Contacts of the strand formed by residues 186 - 191 (chain Y) in PDB entry 5M32
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 186 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32Y LYS* 3.0 30.2 - - - +
36Y GLU* 4.4 2.8 + - - -
175Y ASN* 4.0 12.2 - - - +
176Y LEU 3.7 4.7 - - - +
177Y TYR* 2.4 54.1 + - + -
184Y TRP* 3.8 17.8 - - + -
185Y ILE* 1.3 77.3 - - - +
187Y VAL* 1.3 64.8 + - - +
188Y SER 3.6 22.9 + - - +
189Y SER* 4.4 11.5 + - - -
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Residues in contact with VAL 187 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153Y TYR* 3.4 39.5 - - + +
157Y ARG* 3.6 12.0 + - - +
176Y LEU* 3.3 46.3 + - + +
177Y TYR* 4.6 0.4 - - - +
178Y HIS* 5.1 1.6 - - + -
185Y ILE* 3.7 20.0 - - + +
186Y ARG* 1.3 78.0 - - - +
188Y SER* 1.3 62.5 + - - +
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Residues in contact with SER 188 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157Y ARG* 3.3 32.1 - - - +
174Y VAL* 3.1 13.1 + - - +
175Y ASN* 3.7 6.9 - - - +
176Y LEU* 3.0 34.1 + - - +
186Y ARG* 3.6 19.8 + - - +
187Y VAL* 1.3 82.2 + - - +
189Y SER* 1.3 64.2 + - - +
190Y ASP* 4.2 2.5 - - - -
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Residues in contact with SER 189 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173Y ALA* 4.4 9.8 - - - +
174Y VAL 3.6 6.7 - - - -
175Y ASN* 4.9 1.6 - - - +
186Y ARG* 4.4 11.3 + - - +
188Y SER* 1.3 75.6 - - - +
190Y ASP* 1.3 68.9 + - - +
191Y ASN* 3.8 1.0 + - - +
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Residues in contact with ASP 190 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157Y ARG* 2.5 37.1 + - - +
173Y ALA* 3.3 1.1 - - - -
174Y VAL* 2.6 45.4 + - + +
188Y SER* 3.8 1.3 - - - -
189Y SER* 1.3 82.5 + - - +
191Y ASN* 1.3 64.2 + - - +
194Y ASP* 5.4 8.6 - - + +
195Y LEU* 4.4 9.8 - - + +
198Y LYS* 5.7 3.1 + - - -
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Residues in contact with ASN 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202I ARG* 4.4 15.6 - - - +
172Y GLY 3.4 16.6 - - - +
173Y ALA* 3.7 5.8 - - + +
174Y VAL* 5.0 0.7 - - - -
189Y SER 3.8 1.4 + - - +
190Y ASP* 1.3 74.9 - - - +
192Y VAL* 1.3 67.2 + - - +
193Y ALA* 4.1 12.8 - - - +
194Y ASP* 2.9 36.8 + - - +
195Y LEU* 3.3 25.3 + - - +
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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