Contacts of the strand formed by residues 155 - 160 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ILE* 5.4 1.3 - - + -
151C ALA* 3.7 27.8 - - + -
153C THR 3.3 0.2 + - - -
154C SER* 1.3 75.2 - - - +
156C PHE* 1.3 64.4 + - - +
197C THR* 3.1 8.0 - - - -
198C ILE* 2.9 40.9 + - + +
213C HIS* 4.2 0.2 - - - -
214C THR* 3.3 21.1 - - - +
216C VAL* 3.8 11.0 - - + -
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Residues in contact with PHE 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C MET 3.2 26.0 - - - -
121C PHE* 3.4 46.4 - + + -
124C VAL* 4.0 12.5 - - + +
135C VAL* 3.7 13.6 - - + +
136C ALA* 4.4 2.9 - - - +
147C ILE* 5.9 0.2 - - - +
155C ALA* 1.3 78.2 - - - +
157C LEU* 1.3 63.1 + - - +
195C CYS* 3.7 24.5 - - + -
196C VAL 3.3 13.5 - - - -
197C THR* 3.8 4.3 - - + -
207C ILE* 3.9 14.8 - - + -
208C SER 3.9 8.1 - - - -
209C CYS 4.0 1.6 - - - -
211C ALA 3.1 21.1 - - - -
213C HIS* 3.7 26.2 - + + +
214C THR 3.4 9.0 + - - +
216C VAL* 4.8 7.1 + - - +
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C PHE* 3.4 15.8 - - - -
135C VAL* 3.6 3.8 - - - -
136C ALA* 3.2 14.4 - - + +
138C PRO* 3.9 20.2 - - + -
147C ILE* 4.2 14.1 - - + -
156C PHE* 1.3 80.2 - - - +
158C GLY* 1.3 58.9 + - - +
159C ILE* 2.8 28.2 + - + +
196C VAL* 2.9 26.3 + - + +
198C ILE* 4.1 29.2 - - + +
204C TRP* 3.6 43.5 - - + +
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Residues in contact with GLY 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C PHE* 4.4 0.4 - - - -
135C VAL* 3.5 18.7 - - - +
136C ALA 2.9 14.5 + - - -
137C ILE* 3.4 22.2 - - - +
157C LEU* 1.3 67.9 - - - +
159C ILE* 1.3 60.2 + - - +
170C TYR* 3.4 2.4 - - - -
171C VAL* 2.8 43.7 + - - -
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Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ILE* 4.7 2.0 - - + -
138C PRO* 4.8 5.8 - - + -
157C LEU* 2.8 29.3 + - + +
158C GLY* 1.3 81.1 - - - +
160C THR* 1.3 73.6 + - - +
168C PHE* 3.8 28.0 - - + -
169C MET 3.3 11.2 - - - +
170C TYR* 4.0 13.5 - - + -
171C VAL* 3.9 0.6 - - - +
176C LEU* 3.4 33.2 - - + -
181C TRP* 5.4 0.2 - - + -
195C CYS* 4.7 0.2 - - - +
196C VAL* 3.6 31.5 + - + +
204C TRP* 3.5 26.5 - - + -
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Residues in contact with THR 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C PHE* 3.5 33.9 - - + -
159C ILE* 1.3 86.7 - - - +
161C ASP* 1.3 59.1 + - - +
162C GLU* 3.6 27.6 + - - +
163C VAL* 5.2 1.4 + - - +
167C GLN 3.8 0.5 - - - +
168C PHE* 3.6 8.5 - - - -
169C MET* 2.8 33.5 + - - +
171C VAL* 4.5 6.7 - - + +
194C ASP 3.0 18.6 - - - +
195C CYS* 3.8 10.1 - - - -
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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