Contacts of the strand formed by residues 188 - 192 (chain A) in PDB entry 3P3W
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 ARG 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A TYR 5.5 1.2 + - - -
130A TRP* 3.5 49.3 - - + +
132A LYS 3.9 10.8 + - - +
133A PHE* 3.5 20.5 - - + -
134A VAL* 3.0 31.7 + - - +
186A GLU* 3.7 0.6 - - - +
187A LYS* 1.3 90.1 + - - +
189A TYR* 1.3 62.2 + - - +
214A GLY 4.4 11.7 + - - -
215A TYR 5.8 0.2 + - - -
216A HIS* 3.6 25.7 + - + +
238A ASN* 5.3 5.3 - - - +
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Residues in contact with TYR 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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130A TRP* 3.8 7.8 - - - -
134A VAL* 3.7 29.4 - - + -
136A LEU* 4.4 19.7 - - + -
178A ILE* 3.6 29.0 - - + +
181A MET* 3.3 30.1 - - + +
182A ASP* 3.7 8.3 + - - -
186A GLU 4.0 9.6 + - - -
187A LYS 4.1 0.9 - - - -
188A ARG* 1.3 77.7 - - - +
190A LEU* 1.3 54.9 + - - +
191A ILE* 4.2 5.4 - - + -
215A TYR* 3.7 31.4 - + - -
216A HIS 2.8 11.5 + - - +
217A TYR* 3.7 38.4 - + + -
218A MET* 2.8 31.7 + - - -
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Residues in contact with LEU 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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121A ILE* 4.2 20.0 - - + -
125A LEU* 4.5 7.4 - - + -
130A TRP* 4.7 4.7 - - + -
133A PHE* 4.2 23.8 - - + -
134A VAL 2.7 16.6 + - - +
135A TYR* 3.4 29.1 - - + -
136A LEU* 2.9 29.1 + - - +
149A ILE* 5.0 6.7 - - + -
189A TYR* 1.3 72.7 - - - +
191A ILE* 1.3 63.2 + - - +
218A MET* 3.4 38.6 - - + +
220A ALA* 4.1 19.5 - - + -
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Residues in contact with ILE 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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136A LEU* 3.7 29.6 - - + +
189A TYR* 4.2 16.2 - - + +
190A LEU* 1.3 76.4 - - - +
192A ASP* 1.3 60.2 + - - +
193A CYS* 3.7 13.4 + - - -
198A ILE* 3.8 26.7 - - + +
201A ILE* 3.8 24.5 - - + -
202A LEU* 5.9 1.3 - - + -
217A TYR* 4.4 15.7 - - + -
218A MET 2.8 11.5 + - - +
219A LEU* 3.7 26.9 - - + -
220A ALA* 2.7 34.1 + - - +
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Residues in contact with ASP 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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135A TYR* 3.5 24.3 + - + +
136A LEU 2.7 17.0 + - - +
137A TYR* 4.1 3.7 - - + +
138A ASP* 3.0 24.8 + - - +
141A ARG* 3.1 33.2 + - - +
142A GLY 4.7 1.9 - - - +
145A VAL* 3.2 32.1 - - - +
190A LEU* 5.6 0.2 - - + -
191A ILE* 1.3 73.4 - - - +
193A CYS* 1.3 59.4 + - - +
220A ALA* 3.5 19.5 - - + +
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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