Contacts of the strand formed by residues 186 - 193 (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 GLY 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A LYS* 3.9 9.2 - - - -
184A ASP 3.5 1.2 + - - -
185A ALA* 1.3 75.6 - - - +
187A PHE* 1.4 67.6 + - - -
188A TYR* 3.6 10.6 - - - -
205A GLN* 3.7 2.1 - - - -
206A LEU 2.8 35.5 + - - -
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Residues in contact with PHE 187 (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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135A SER* 5.9 0.2 - - - -
162A LYS* 3.4 8.7 - - - +
163A MET* 2.8 44.1 + - - +
186A GLY* 1.4 72.9 - - - -
188A TYR* 1.3 63.5 + - - +
203A TRP* 3.6 30.7 - + + -
204A SER 3.3 13.7 - - - -
205A GLN* 3.5 40.8 - - + -
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Residues in contact with TYR 188 (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* 5.1 0.2 - - - +
146A LEU* 3.7 26.2 - - + -
160A TRP* 4.2 8.6 - + + -
161A PHE 3.2 15.5 - - - +
162A LYS* 3.4 24.0 - - + +
167A ILE* 3.6 21.1 - - + -
175A LEU* 3.6 20.9 - - + -
177A PHE* 3.6 19.0 - + - -
184A ASP* 2.5 32.7 + - - -
186A GLY 3.6 20.9 - - - -
187A PHE* 1.3 74.3 - - - +
189A VAL* 1.3 60.9 + - - +
202A GLN 3.9 1.0 - - - +
203A TRP* 3.4 7.9 - - - -
204A SER* 2.8 42.6 + - - +
206A LEU* 4.0 13.7 - - + -
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Residues in contact with VAL 189 (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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160A TRP* 3.5 7.8 - - - -
161A PHE* 2.9 47.1 + - + +
163A MET 4.4 0.9 - - - +
188A TYR* 1.3 76.0 - - - +
190A CYS* 1.3 62.9 + - - +
200A PHE* 4.0 26.2 - - + -
201A SER* 3.2 36.3 - - - +
202A GLN 4.2 3.6 - - - +
203A TRP* 3.7 35.9 - - + +
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Residues in contact with CYS 190 (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* 3.8 27.1 - - + -
158A TYR* 4.0 15.3 - - - -
159A GLN 3.6 9.0 - - - -
160A TRP* 3.5 45.1 - - + -
189A VAL* 1.3 74.1 - - - +
191A ARG* 1.3 70.4 + - - +
192A VAL* 4.0 2.1 + - - +
199A GLU 3.7 0.9 - - - +
200A PHE* 3.5 4.4 - - - -
201A SER* 2.7 43.6 + - - +
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Residues in contact with ARG 191 (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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157A GLN* 3.7 0.7 - - - +
158A TYR* 3.4 4.4 - - - -
159A GLN* 2.8 62.5 + - - +
161A PHE* 4.0 17.7 - - + -
166A GLU* 4.3 8.7 + - - -
189A VAL 4.2 0.4 - - - -
190A CYS* 1.3 73.9 - - - +
192A VAL* 1.3 65.5 + - - +
193A ASN* 4.0 22.7 + - - +
198A PHE* 5.1 8.7 - - + -
199A GLU 3.4 10.8 - - - +
200A PHE* 3.5 42.7 - - + -
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Residues in contact with VAL 192 (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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127A SER 3.6 27.9 + - - +
129A ILE* 3.8 19.1 - - + -
148A CYS* 3.8 28.7 - - - -
150A ALA* 3.7 22.2 - - + -
156A VAL* 4.7 3.6 - - + -
157A GLN 3.2 9.4 - - - +
158A TYR* 4.2 14.8 - - + -
190A CYS 4.5 0.9 - - - +
191A ARG* 1.3 76.6 - - - +
193A ASN* 1.3 63.1 + - - +
198A PHE* 3.5 0.9 - - - -
199A GLU* 2.9 31.2 + - - +
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Residues in contact with ASN 193 (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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127A SER 4.1 2.7 - - - +
156A VAL* 3.4 8.5 - - - +
157A GLN* 2.8 70.3 + - - +
158A TYR 5.9 0.3 - - - -
191A ARG* 4.0 26.8 + - - +
192A VAL* 1.3 74.4 - - - +
194A ASN* 1.3 62.9 + - - +
195A ASN* 4.7 4.8 - - - +
197A THR 3.8 17.3 - - - +
198A PHE* 4.3 6.1 - - + +
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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