Contacts of the strand formed by residues 160 - 165 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 2.8 22.5 + - - -
155A GLU* 2.8 34.1 + - + +
158A SER* 4.0 12.1 - - - +
159A GLY* 1.3 85.2 - - - +
161A SER* 1.3 62.7 + - - +
174A GLY* 3.9 22.0 - - - +
175A VAL 3.0 24.2 - - - +
177A VAL* 3.7 5.5 - - - +
27N LYS* 3.4 31.0 - - + -
43N LYS* 4.4 9.9 - - + +
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Residues in contact with SER 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TYR* 3.7 9.2 - - - -
148A TRP* 3.8 19.8 - - - -
149A ILE 2.4 31.2 + - - -
151A GLN* 3.5 20.9 + - - -
155A GLU* 3.2 14.8 - - - -
160A VAL* 1.3 77.7 - - - +
162A SER* 1.3 63.9 + - - +
174A GLY 4.1 1.2 + - - -
175A VAL* 3.0 31.8 + - - +
177A VAL* 4.8 0.2 - - - -
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Residues in contact with SER 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLN* 5.9 3.4 - - - -
148A TRP* 3.7 2.1 - - - -
149A ILE* 3.3 33.7 + - - -
155A GLU* 3.0 26.1 + - - -
161A SER* 1.3 81.0 + - - +
163A THR* 1.3 75.0 + - - +
172A LEU 3.5 8.7 - - - -
173A PRO* 3.8 16.2 - - - +
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Residues in contact with THR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLN* 4.5 2.6 - - - +
146A THR* 3.7 21.5 - - + +
147A ALA 3.1 16.8 - - - +
148A TRP* 4.0 15.9 - - + -
149A ILE* 3.8 7.6 - - - +
162A SER* 1.3 88.6 - - - +
164A TYR* 1.3 62.8 + - - +
170A ASN 5.2 0.7 + - - -
171A PRO* 3.3 7.4 - - - +
172A LEU* 2.8 52.5 + - - +
175A VAL* 3.5 20.9 - - + +
182A VAL* 4.1 6.7 - - + -
30N ILE* 5.3 0.3 - - - +
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Residues in contact with TYR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLN* 3.6 36.8 - - + -
123A LEU* 3.9 34.3 - - + -
124A SER* 3.6 32.4 + - - -
127A TYR* 4.1 9.2 - - + +
128A ASP* 5.3 0.5 + - - -
146A THR* 3.5 4.4 - - - -
147A ALA* 2.7 32.1 + - - +
149A ILE* 4.2 7.8 - - + +
163A THR* 1.3 74.8 - - - +
165A ASN* 1.3 87.1 + - - +
166A LEU* 4.0 5.2 - - + -
169A GLN* 3.3 39.6 + - + +
170A ASN 4.8 1.1 - - - -
171A PRO* 3.8 22.9 - - + -
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Residues in contact with ASN 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TYR* 5.0 0.3 - - - -
144A SER* 2.8 25.5 + - - -
145A ILE 3.4 7.8 + - - -
146A THR* 3.1 21.5 + - + +
164A TYR* 1.3 83.1 - - - +
166A LEU* 1.3 58.3 + - - +
167A ILE* 2.7 22.4 + - - +
168A THR* 2.6 37.1 + - - +
169A GLN* 2.6 54.7 + - - +
170A ASN* 4.6 3.8 - - + +
34N GLY* 3.9 8.1 + - - -
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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