Contacts of the helix formed by residues 192 - 200 (chain B) in PDB entry 1M2V
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 ASN 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B PRO* 3.1 3.9 + - - +
191B LYS* 1.3 88.4 + - - +
193B SER* 1.3 62.0 + - - +
194B SER* 3.1 13.0 + - - +
195B LEU* 2.8 39.3 + - - +
196B LEU* 3.2 18.7 + - - +
600B VAL* 4.3 9.2 - - - -
602B GLU 3.1 19.1 - - - +
603B SER* 3.7 10.5 - - - +
637B GLU* 4.6 14.6 + - - +
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASN* 1.3 68.6 - - - +
194B SER* 1.3 62.9 + - - +
196B LEU* 3.2 10.8 + - - +
197B LYS* 2.8 32.2 + - - +
600B VAL 3.4 10.2 + - - -
601B ASP 3.4 24.0 + - - -
602B GLU* 2.9 20.5 + - - +
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Residues in contact with SER 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASN* 3.1 10.7 + - - +
193B SER* 1.3 80.1 + - - +
195B LEU* 1.3 64.7 + - - +
197B LYS* 3.1 8.0 + - - +
198B LYS* 2.9 24.6 + - - +
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PRO* 4.0 12.5 - - + +
191B LYS 4.3 1.1 - - - +
192B ASN* 2.8 28.6 + - - +
194B SER* 1.3 73.9 - - - +
196B LEU* 1.3 62.7 + - - +
198B LYS* 3.4 10.8 + - + +
199B SER* 3.1 21.1 + - - -
636B THR 3.3 26.5 - - - +
637B GLU* 3.4 28.0 - - + +
638B SER 4.0 0.9 - - - +
639B LEU* 3.8 33.7 - - + +
642B VAL* 4.3 8.7 - - + -
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B LEU* 4.0 14.8 - - + -
190B PRO* 3.6 27.3 - - + +
192B ASN 3.2 13.1 + - - +
193B SER* 3.2 12.2 + - - +
195B LEU* 1.3 76.8 - - - +
197B LYS* 1.3 65.4 + - + +
199B SER* 2.5 25.4 + - - +
200B LYS* 3.7 1.9 + - - -
201B LEU 3.5 22.3 + - - +
203B PHE* 4.3 13.0 - - + +
598B VAL 4.9 2.9 - - - +
599B ASN* 5.1 3.1 - - - +
600B VAL* 3.7 36.3 - - + +
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Residues in contact with LYS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B SER 2.8 17.2 + - - +
194B SER* 3.5 7.0 - - - +
196B LEU* 1.3 80.0 - - + +
198B LYS* 1.3 62.2 + - - +
200B LYS* 3.2 34.1 + - - +
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Residues in contact with LYS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B SER 2.9 15.6 + - - +
195B LEU* 3.8 14.6 - - + +
197B LYS* 1.3 76.5 - - - +
199B SER* 1.3 62.8 + - - +
200B LYS* 3.0 7.5 + - - +
639B LEU* 4.8 11.9 - - + -
685B THR* 3.2 21.2 - - - +
689B GLU* 4.1 35.4 + - + +
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Residues in contact with SER 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU 3.1 12.8 + - - -
196B LEU* 2.5 26.4 + - - +
198B LYS* 1.3 76.8 - - - +
200B LYS* 1.3 59.8 + - - +
201B LEU* 2.9 25.7 + - - +
639B LEU* 3.6 23.1 - - - +
642B VAL* 4.2 15.5 - - - +
643B TYR* 2.5 30.9 + - - -
685B THR* 4.7 0.2 - - - -
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B LEU 3.7 1.0 + - - -
197B LYS* 3.2 25.8 + - - +
198B LYS* 3.0 12.5 + - - +
199B SER* 1.3 78.6 + - - +
201B LEU* 1.3 58.9 + - - +
643B TYR* 4.4 1.3 - - - +
655B TYR* 3.8 12.2 + - - -
677B LYS* 5.9 2.8 - - - +
681B ASP* 4.1 37.8 + - + +
682B ILE* 3.6 15.1 - - + +
685B THR* 3.0 26.2 - - + +
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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