Contacts of the strand formed by residues 1000 - 1004 (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 VAL1000 (chain v).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994v GLN 4.3 3.8 - - - +
995v THR* 5.1 2.9 - - - +
999v ARG* 1.3 76.9 - - - +
1001v ILE* 1.3 59.3 - - - +
1002v VAL* 3.8 1.7 + - + -
1010v ILE 3.4 4.9 - - - +
1011v TRP* 3.6 3.1 - - - -
1012v VAL* 2.9 50.3 + - + +
1014v TYR* 5.9 5.4 - - + +
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Residues in contact with ILE1001 (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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992v GLY 3.9 0.9 - - - +
993v ILE* 3.5 7.8 - - - +
994v GLN* 3.1 42.7 + - + +
999v ARG 4.3 0.4 - - - -
1000v VAL* 1.3 72.9 - - - +
1002v VAL* 1.3 59.7 + - - +
1003v SER 4.0 0.6 + - - -
1009v PHE* 5.7 7.2 - - + -
1010v ILE 3.7 4.3 - - - -
1011v TRP* 5.2 0.7 - - - +
1044v VAL* 5.8 8.3 - - + -
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Residues in contact with VAL1002 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986v ILE* 6.0 5.8 - - + -
992v GLY 4.0 2.7 - - - -
993v ILE* 5.0 3.1 - - + +
1000v VAL* 3.8 2.2 + - + +
1001v ILE* 1.3 72.5 - - - +
1003v SER* 1.3 62.1 + - - +
1004v ASP 3.6 1.4 + - - -
1008v SER 3.8 0.5 - - - +
1009v PHE* 3.4 5.4 - - - +
1010v ILE* 2.9 51.6 + - + +
1012v VAL* 5.7 5.8 - - + -
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Residues in contact with SER1003 (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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990v ILE* 3.7 5.9 - - - +
991v SER* 2.9 29.5 + - - -
992v GLY* 2.9 31.8 + - - +
1001v ILE 4.0 0.4 + - - -
1002v VAL* 1.3 71.9 - - - +
1004v ASP* 1.3 65.6 + - - +
1008v SER 4.3 3.1 - - - -
1009v PHE* 4.7 3.8 - - - +
1033v VAL* 4.7 12.6 - - - -
1034v THR 5.4 4.0 - - - -
1035v THR 5.7 1.8 - - - -
1036v ALA* 5.4 12.8 - - - -
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Residues in contact with ASP1004 (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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987v ALA* 4.9 15.7 - - + -
988v ASN 5.8 0.2 - - - +
989v TYR 3.7 8.3 - - - +
990v ILE* 5.0 0.4 - - - +
991v SER* 4.1 0.8 - - - -
1002v VAL 3.6 1.8 + - - -
1003v SER* 1.3 74.9 - - - +
1005v VAL* 1.3 64.4 + - - +
1006v GLN* 3.2 1.3 + - + +
1007v GLU* 3.8 23.4 + - + +
1008v SER 3.2 25.2 + - - +
1033v VAL* 3.4 23.6 + - - +
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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