Contacts of the strand formed by residues 973 - 980 (chain A) 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 CYS 973 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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971A GLY 3.4 6.6 + - - +
972A GLU* 1.3 74.0 - - - +
974A ASN* 1.3 62.4 + - - +
975A VAL* 4.2 2.4 + - + +
1100A ARG* 3.4 5.9 - - - +
1101A PHE* 2.9 35.7 + - + +
1177A VAL* 6.2 1.1 - - + -
1178A TYR 3.4 13.7 - - - +
1179A SER* 3.8 20.2 - - - +
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Residues in contact with ASN 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A VAL 4.8 12.9 + - - +
966A TRP* 6.5 0.4 - - + -
973A CYS* 1.3 73.4 - - - +
975A VAL* 1.3 64.1 + - - +
1099A PHE 3.9 4.0 - - - +
1100A ARG* 4.5 5.8 - - + +
1177A VAL* 3.5 1.7 - - - +
1178A TYR* 2.8 45.5 + - + +
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Residues in contact with VAL 975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A CYS* 5.3 2.7 - - + +
974A ASN* 1.3 76.9 - - - +
976A MET* 1.3 59.8 + - - +
1097A ILE 4.0 0.5 - - - +
1098A PHE* 4.9 0.4 - - - -
1099A PHE* 2.9 39.8 + - - +
1149A LEU* 6.5 1.1 - - + -
1150A GLY* 6.4 1.8 - - - -
1176A SER 3.4 12.8 - - - +
1177A VAL* 3.9 11.9 - - + +
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Residues in contact with MET 976 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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975A VAL* 1.3 74.7 - - - +
977A LEU* 1.3 62.3 + - - +
1097A ILE 3.1 12.1 - - - +
1098A PHE* 4.7 5.8 - - + -
1174A PHE 4.1 0.8 - - - +
1175A VAL* 3.4 4.3 - - - +
1176A SER* 2.9 36.6 + - - +
1186A LEU 5.3 3.1 - - - +
1187A PHE* 4.8 18.2 - - + -
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Residues in contact with LEU 977 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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975A VAL 4.4 0.2 + - - -
976A MET* 1.3 77.1 - - - +
978A GLU* 1.3 61.2 + - - +
979A SER* 4.3 2.5 - - - -
1095A ILE 4.0 0.6 - - - +
1096A HIS* 3.5 3.6 - - - +
1097A ILE* 2.9 43.3 + - + +
1153A VAL* 6.5 2.7 - - + -
1154A PHE* 6.5 1.1 - - - -
1174A PHE 3.7 4.0 - - - -
1175A VAL* 4.5 7.4 - - + +
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Residues in contact with GLU 978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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977A LEU* 1.3 74.9 - - - +
979A SER* 1.3 61.4 + - - +
1095A ILE 3.5 8.1 - - - +
1096A HIS* 5.2 4.3 - - + -
1172A ASN 4.5 0.6 - - - +
1173A SER* 3.3 4.3 - - - -
1174A PHE* 2.9 51.7 + - + +
1187A PHE* 5.9 4.5 - - + -
1188A ASN* 4.9 16.4 - - + +
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Residues in contact with SER 979 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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977A LEU* 4.3 2.4 - - - -
978A GLU* 1.3 76.1 - - - +
980A ARG* 1.3 64.4 + - - +
1094A ARG* 3.3 6.0 - - - +
1095A ILE* 2.9 36.0 + - - +
1168A VAL* 5.0 14.4 - - - -
1169A GLN 5.4 1.1 - - - -
1172A ASN 4.8 2.0 - - - -
1173A SER* 4.1 18.8 - - - +
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Residues in contact with ARG 980 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979A SER* 1.3 76.4 - - - +
981A PHE* 1.3 63.3 + - - +
982A GLU* 2.9 14.8 + - + +
1093A ASP* 3.3 13.7 - - + +
1094A ARG* 4.3 4.5 - - + +
1167A THR 3.6 6.4 - - - +
1168A VAL* 4.3 9.1 - - - +
1169A GLN 4.7 2.6 + - - -
1172A ASN* 4.7 20.8 + - + +
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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