Contacts of the strand formed by residues 1063 - 1069 (chain D) in PDB entry 6VVT
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 PHE1063 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1056D LEU* 3.5 39.0 - - + -
1057D GLU 3.6 17.7 - - - -
1058D GLU* 3.0 39.7 - - + -
1059D SER 5.1 0.4 - - - +
1062D PHE* 1.3 73.1 - - - +
1064D LYS* 1.3 57.4 + - - +
1065D ILE* 4.5 1.1 - - + -
1079D ASP 2.6 25.7 - - - +
1081D LEU* 2.9 25.1 + - + +
1083D LYS* 4.9 21.2 - - + +
1087D LEU* 4.8 17.7 - - + -
1113D MET* 3.6 31.0 - - + -
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Residues in contact with LYS1064 (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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1055D ARG 3.4 1.7 - - - +
1056D LEU* 3.7 1.9 - - - -
1057D GLU* 2.8 76.0 + - + +
1059D SER* 4.9 5.6 - - - +
1062D PHE 3.9 0.6 + - - -
1063D PHE* 1.3 74.5 - - - +
1065D ILE* 1.3 66.4 + - - +
1066D THR* 4.0 13.7 - - - +
1077D VAL* 4.6 9.1 - - + +
1078D TYR 3.8 2.7 - - - -
1079D ASP* 3.0 43.4 + - - +
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Residues in contact with ILE1065 (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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1054D VAL* 3.5 22.9 - - + -
1055D ARG 3.6 2.5 - - - -
1056D LEU* 3.2 31.0 - - + -
1063D PHE* 4.5 1.8 - - + -
1064D LYS* 1.3 73.3 - - - +
1066D THR* 1.3 61.9 + - - +
1067D ILE* 4.6 2.2 - - + -
1077D VAL 3.9 0.2 - - - -
1078D TYR* 2.9 41.8 + - + +
1081D LEU* 3.8 23.3 - - + +
1087D LEU* 4.1 17.0 - - + -
1100D LEU* 4.8 4.9 - - + -
1112D LEU* 3.9 41.5 - - + +
1113D MET* 4.4 3.8 - - + -
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Residues in contact with THR1066 (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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1054D VAL* 3.2 4.0 - - - +
1055D ARG* 2.6 61.3 + - - +
1057D GLU* 4.0 10.4 + - - -
1064D LYS* 4.0 16.8 - - - +
1065D ILE* 1.3 74.6 - - - +
1067D ILE* 1.3 65.3 + - - +
1068D VAL 4.0 0.6 + - - -
1075D GLU* 3.6 29.2 - - + +
1076D VAL 3.5 10.1 - - - +
1077D VAL* 4.1 19.6 - - + +
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Residues in contact with ILE1067 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1048D ALA* 3.8 30.1 - - + -
1049D ASP 4.6 2.5 - - - +
1050D VAL* 3.7 32.3 - - + +
1052D GLY 4.6 7.4 - - - +
1053D ARG 3.2 12.1 - - - +
1054D VAL* 4.8 5.8 - - + -
1065D ILE* 4.6 9.2 - - + -
1066D THR* 1.3 75.6 - - - +
1068D VAL* 1.3 66.8 + - - +
1069D PRO* 3.2 6.4 - - - +
1075D GLU* 3.6 3.8 - - - +
1076D VAL* 2.8 37.5 + - + +
1078D TYR* 3.8 25.4 - - + +
1106D VAL* 4.8 9.0 - - + -
1112D LEU* 4.1 5.8 - - + -
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Residues in contact with VAL1068 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1052D GLY* 3.2 1.0 - - - -
1053D ARG* 2.8 49.7 + - + +
1054D VAL 5.7 0.4 - - - -
1055D ARG* 3.7 36.8 - - + +
1066D THR 5.1 2.0 - - - +
1067D ILE* 1.3 71.4 - - - +
1069D PRO* 1.3 75.9 - - + +
1070D ASP* 4.0 1.4 - - - +
1075D GLU* 3.7 18.4 - - + +
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Residues in contact with PRO1069 (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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1050D VAL* 4.1 15.3 - - + -
1051D ALA 3.2 15.0 - - - +
1052D GLY* 4.0 0.2 - - - -
1067D ILE* 3.2 12.8 - - + +
1068D VAL* 1.3 98.7 - - + +
1070D ASP* 1.3 60.4 + - - +
1071D ASP* 3.2 23.5 + - - +
1072D GLY* 3.7 8.2 - - - -
1073D GLY 3.4 35.2 - - - +
1074D GLU 3.6 15.3 - - - +
1075D GLU* 4.0 5.2 - - + -
1076D VAL 4.9 0.2 - - - +
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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