Contacts of the helix formed by residues 1012 - 1017 (chain U) in PDB entry 6FF7
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 ARG1012 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140M LEU* 5.4 8.1 - - + -
174M LYS* 5.3 6.5 - - + -
175M LEU* 5.0 4.9 - - + +
929U CYS* 3.6 27.4 - - + -
930U GLU* 5.3 0.9 - - - +
1008U LEU 3.0 5.2 + - - +
1009U GLU* 3.6 15.5 - - - +
1010U GLU 3.3 1.0 - - - -
1011U PHE* 1.3 77.2 - - - +
1013U ALA* 1.3 53.6 + - - +
1015U GLU* 2.8 32.4 + - + +
1016U LEU* 3.3 7.2 + - - +
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Residues in contact with ALA1013 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174M LYS 4.2 7.1 + - - +
175M LEU* 4.0 25.8 - - + +
1009U GLU 4.8 0.4 + - - -
1010U GLU 3.9 13.1 + - - +
1011U PHE 3.1 0.6 - - - -
1012U ARG* 1.3 79.4 - - - +
1014U SER* 1.3 55.2 + - - +
1015U GLU 3.1 0.2 - - - -
1016U LEU* 3.1 2.9 + - - +
1017U LEU* 2.8 34.2 + - + +
1023U ARG* 6.3 0.7 - - - -
1026U TYR* 4.3 23.6 - - + -
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Residues in contact with SER1014 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901U VAL* 5.6 10.5 - - - -
902U LEU* 5.9 7.4 - - - -
905U ARG* 6.3 2.9 - - - -
1011U PHE* 3.0 16.9 + - - -
1013U ALA* 1.3 78.2 - - - +
1015U GLU* 1.3 57.8 + - - +
1017U LEU* 3.2 20.6 - - - +
1018U ARG* 4.9 1.9 - - - -
1023U ARG* 5.4 10.5 - - - -
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Residues in contact with GLU1015 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928U THR* 6.1 4.3 - - - -
929U CYS* 5.5 7.4 - - + +
1011U PHE 4.0 1.2 + - - +
1012U ARG* 2.8 17.7 + - + +
1014U SER* 1.3 78.1 - - - +
1016U LEU* 1.3 58.8 + - - +
1017U LEU 3.4 1.6 + - - -
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Residues in contact with LEU1016 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M LEU* 4.5 13.2 - - + -
1012U ARG 3.3 8.5 + - - +
1013U ALA* 3.1 11.1 + - - +
1015U GLU* 1.3 77.6 - - - +
1017U LEU* 1.3 60.5 + - + +
1018U ARG 4.2 0.8 + - - -
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Residues in contact with LEU1017 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013U ALA* 2.8 15.5 + - + +
1014U SER* 3.2 20.4 - - - +
1015U GLU 4.9 0.9 - - - -
1016U LEU* 1.3 79.7 - - + +
1018U ARG* 1.3 64.3 + - - +
1019U SER 3.7 3.6 - - - +
1022U ASP* 3.9 28.0 - - + +
1023U ARG* 4.3 14.7 - - - +
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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