Contacts of the strand formed by residues 155 - 164 (chain B) in PDB entry 1KWV
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 ALA 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ILE* 5.7 0.9 - - + -
151B ALA* 4.0 7.2 - - + -
153B THR 3.2 6.5 + - - +
154B SER* 1.3 76.3 - - - +
156B PHE* 1.3 64.9 + - - +
197B THR* 3.1 6.5 - - - -
198B ILE* 2.9 38.2 + - + +
213B HIS* 4.1 0.4 - - - -
214B THR* 3.2 28.9 - - - +
216B VAL* 3.9 18.6 - - + -
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Residues in contact with PHE 156 (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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119B MET 3.0 28.5 - - - -
121B PHE* 3.5 45.8 - + + -
124B VAL* 4.1 11.9 - - + -
135B VAL* 3.6 14.3 - - + +
136B ALA* 4.4 2.4 + - - +
155B ALA* 1.3 79.6 - - - +
157B LEU* 1.3 64.8 + - - +
195B CYS* 3.9 15.9 - - + -
196B VAL 3.3 9.0 - - - -
197B THR* 3.8 7.6 - - + -
207B ILE* 3.8 22.7 - - + -
208B SER 3.9 5.8 - - - -
209B CYS 4.2 0.4 - - - -
211B ALA 3.1 21.3 - - - -
213B HIS* 3.5 24.9 - + + +
214B THR 3.4 9.0 + - - +
216B VAL* 4.8 6.2 + - - +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 3.4 16.1 - - - -
135B VAL* 3.6 3.4 - - - -
136B ALA* 3.2 11.4 - - + +
138B PRO* 3.7 28.5 - - + -
147B ILE* 4.2 12.6 - - + -
155B ALA* 5.8 0.2 - - + -
156B PHE* 1.3 81.3 - - - +
158B GLY* 1.3 58.8 + - - +
159B ILE* 2.8 26.3 + - + +
196B VAL* 2.9 24.3 + - + +
198B ILE* 3.9 34.5 - - + +
204B TRP* 3.6 41.5 - - + +
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Residues in contact with GLY 158 (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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121B PHE* 4.6 0.2 - - - -
135B VAL* 3.5 17.8 - - - +
136B ALA 2.8 14.6 + - - -
137B ILE* 3.5 17.2 - - - +
157B LEU* 1.3 70.1 - - - +
159B ILE* 1.3 60.3 + - - +
170B TYR* 3.2 6.8 - - - -
171B VAL* 2.8 40.9 + - - -
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 4.7 1.6 - - + -
138B PRO* 4.5 7.9 - - + -
157B LEU* 2.8 25.3 + - + +
158B GLY* 1.3 82.2 - - - +
160B THR* 1.3 72.6 + - - +
168B PHE* 3.5 32.8 - - + -
169B MET 3.2 10.5 - - - +
170B TYR* 3.8 17.7 - - + -
171B VAL* 4.1 0.8 - - - +
176B LEU* 3.9 17.7 - - + -
181B TRP* 5.8 0.2 - - + -
195B CYS* 4.7 0.2 - - - +
196B VAL* 3.6 30.7 + - + +
204B TRP* 3.7 34.3 - - + -
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Residues in contact with THR 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 3.7 31.6 - - + -
159B ILE* 1.3 82.4 - - - +
161B ASP* 1.3 59.4 + - - +
162B GLU* 3.2 30.4 + - - +
168B PHE* 3.7 6.7 - - - -
169B MET* 2.8 35.3 + - - +
171B VAL* 4.6 6.6 - - + +
194B ASP 2.9 18.4 - - - +
195B CYS* 3.8 10.3 - - - -
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Residues in contact with ASP 161 (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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160B THR* 1.3 72.8 - - - +
162B GLU* 1.3 59.2 + - - +
163B VAL 3.1 7.6 + - - +
164B THR 3.7 17.7 - - - +
165B GLU* 2.9 22.3 + - - +
166B GLY 3.1 7.3 + - - +
167B GLN 3.6 23.3 - - - +
168B PHE* 3.3 24.5 - - + -
169B MET* 5.9 0.2 - - - -
194B ASP* 2.8 24.7 + - - +
602B CA 2.4 30.0 - - - -
604B CA 4.0 2.6 - - - -
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Residues in contact with GLU 162 (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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121B PHE* 5.0 4.4 - - - -
125B LYS* 5.2 8.8 + - - -
160B THR* 3.2 29.1 + - - +
161B ASP* 1.3 75.7 - - - +
163B VAL* 1.3 63.9 + - + +
194B ASP* 3.6 27.7 - - + +
195B CYS* 4.6 0.2 - - - -
209B CYS* 3.6 20.8 - - - +
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Residues in contact with VAL 163 (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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161B ASP* 3.1 1.6 - - - +
162B GLU* 1.3 85.9 - - + +
164B THR* 1.3 72.9 + - - +
165B GLU 4.1 0.8 + - - -
167B GLN 5.6 0.4 - - - +
169B MET* 5.5 13.7 - - + -
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Residues in contact with THR 164 (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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161B ASP 3.7 5.2 - - - +
163B VAL* 1.3 91.2 + - - +
165B GLU* 1.3 60.1 + - - +
166B GLY 3.2 0.3 + - - -
167B GLN* 2.7 64.0 + - + +
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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