Contacts of the strand formed by residues 202 - 212 (chain A) in PDB entry 4ZMQ
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 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A PRO* 4.9 0.9 - - - -
192A GLN* 3.8 28.9 - - + +
193A ALA 3.2 4.5 - - - +
194A THR* 2.6 31.4 + - - +
200A GLY 4.2 2.1 + - - -
201A SER* 1.3 78.2 - - - +
203A THR* 1.3 75.8 + - - +
204A THR* 4.9 1.8 - - - +
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Residues in contact with THR 203 (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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106A PRO* 3.2 36.9 + - + +
107A LYS* 3.8 12.6 - - - +
108A PHE* 3.6 16.2 + - + +
192A GLN* 3.3 6.2 - - - -
193A ALA* 2.9 42.4 + - + +
202A THR* 1.3 75.9 - - - +
204A THR* 1.3 73.6 + - - +
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Residues in contact with THR 204 (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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108A PHE* 3.6 6.4 - - - +
111A ASP* 5.7 1.2 - - - +
151A HIS* 5.8 1.4 - - - -
190A THR* 4.1 22.0 - - + +
191A ILE 3.4 7.1 + - - -
192A GLN* 4.2 10.9 + - - +
202A THR* 4.9 2.1 - - - +
203A THR* 1.3 85.2 + - - +
205A ALA* 1.3 68.5 + - - +
206A VAL* 6.0 1.3 - - + -
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Residues in contact with ALA 205 (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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108A PHE* 3.4 27.1 - - + -
110A GLN 3.8 10.3 - - - +
111A ASP* 3.5 16.4 - - - +
113A PHE* 4.2 5.2 - - + -
190A THR* 3.5 7.1 - - - +
191A ILE* 2.8 36.6 + - + -
204A THR* 1.3 77.6 - - - +
206A VAL* 1.3 68.5 + - - +
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Residues in contact with VAL 206 (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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111A ASP 3.0 10.6 + - - +
112A THR* 3.3 11.8 - - + +
113A PHE* 2.8 29.3 + - - -
188A THR* 3.5 30.5 - - + -
189A LEU 3.3 5.8 - - - +
190A THR* 4.7 11.7 - - + +
191A ILE* 4.5 2.2 - - - -
204A THR* 6.0 1.1 - - + -
205A ALA* 1.3 81.9 - - - +
207A ALA* 1.3 61.6 + - - +
208A VAL* 4.0 16.2 - - + -
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Residues in contact with ALA 207 (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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113A PHE* 3.3 7.2 - - + -
128A MET* 3.9 15.3 - - + -
172A ILE* 3.8 28.9 - - + -
187A TYR 3.8 0.7 - - - +
188A THR* 3.7 1.0 - - - -
189A LEU* 2.8 45.9 + - + +
191A ILE* 4.2 10.5 - - + +
206A VAL* 1.3 72.6 - - - +
208A VAL* 1.3 62.0 + - - +
209A VAL 4.0 0.4 - - - -
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Residues in contact with VAL 208 (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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112A THR* 4.0 21.3 - - + -
113A PHE 2.8 11.0 + - - +
114A ARG* 3.5 32.3 - - + +
115A GLY 3.3 23.9 + - - +
128A MET* 3.7 1.2 - - - +
186A GLU* 3.5 37.2 - - + +
187A TYR 3.4 4.3 - - - +
188A THR* 4.5 9.2 - - - +
206A VAL* 4.0 12.6 - - + -
207A ALA* 1.3 75.1 - - - +
209A VAL* 1.3 64.0 + - - +
210A GLU* 4.0 2.9 + - + +
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Residues in contact with VAL 209 (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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115A GLY 3.6 2.9 - - - -
117A VAL* 4.6 5.8 - - + -
127A VAL* 3.9 20.4 - - + -
128A MET* 3.5 23.3 - - + -
163A PHE* 3.9 30.5 - - + -
172A ILE* 5.0 0.7 - - + -
186A GLU* 3.2 6.8 - - - +
187A TYR* 2.8 45.6 + - + +
189A LEU* 4.3 19.3 - - + -
208A VAL* 1.3 73.4 - - - +
210A GLU* 1.3 69.2 + - - +
211A ILE* 3.9 11.2 + - + -
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Residues in contact with GLU 210 (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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115A GLY 3.0 14.6 + - - +
116A SER* 3.2 9.5 - - - -
117A VAL 3.1 24.8 + - - -
181A ARG* 3.9 16.0 + - - +
185A PRO 3.8 5.8 - - - +
186A GLU* 4.6 7.6 - - - +
208A VAL* 4.0 3.0 + - + +
209A VAL* 1.3 73.6 - - - +
211A ILE* 1.3 73.5 + - - +
212A LEU* 3.9 23.9 - - - +
213A ASP 5.3 0.3 + - - -
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Residues in contact with ILE 211 (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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117A VAL* 3.5 18.8 - - + +
119A GLU* 3.7 32.8 - - + -
163A PHE* 5.3 0.2 - - + -
179A LEU* 3.8 29.8 - - + -
180A ASP 4.6 0.7 - - - +
181A ARG* 2.6 53.2 + - + +
184A VAL 3.6 20.6 - - - +
185A PRO 2.9 14.5 + - - +
187A TYR* 4.1 20.0 - - + -
209A VAL* 4.3 7.2 - - + +
210A GLU* 1.3 75.1 - - - +
212A LEU* 1.3 57.2 + - - +
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Residues in contact with LEU 212 (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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116A SER* 3.7 26.7 - - - +
117A VAL* 2.8 25.5 + - - +
118A LEU* 4.2 22.2 - - + +
119A GLU* 4.4 11.6 + - - +
181A ARG* 3.8 7.9 - - - +
210A GLU* 3.9 26.2 - - - +
211A ILE* 1.3 77.8 - - - +
213A ASP* 1.3 71.0 + - - +
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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