Contacts of the strand formed by residues 157 - 162 (chain A) in PDB entry 3K0W
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 GLN 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A VAL* 1.3 76.0 - - - +
158A TYR* 1.3 64.5 + - - +
191A ARG* 3.7 0.6 - - - +
192A VAL* 3.2 10.2 - - - +
193A ASN* 2.8 64.6 + - - +
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Residues in contact with TYR 158 (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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148A CYS 3.4 20.2 - - - -
149A ARG* 3.7 2.3 - - - -
150A ALA 3.2 25.0 + - - -
153A HIS* 2.7 39.2 + + - +
154A PRO* 5.6 1.6 - - + -
156A VAL* 3.6 25.2 - - + +
157A GLN* 1.3 77.7 - - - +
159A GLN* 1.3 63.1 + - - +
171A ASN* 3.0 29.4 + - - +
172A THR* 3.5 23.1 - - - +
173A SER* 3.5 23.6 - - - -
190A CYS* 4.0 18.8 - - - -
191A ARG* 3.4 3.4 - - - -
192A VAL* 4.2 15.7 - - + -
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Residues in contact with GLN 159 (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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158A TYR* 1.3 75.9 - - - +
160A TRP* 1.3 81.5 + - - +
161A PHE* 3.7 11.8 - - + -
166A GLU* 3.7 34.6 - - + +
167A ILE 2.8 28.8 + - - +
169A ASN 5.6 0.9 + - - -
170A GLY 3.4 9.3 + - - +
171A ASN* 4.3 12.3 - - - +
190A CYS* 3.6 1.3 - - - -
191A ARG* 2.8 64.7 + - - +
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Residues in contact with TRP 160 (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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133A PRO* 3.7 31.2 - - + -
146A LEU* 3.7 41.1 - - + -
147A CYS 4.0 0.7 - - - -
148A CYS* 3.8 12.3 - - + -
159A GLN* 1.3 90.5 + - - +
161A PHE* 1.3 65.1 + - - +
166A GLU 4.0 0.2 - - - -
167A ILE* 3.1 26.0 + - + +
170A GLY* 2.8 28.5 + - - +
172A THR* 2.9 28.7 + - + -
173A SER 3.5 20.3 + - - -
175A LEU* 3.8 34.5 - - + +
188A TYR* 4.2 10.5 - - + -
189A VAL 3.5 20.6 - - - -
190A CYS* 3.5 20.9 - - + -
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Residues in contact with PHE 161 (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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159A GLN* 3.7 24.2 - - + -
160A TRP* 1.3 78.1 - - - +
162A LYS* 1.3 57.6 + - - +
163A MET 3.2 19.6 + - - +
164A ASN* 4.1 8.7 - - - -
165A LYS 3.2 16.6 - - - -
166A GLU* 3.5 39.9 - - + -
167A ILE* 3.8 6.7 - - - -
188A TYR* 3.2 8.5 - - - -
189A VAL* 2.9 45.4 + - + -
191A ARG* 4.0 27.4 - - + -
200A PHE* 4.2 13.5 - + - -
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Residues in contact with LYS 162 (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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161A PHE* 1.3 69.6 - - - +
163A MET* 1.3 65.9 + - + +
165A LYS* 2.9 41.3 + - + +
167A ILE* 3.7 10.4 - - + +
183A LYS 3.0 20.2 + - - -
184A ASP* 3.7 4.6 + - - +
185A ALA 2.8 29.1 + - - -
186A GLY* 3.9 9.4 - - - -
187A PHE 3.4 10.5 - - - +
188A TYR* 3.4 35.0 + - + +
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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