Contacts of the strand formed by residues 185 - 191 (chain A) in PDB entry 5JPM
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 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A MET* 4.2 33.8 - - + +
178A VAL 3.3 10.5 - - - +
179A GLU* 4.2 3.5 - - - +
183A GLY 4.2 0.8 + - - -
184A LEU* 1.3 86.7 - - + +
186A VAL* 1.3 60.1 + - - +
187A ARG 4.4 6.3 - - - +
188A LYS* 3.7 29.5 - - - +
1053B TYR* 3.2 24.8 + - - +
1057B GLN* 4.5 1.6 + - - +
1094B GLY 2.9 29.1 + - - -
1095B GLY 3.6 11.7 + - - -
1096B SER* 4.2 21.2 - - - +
1099B LYS* 5.4 4.4 - - - +
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Residues in contact with VAL 186 (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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178A VAL* 2.7 39.3 + - + +
179A GLU 4.6 0.2 - - - +
180A ASN* 4.4 11.0 - - + +
184A LEU* 3.7 12.8 - - + +
185A ARG* 1.3 74.8 - - - +
187A ARG* 1.3 66.4 + - + +
202A PHE* 5.2 0.4 - - + -
213A TRP* 4.2 14.1 - - + -
1050B GLN* 5.0 1.7 - - - +
1053B TYR* 3.4 26.5 - - - -
1054B MET* 3.9 30.6 - - + +
1057B GLN* 4.9 7.9 - - + -
1058B GLN* 3.5 28.0 - - - +
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Residues in contact with ARG 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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158A TYR* 4.6 2.6 + - - +
176A VAL 4.6 0.7 - - - +
177A MET* 3.3 7.1 - - - +
178A VAL* 3.1 37.8 + - + +
185A ARG* 4.4 4.4 - - - +
186A VAL* 1.3 87.3 - - + +
188A LYS* 1.3 62.3 + - - +
189A LYS* 3.3 22.9 - - + +
200A ASP* 2.7 39.2 + - - -
201A ASP 3.7 8.9 + - - -
202A PHE* 3.5 43.8 - - - +
1050B GLN* 3.3 40.2 + - + +
1053B TYR* 5.1 0.9 - - - -
1054B MET* 4.2 13.9 - - - +
1093B VAL 4.9 2.0 - - - -
1094B GLY 5.2 0.2 - - - -
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Residues in contact with LYS 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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175A THR* 5.2 7.9 - - - -
176A VAL 3.6 7.9 - - - +
177A MET* 4.4 6.5 - - + +
185A ARG* 3.7 29.4 - - - +
187A ARG* 1.3 76.6 - - - +
189A LYS* 1.3 68.2 + - - +
190A GLU* 2.7 42.0 + - - +
1050B GLN* 4.7 1.6 + - - +
1093B VAL 4.1 8.3 + - - +
1094B GLY* 3.4 40.5 + - - +
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Residues in contact with LYS 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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158A TYR* 4.8 3.4 - - - +
174A ILE 4.1 0.2 - - - +
175A THR* 3.3 3.5 - - - -
176A VAL* 2.9 46.3 + - + +
187A ARG* 3.3 34.5 - - + +
188A LYS* 1.3 84.5 - - - +
190A GLU* 1.3 65.5 + - - +
191A VAL* 4.2 0.7 - - + -
198A PHE* 4.7 13.0 - - + -
200A ASP* 3.7 16.2 - - - +
1050B GLN* 4.3 16.9 + - - +
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Residues in contact with GLU 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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173A THR* 4.8 6.8 - - + +
174A ILE 3.4 6.5 - - - +
175A THR* 3.6 26.8 - - + +
188A LYS* 2.7 32.8 + - - +
189A LYS* 1.3 77.1 - - - +
191A VAL* 1.3 62.2 - - - +
192A TYR* 5.7 1.8 - - - -
220A SER* 4.3 7.1 + - - -
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Residues in contact with VAL 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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173A THR* 3.5 4.6 - - - +
174A ILE* 2.9 47.8 + - + +
176A VAL* 4.8 4.9 - - + -
189A LYS* 5.3 0.9 - - + -
190A GLU* 1.3 76.3 - - - +
192A TYR* 1.3 77.7 + - - +
193A MET* 4.0 8.9 + - + +
198A PHE* 3.8 53.2 - - + -
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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