Contacts of the helix formed by residues 1195 - 1200 (chain B) in PDB entry 5XA0
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 ARG1195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1192B ALA* 5.2 1.5 - - - +
1193B SER 3.0 6.3 + - - +
1194B VAL* 1.3 68.3 - - - +
1196B LYS* 1.3 65.6 + - - +
1197B SER 3.2 1.1 - - - -
1198B ARG* 3.1 7.5 + - - +
1199B LYS 2.9 7.8 + - - -
1239B GLU 5.1 0.4 - - - -
1240B PHE* 2.7 44.6 - - + +
1241B LEU* 4.1 9.2 - - + +
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Residues in contact with LYS1196 (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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1109B VAL* 6.2 0.7 - - + -
1194B VAL* 2.1 22.4 + - + +
1195B ARG* 1.3 70.0 - - - +
1197B SER* 1.3 56.1 + - - +
1199B LYS* 2.7 27.9 + - - +
1200B GLN* 2.8 19.8 + - + +
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Residues in contact with SER1197 (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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1108B ASP 4.3 1.1 - - - -
1109B VAL* 4.7 4.9 - - - +
1112B TYR* 3.3 34.3 - - - -
1190B GLU* 3.8 15.3 - - - +
1193B SER* 3.1 20.2 - - - -
1194B VAL* 3.2 3.4 + - - +
1195B ARG 3.2 0.2 - - - -
1196B LYS* 1.3 77.5 - - - +
1198B ARG* 1.3 66.9 + - - +
1200B GLN* 3.6 13.8 + - - +
1201B GLN* 5.3 0.5 - - - -
1237B ALA 4.2 3.1 - - - +
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Residues in contact with ARG1198 (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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1190B GLU 3.6 2.9 + - - -
1191B SER 3.2 13.0 - - - +
1192B ALA* 5.4 0.2 - - - -
1193B SER 4.2 1.0 + - - +
1195B ARG* 3.1 7.5 + - - +
1197B SER* 1.3 82.6 - - - +
1199B LYS* 1.3 59.9 + - - +
1200B GLN 3.2 0.7 + - - -
1201B GLN* 4.1 2.9 + - - +
1237B ALA 3.6 4.7 - - - +
1238B HIS* 2.9 34.1 - - - +
1239B GLU 2.7 46.0 - - - +
1240B PHE* 3.0 3.1 - - - +
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Residues in contact with LYS1199 (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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1195B ARG 2.9 11.8 + - - +
1196B LYS* 2.7 19.2 + - - +
1198B ARG* 1.3 72.7 - - - +
1200B GLN* 1.3 56.0 + - + +
1201B GLN* 3.3 6.7 + - - +
1238B HIS* 5.3 2.0 - - - -
1240B PHE* 3.8 13.9 - - + +
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Residues in contact with GLN1200 (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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1196B LYS* 2.8 19.7 + - + +
1197B SER* 4.2 9.5 - - - +
1198B ARG 3.2 0.6 + - - -
1199B LYS* 1.3 71.0 - - + +
1201B GLN* 1.3 56.8 + - - +
1202B GLN* 3.2 11.4 + - - +
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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