Contacts of the strand formed by residues 1077 - 1080 (chain D) in PDB entry 7C97
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 ALA1077 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1038D THR* 2.3 49.5 + - - +
1040D MET* 3.1 14.6 - - - +
1075D ARG 3.4 0.2 + - - -
1076D PRO* 1.3 76.6 - - - +
1078D LEU* 1.3 53.7 + - - +
1098D GLN* 3.4 30.7 - - + -
1099D TYR 4.0 6.3 - - - -
1100D PHE* 3.8 24.9 - - + +
1101D LEU* 4.9 1.1 - - - +
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Residues in contact with LEU1078 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035D VAL* 3.7 21.4 - - + +
1036D ARG 3.4 6.5 - - - +
1037D PHE* 3.4 38.4 - - + -
1040D MET* 3.3 41.3 - - + -
1077D ALA* 1.3 72.6 - - - +
1079D LYS* 1.3 64.7 + - - +
1080D ILE* 3.1 12.3 + - - +
1097D ALA 4.4 2.1 - - - +
1098D GLN* 5.2 0.7 - - - -
1099D TYR* 4.5 11.7 + - - +
1101D LEU* 4.4 16.7 - - + +
1107D VAL* 5.5 2.0 - - + -
1109D LEU* 3.9 26.9 - - + +
1121D LEU* 6.1 0.7 - - - +
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Residues in contact with LYS1079 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034D PHE 3.7 1.7 - - - +
1035D VAL* 5.0 0.9 - - - -
1036D ARG* 3.1 53.9 + - + +
1038D THR* 3.1 27.3 - - + +
1078D LEU* 1.3 67.6 - - - +
1080D ILE* 1.3 69.4 + - - +
1081D VAL* 3.4 10.0 + - + +
1087D ASP* 3.1 49.8 + - + +
1095D MET* 4.2 19.2 - - - +
1096D PRO* 4.7 0.2 - - - +
1097D ALA 3.7 11.7 - - - +
1098D GLN* 4.7 12.5 - - + +
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Residues in contact with ILE1080 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029D THR* 5.0 2.7 - - + +
1030D GLU 5.0 2.0 - - - +
1031D VAL* 2.9 51.4 - - + +
1032D SER* 3.0 25.4 - - - +
1034D PHE 4.2 4.5 - - - +
1035D VAL* 6.2 0.7 - - - -
1078D LEU 3.1 9.1 + - - +
1079D LYS* 1.3 75.2 - - - +
1081D VAL* 1.3 57.7 + - - +
1087D ASP* 3.5 6.9 - - - -
1088D VAL* 3.1 37.7 + - + +
1097D ALA* 3.1 12.1 + - + +
1099D TYR* 3.5 33.2 - - + +
1121D LEU* 5.2 9.9 - - + -
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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