Contacts of the helix formed by residues 1252 - 1256 (chain R) in PDB entry 3F5P
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 ASN1252 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1250R GLN* 3.4 7.1 - - - +
1251R TYR* 1.3 79.5 - - + +
1253R PRO* 1.3 81.5 - - - +
1254R LYS* 3.3 27.2 + - - +
1255R MET* 2.9 46.2 + - + +
1256R ARG 3.9 2.3 + - - -
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Residues in contact with PRO1253 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182R GLU* 3.2 35.2 - - + +
1190R THR* 5.1 0.7 - - - +
1192R TYR* 3.6 44.5 - - + +
1251R TYR* 3.3 7.4 - - + +
1252R ASN* 1.3 93.8 - - - +
1254R LYS* 1.3 61.7 + - + +
1255R MET 3.2 0.9 + - - -
1256R ARG* 3.4 29.5 + - - +
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Residues in contact with LYS1254 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049K ASN* 4.4 4.0 - - - +
1192R TYR* 4.3 31.6 - - + +
1252R ASN* 3.0 22.9 + - - +
1253R PRO* 1.3 78.4 - - + +
1255R MET* 1.3 69.7 + - + +
1256R ARG 3.4 6.3 + - - +
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Residues in contact with MET1255 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987K TYR* 2.8 32.8 + - - -
1042K ARG* 5.2 9.6 - - - +
1045K ILE* 3.6 15.0 - - + +
1046K GLU* 3.9 31.0 - - + +
1049K ASN* 3.2 34.5 - - + +
1250R GLN* 3.7 25.2 - - + +
1252R ASN* 2.9 37.7 + - + +
1254R LYS* 1.3 85.5 - - + +
1256R ARG* 1.3 52.5 + - - +
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Residues in contact with ARG1256 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987K TYR* 3.6 3.4 - - - -
1180R SER* 4.1 0.2 - - - -
1181R PRO* 4.2 3.6 - - - +
1182R GLU* 2.9 41.0 + - - -
1192R TYR* 3.0 35.0 + - + -
1195R VAL* 4.3 6.1 - - + -
1196R TRP* 3.9 25.9 - - - +
1247R MET 3.4 15.9 - - - +
1248R CYS 3.4 16.6 + - - +
1250R GLN* 2.8 22.2 + - + -
1251R TYR* 3.0 20.4 + - - +
1252R ASN 4.3 0.2 - - - +
1253R PRO* 3.4 25.0 + - - +
1254R LYS 4.0 6.4 - - - +
1255R MET* 1.3 80.6 - - - +
1257R PRO* 1.3 76.9 - - + +
1258R SER 4.0 0.2 + - - -
1261R GLU* 4.4 1.2 - - - +
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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