Contacts of the strand formed by residues 1021 - 1025 (chain v) 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 LEU1021 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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967v LEU* 5.5 6.3 - - + +
981v CYS* 5.1 9.0 - - + +
982v GLU 5.4 1.5 + - - -
983v ASN* 4.0 31.0 - - + +
1012v VAL* 5.3 11.0 - - + -
1013v ARG 3.6 5.8 - - - -
1014v TYR* 5.1 2.7 - - + +
1019v ASN 3.7 1.9 + - - +
1020v GLN* 1.3 72.4 - - - +
1022v ILE* 1.3 61.1 + - - +
1023v ILE 3.9 1.4 + - - -
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Residues in contact with ILE1022 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012v VAL* 4.5 1.1 - - - -
1013v ARG* 3.0 40.1 + - + +
1020v GLN* 3.8 8.7 - - + +
1021v LEU* 1.3 73.6 - - - +
1023v ILE* 1.3 67.1 + - - +
1024v PHE* 3.7 2.3 + - + +
1066v VAL* 3.9 23.6 - - + +
1068v GLU* 5.3 11.9 - - + +
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Residues in contact with ILE1023 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985v HIS* 6.0 6.7 - - + -
1010v ILE* 5.8 6.3 - - + -
1011v TRP 3.4 12.6 - - - +
1012v VAL* 4.4 4.6 - - + +
1021v LEU 3.9 2.8 + - - -
1022v ILE* 1.3 77.6 - - - +
1024v PHE* 1.3 61.3 + - - +
1025v ALA 5.0 2.7 - - - +
1066v VAL* 5.1 4.9 - - - +
1085v ALA* 5.1 10.9 - - + +
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Residues in contact with PHE1024 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011v TRP* 3.3 7.6 + - + +
1013v ARG* 5.8 4.5 - - + +
1022v ILE* 3.7 4.4 + - + +
1023v ILE* 1.3 75.6 - - - +
1025v ALA* 1.3 63.3 + - + +
1063v ASN 4.5 16.4 - - - +
1064v ASP* 4.8 8.3 - - - +
1066v VAL* 4.7 14.1 - - + -
1085v ALA* 4.2 8.3 - - - -
1086v SER 4.7 0.9 + - - +
1087v GLN* 3.3 26.3 + - - +
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Residues in contact with ALA1025 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010v ILE* 3.7 3.1 - - - +
1011v TRP* 2.9 44.4 + - + +
1023v ILE* 5.4 1.7 - - - +
1024v PHE* 1.3 81.9 - - + +
1026v ASP* 1.3 65.3 + - - +
1062v THR* 5.9 5.2 - - - -
1085v ALA* 4.0 6.1 - - - +
1087v GLN* 3.5 18.4 - - + +
1089v ALA* 5.6 4.5 - - + -
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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