Contacts of the strand formed by residues 186 - 194 (chain B) in PDB entry 4ZMV
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PRO* 3.5 18.5 - - - +
184B VAL* 3.4 7.8 + - - +
185B PRO* 1.3 88.1 - - + +
187B TYR* 1.3 69.3 + - - +
188B THR* 4.3 7.1 + - - -
208B VAL* 3.5 32.2 - - + +
209B VAL 3.5 12.1 - - - +
210B GLU* 4.8 9.2 - - + +
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Residues in contact with TYR 187 (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 GLN* 3.8 17.9 - - + -
154B GLU 3.3 4.7 - - - +
155B PRO* 3.6 28.7 - - + -
157B ASP 2.7 30.2 + - - -
158B PRO* 3.5 10.9 - - - +
162B MET* 4.2 5.2 - - + +
163B PHE* 3.7 26.5 - + + -
179B LEU* 3.5 31.5 - - + +
180B ASP 5.4 1.0 + - - -
184B VAL* 3.7 23.6 + - + +
186B GLU* 1.3 77.7 - - - +
188B THR* 1.3 65.1 + - - +
189B LEU* 4.7 8.3 - - + -
207B ALA 3.9 0.2 - - - +
208B VAL* 3.5 3.5 - - - -
209B VAL* 3.0 35.4 + - + +
211B ILE* 3.9 17.0 - - + -
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B SER 3.9 0.7 - - - +
153B GLN* 3.6 2.8 - - - -
154B GLU* 2.7 45.0 + - - +
186B GLU* 4.3 10.2 + - - -
187B TYR* 1.3 74.3 + - - +
189B LEU* 1.3 66.4 + - - +
190B THR* 4.0 4.0 + - - +
206B VAL* 4.1 28.5 - - + -
207B ALA 3.7 2.5 - - - -
208B VAL* 4.2 15.7 - - + +
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Residues in contact with LEU 189 (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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150B ILE* 4.4 15.3 - - + -
152B SER 3.5 3.4 - - - +
153B GLN* 3.6 35.4 - - + +
163B PHE* 4.0 34.5 - - + +
172B ILE* 4.1 21.3 - - + -
187B TYR* 4.7 2.7 - - + -
188B THR* 1.3 74.9 - - - +
190B THR* 1.3 62.9 + - - +
191B ILE* 3.4 12.1 + - + -
206B VAL* 3.1 7.7 - - - -
207B ALA* 2.8 39.9 + - + +
209B VAL* 4.0 23.8 - - + -
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Residues in contact with THR 190 (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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150B ILE* 3.5 2.8 - - - +
151B HIS* 2.6 50.3 + - + +
152B SER* 2.8 32.4 + - - -
188B THR* 4.0 4.4 + - - +
189B LEU* 1.3 71.3 - - - +
191B ILE* 1.3 57.0 + - - +
204B THR* 3.6 27.8 - - + -
205B ALA 3.7 4.3 - - - +
206B VAL* 4.5 11.1 - - + +
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Residues in contact with ILE 191 (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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108B PHE* 3.6 16.9 - - + -
113B PHE* 4.1 5.2 - - + -
130B VAL* 3.8 37.2 - - + -
149B SER 3.4 9.9 - - - +
150B ILE* 4.4 9.0 - - + -
165B ILE* 4.8 5.8 - - + -
172B ILE* 4.4 11.4 - - + -
189B LEU* 3.8 21.8 - - + +
190B THR* 1.3 78.8 - - - +
192B GLN* 1.3 63.1 + - - +
204B THR* 3.4 5.4 - - - +
205B ALA* 2.9 44.5 + - + +
206B VAL 3.9 17.9 - - - +
207B ALA* 4.2 5.4 - - + -
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Residues in contact with GLN 192 (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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108B PHE* 3.6 7.3 - - - -
147B ALA 3.8 0.2 - - - +
148B TYR* 3.4 5.4 - - - +
149B SER* 2.8 52.0 + - - +
150B ILE 5.1 0.2 - - - -
151B HIS* 3.6 42.6 - - + +
191B ILE* 1.3 82.3 - - - +
193B ALA* 1.3 60.4 + - - +
194B THR* 4.9 2.4 + - - +
202B THR* 3.8 19.6 - - + +
203B THR 3.3 6.5 - - - +
204B THR* 3.5 22.7 + - + +
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Residues in contact with ALA 193 (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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106B PRO* 3.7 7.5 - - + +
108B PHE* 3.7 11.4 - - + -
132B ALA* 3.6 31.2 - - + -
146B VAL* 3.6 13.0 - - + -
147B ALA 3.4 4.7 - - - -
148B TYR* 4.2 2.2 - - + -
192B GLN* 1.3 74.3 - - - +
194B THR* 1.3 62.3 + - - +
202B THR* 3.3 2.4 - - - -
203B THR* 3.0 35.3 + - + -
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PRO* 4.4 0.9 - - - -
146B VAL* 3.5 2.4 - - - +
147B ALA* 2.8 35.7 + - - -
149B SER* 5.0 3.3 + - - -
192B GLN* 4.9 3.6 + - - +
193B ALA* 1.3 76.6 + - - +
195B ASP* 1.3 69.9 + - - +
198B GLY* 3.4 34.2 + - - +
200B GLY 3.6 14.6 - - - +
201B SER 3.2 7.6 - - - +
202B THR* 2.6 28.9 + - - +
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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