - - +
161B SER 4.1 2.5 - - - +
162B SER* 1.3 84.8 - - - +
164B TYR* 1.3 61.2 + - - +
170B ASN 3.8 1.3 + - - +
171B PRO* 3.1 26.7 - - - +
172B LEU* 3.1 23.7 + - - +
175B VAL* 4.0 26.1 - - + +
182B VAL* 5.0 2.7 - - + -
30D ILE* 5.1 0.5 - - - +
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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
----------------------------------------------------------
120B GLN* 4.1 13.0 - - + -
123B LEU* 3.9 31.4 - - + +
124B SER* 3.5 34.2 + - - -
127B TYR* 3.9 13.6 - - + +
145B ILE 3.5 2.3 - - - +
146B THR* 4.3 1.8 - - - -
147B ALA* 3.0 30.9 + - - +
149B ILE* 3.8 14.8 - - + +
163B THR* 1.3 74.4 - - - +
165B ASN* 1.3 67.4 + - - +
166B LEU* 3.7 6.6 + - + +
169B GLN* 2.6 62.6 + - + +
170B ASN 4.6 0.2 - - - -
171B PRO* 3.8 25.4 - - + -
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Residues in contact with ASN 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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127B TYR* 5.1 0.2 - - - -
144B SER* 2.5 34.9 + - - -
145B ILE 2.8 19.4 + - - +
146B THR* 3.4 11.1 + - + +
164B TYR* 1.3 75.6 - - - +
166B LEU* 1.3 58.0 + - - +
167B ILE* 2.6 34.7 + - - +
168B THR* 2.6 26.1 + - - +
169B GLN* 2.6 49.3 + - - +
170B ASN* 4.5 4.8 + - + +
34D GLY* 4.1 7.0 - - - +
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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