Contacts of the strand formed by residues 186 - 194 (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 GLU 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ARG* 4.6 5.8 + - - -
155A PRO* 3.7 9.4 - - - +
184A VAL* 3.3 16.3 + - - +
185A PRO* 1.3 87.9 - - + +
187A TYR* 1.3 68.1 + - - +
188A THR* 4.3 8.3 + - - +
208A VAL* 3.5 32.5 - - + +
209A VAL 3.2 8.7 - - - +
210A GLU* 4.9 6.4 - - + +
211A ILE* 4.4 0.4 - - - +
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Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLN* 4.1 7.9 - - + -
154A GLU 3.5 2.9 - - - +
155A PRO* 3.6 28.0 - - + -
157A ASP 2.5 30.0 + - - -
158A PRO* 3.4 5.0 - - - +
162A MET* 3.4 31.2 - - + +
163A PHE* 3.7 29.8 - + + -
178A GLY 5.1 0.9 + - - -
179A LEU* 4.2 7.1 - - + +
180A ASP 5.4 1.2 + - - -
184A VAL* 3.4 25.6 + - + +
186A GLU* 1.3 75.3 - - - +
188A THR* 1.3 61.5 + - - +
189A LEU* 4.1 6.1 - - + -
207A ALA 3.8 0.7 - - - +
208A VAL* 3.4 4.0 - - - +
209A VAL* 2.8 37.4 + - + +
211A ILE* 4.1 27.8 - - + -
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Residues in contact with THR 188 (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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152A SER 3.9 0.7 - - - +
153A GLN* 3.6 1.9 - - - -
154A GLU* 2.8 42.9 + - + +
186A GLU* 4.3 10.8 + - - +
187A TYR* 1.3 74.1 + - - +
189A LEU* 1.3 65.3 + - - +
190A THR* 4.1 4.1 + - - +
206A VAL* 3.5 28.0 - - + -
207A ALA 3.7 2.2 - - - -
208A VAL* 4.5 9.4 - - + +
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Residues in contact with LEU 189 (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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150A ILE* 4.6 13.9 - - + -
152A SER 3.4 4.5 - - - +
153A GLN* 3.7 35.7 - - + +
163A PHE* 3.9 29.4 - - + -
172A ILE* 4.1 35.7 - - + -
187A TYR* 4.9 2.5 - - + +
188A THR* 1.3 76.5 - - - +
190A THR* 1.3 61.1 + - - +
191A ILE* 3.6 12.0 + - + -
206A VAL* 3.3 5.0 - - - +
207A ALA* 2.8 40.2 + - + +
209A VAL* 4.3 14.4 - - + -
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Residues in contact with THR 190 (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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150A ILE* 3.8 3.3 - - - +
151A HIS* 2.8 49.7 + - + +
152A SER* 3.0 26.0 + - - +
188A THR* 4.1 4.6 + - - +
189A LEU* 1.3 72.2 - - - +
191A ILE* 1.3 56.1 + - - +
204A THR* 4.1 21.3 - - + +
205A ALA 3.5 10.3 - - - +
206A VAL* 4.6 10.3 - - + +
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Residues in contact with ILE 191 (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* 3.8 27.3 - - + -
113A PHE* 4.1 12.6 - - + -
130A VAL* 3.8 28.5 - - + -
149A SER 3.6 10.8 - - - +
150A ILE* 4.4 9.9 - - + -
165A ILE* 4.7 5.2 - - + -
172A ILE* 4.3 10.8 - - + -
189A LEU* 4.1 19.5 - - + +
190A THR* 1.3 77.4 - - - +
192A GLN* 1.3 64.8 + - - +
204A THR* 3.4 7.1 + - - +
205A ALA* 2.8 46.1 + - + +
206A VAL 4.2 2.0 - - - +
207A ALA* 4.2 11.9 - - + -
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Residues in contact with GLN 192 (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 7.1 - - - -
147A ALA 4.5 0.4 - - - -
148A TYR* 3.3 6.6 - - - +
149A SER* 2.8 51.9 + - - +
150A ILE 4.1 1.8 + - - -
151A HIS* 3.4 46.7 - - + +
191A ILE* 1.3 79.9 - - - +
193A ALA* 1.3 60.8 + - - +
194A THR* 4.8 1.8 - - - +
202A THR* 3.8 24.8 - - + +
203A THR 3.3 4.5 - - - +
204A THR* 4.2 9.2 + - - +
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Residues in contact with ALA 193 (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* 3.8 4.8 - - + +
108A PHE* 3.6 14.1 - - + -
132A ALA* 3.5 33.2 - - + -
146A VAL* 3.8 10.5 - - + -
147A ALA 3.5 5.6 - - - -
148A TYR* 4.1 2.0 - - + -
192A GLN* 1.3 73.0 - - - +
194A THR* 1.3 61.8 + - - +
201A SER 3.7 1.0 - - - +
202A THR* 3.2 2.1 - - - -
203A THR* 2.9 37.8 + - + +
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Residues in contact with THR 194 (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* 4.5 0.7 - - - -
146A VAL* 3.4 3.0 - - - +
147A ALA 2.8 40.3 + - - +
149A SER* 5.2 2.4 + - - -
192A GLN* 4.8 2.9 - - - +
193A ALA* 1.3 75.5 + - - +
195A ASP* 1.3 67.8 + - - +
198A GLY* 3.3 41.3 + - - +
200A GLY 3.7 10.3 - - - +
201A SER 3.2 7.2 - - - +
202A THR* 2.6 30.8 + - - +
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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