Contacts of the strand formed by residues 167 - 178 (chain B) in PDB entry 1KTW
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 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B VAL* 3.7 42.0 - - + +
135B VAL* 3.2 20.2 - - + +
138B PHE* 4.8 2.2 - - + -
164B LEU* 4.3 9.6 - - + -
165B GLY 3.0 8.0 + - - +
166B ASP* 1.3 73.8 + - - +
168B ARG* 1.3 68.4 + - - +
170B TYR* 4.0 31.4 - - + -
200B TRP 4.4 0.2 + - - -
201B SER* 3.2 43.4 - - - +
202B ARG 3.2 4.0 + - - +
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Residues in contact with ARG 168 (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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135B VAL 3.2 6.3 + - - -
136B ARG* 3.5 46.4 - - - +
137B ASN 3.1 15.6 + - - -
166B ASP* 4.7 4.5 + - - +
167B VAL* 1.3 82.3 - - - +
169B ASN* 1.3 75.2 + - + +
170B TYR* 3.7 2.2 - - - -
200B TRP 5.0 3.1 + - - +
202B ARG* 3.1 57.8 - - + +
203B ASN* 4.9 9.8 - - - +
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Residues in contact with ASN 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE 4.2 1.6 - - - +
39B TYR* 3.5 11.2 - - - -
40B VAL* 2.9 52.0 + - - +
136B ARG* 6.1 0.2 - - + -
137B ASN* 3.0 30.5 + - - +
138B PHE 3.2 18.5 + - - -
168B ARG* 1.3 79.8 - - + +
170B TYR* 1.3 55.9 + - - +
202B ARG 3.2 1.8 + - - -
203B ASN* 3.0 25.0 + - + +
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Residues in contact with TYR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR* 3.4 12.0 - - - -
129B VAL* 6.4 0.2 - - + -
138B PHE* 3.1 20.4 - + + +
164B LEU* 3.5 29.2 - - + +
167B VAL* 4.0 33.9 - - + -
169B ASN* 1.3 76.8 - - - +
171B LYS* 1.3 65.2 + - - +
172B ILE* 4.2 15.7 - - + -
189B VAL* 4.4 2.3 - - - +
201B SER* 3.0 36.8 + - - -
202B ARG 4.1 6.1 - - - -
203B ASN 3.1 12.0 + - - -
204B GLY* 3.2 16.6 - - - -
205B ILE 3.1 21.0 + - - -
206B ILE* 4.0 24.2 - - + +
229B ILE* 3.5 16.9 - - + +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASP* 5.0 9.7 + - - -
39B TYR* 4.0 34.5 - - + -
106B ARG* 6.3 0.4 - - - +
138B PHE* 3.2 5.1 + - - -
139B SER* 3.2 9.7 - - - -
140B PHE 2.9 25.3 + - - +
141B GLN* 3.8 26.5 + - + +
170B TYR* 1.3 80.3 - - - +
172B ILE* 1.3 72.2 + - - +
173B SER* 4.5 2.5 - - - -
205B ILE* 3.3 26.1 - - + +
207B GLU* 3.5 28.1 + - - -
232B ARG* 5.6 0.4 - - - +
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 4.8 7.9 - - + -
140B PHE* 3.3 8.7 - - + +
162B PHE* 3.8 46.7 - - + -
164B LEU* 4.0 30.1 - - + -
170B TYR* 4.2 19.1 - - + -
171B LYS* 1.3 78.4 - - - +
173B SER* 1.3 64.8 + - - +
175B PHE* 3.9 15.0 - - + -
187B ILE* 4.7 7.2 - - + -
205B ILE 3.0 9.0 + - - +
206B ILE* 3.4 13.2 - - + +
207B GLU 3.1 22.7 + - - +
209B ILE* 4.6 6.9 - - + +
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Residues in contact with SER 173 (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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140B PHE 2.9 11.8 + - - +
141B GLN* 3.4 25.2 + - - -
142B GLY 2.9 24.1 + - - -
171B LYS* 4.5 5.8 - - - -
172B ILE* 1.3 79.6 - - - +
174B ASN* 1.3 69.7 + - - +
175B PHE* 3.6 12.9 - - - -
207B GLU* 2.9 38.4 + - - +
208B ARG* 4.1 3.5 - - - -
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Residues in contact with ASN 174 (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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141B GLN* 4.7 0.2 - - + -
142B GLY* 3.0 35.8 + - - +
143B LEU 3.9 0.4 - - - -
144B GLY 3.0 24.7 + - - -
145B ASN 3.9 4.0 - - - +
146B GLY* 3.3 27.7 + - - +
147B PHE 3.6 0.5 + - - -
173B SER* 1.3 84.8 + - - +
175B PHE* 1.3 63.5 + - - +
207B GLU 3.2 3.0 + - - -
208B ARG* 3.0 52.7 + - - +
209B ILE* 4.6 0.2 - - - +
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Residues in contact with PHE 175 (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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140B PHE* 5.2 2.5 - + - -
146B GLY* 4.5 1.6 - - - -
147B PHE* 3.3 46.0 - + + +
149B VAL* 4.2 11.4 - - + -
161B VAL* 4.6 10.5 - - + -
162B PHE* 4.0 25.4 - + - -
172B ILE* 3.9 19.1 - - + -
173B SER 3.6 13.9 - - - -
174B ASN* 1.3 78.8 + - - +
176B THR* 1.3 64.7 + - - +
177B ILE* 4.0 24.0 - - + -
187B ILE* 4.7 2.2 - - + -
208B ARG 3.2 4.7 + - - +
209B ILE* 3.3 42.8 - - + +
210B LYS 3.3 20.1 + - - -
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Residues in contact with THR 176 (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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145B ASN 5.7 0.9 + - - -
147B PHE 2.9 10.8 + - - -
148B LEU* 3.6 10.9 - - + +
149B VAL* 2.9 29.6 + - - +
175B PHE* 1.3 77.2 + - - +
177B ILE* 1.3 66.2 + - - +
178B ASP* 4.1 8.3 - - - +
210B LYS* 3.3 25.2 - - + +
212B ASN* 3.7 25.6 - - - +
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B VAL* 3.5 21.8 - - + +
151B PHE* 4.6 10.8 - - + -
161B VAL* 4.0 13.2 - - + -
175B PHE* 4.0 19.1 - - + -
176B THR* 1.3 77.9 - - - +
178B ASP* 1.3 62.9 + - - +
179B ASP* 3.3 11.6 + - + +
186B SER* 3.6 36.3 - - - +
187B ILE* 5.6 1.6 - - + -
209B ILE* 4.0 18.6 - - + -
210B LYS 2.8 13.6 + - - +
211B GLN* 3.5 16.3 - - + +
212B ASN* 2.9 27.9 + - - +
220B LEU* 4.2 1.6 - - + -
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Residues in contact with ASP 178 (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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14B NA 2.1 31.6 - - - -
148B LEU* 3.8 17.4 - - + +
149B VAL 2.9 12.7 + - - +
150B ASP* 3.8 5.8 - - - +
151B PHE* 3.0 24.8 + - - +
152B LYS* 2.7 40.3 + - + +
176B THR* 4.1 2.5 - - - +
177B ILE* 1.3 70.0 - - - +
179B ASP* 1.3 64.5 + - - +
212B ASN* 3.1 27.0 + - - +
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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