Contacts of the strand formed by residues 1016 - 1023 (chain B) in PDB entry 1VDV
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 GLN1016 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1121A TYR* 3.2 51.7 + - - -
1124A ARG* 3.6 20.4 - - + +
1125A VAL 5.0 2.6 + - - +
1126A SER* 5.5 0.3 - - - -
1013B PHE 2.8 23.9 + - - +
1014B LEU 3.0 7.4 + - - +
1015B ASN* 1.3 77.9 - - - +
1017B ALA* 1.3 64.2 + - - +
1073B ASN* 4.4 8.5 - - - +
1074B SER* 5.9 0.3 - - - -
1075B SER* 4.0 13.6 + - - +
1085B ILE* 3.7 10.6 - - - +
1086B TYR* 4.8 2.3 + - - -
1132B PHE* 3.5 29.0 - - + -
1133B TYR 3.2 7.9 - - - +
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Residues in contact with ALA1017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016B GLN* 1.3 77.3 - - - +
1018B GLY* 1.3 59.5 + - - +
1085B ILE* 3.5 35.0 - - + +
1086B TYR* 3.5 28.9 - - + -
1089B ALA* 3.4 2.8 - - - +
1132B PHE* 3.2 13.4 - - - -
1133B TYR 2.9 32.5 + - - +
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Residues in contact with GLY1018 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017B ALA* 1.3 74.8 - - - +
1019B ALA* 1.3 61.9 + - - +
1033B HIS* 3.5 3.5 - - - +
1034B GLY 3.2 24.9 + - - -
1071B VAL* 3.9 17.6 - - - +
1074B SER* 6.3 0.8 - - - +
1086B TYR* 3.7 7.0 - - - -
1089B ALA* 3.9 1.8 - - - -
1131B GLY 3.3 8.3 - - - -
1132B PHE* 4.1 8.9 - - - -
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Residues in contact with ALA1019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018B GLY* 1.3 74.9 - - - +
1020B LEU* 1.3 60.6 - - - +
1021B ILE* 4.3 1.3 - - + -
1032B SER 3.3 12.3 - - - +
1033B HIS* 4.0 2.2 - - + +
1071B VAL* 4.1 5.1 - - - +
1089B ALA* 3.7 32.1 - - + +
1090B VAL* 3.9 17.5 - - + +
1093B ALA* 4.8 4.0 - - + -
1130B THR* 3.1 8.8 - - - +
1131B GLY 2.8 28.0 + - - +
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Residues in contact with LEU1020 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020A LEU* 4.0 26.9 - - + -
1069A ASN 4.0 4.9 - - - +
1070A THR 5.1 0.2 - - - +
1130A THR* 4.6 1.6 - - + -
1019B ALA* 1.3 75.4 - - - +
1021B ILE* 1.3 62.8 + - - +
1022B HIS* 3.6 36.4 - - + +
1030B LEU 3.9 0.9 - - - +
1031B VAL* 3.7 0.5 - - - -
1032B SER* 2.7 46.2 + - - +
1070B THR* 3.8 39.3 - - + +
1071B VAL* 4.1 1.8 - - + +
1128B SER* 4.3 3.6 - - - +
1129B THR 3.5 17.3 - - - +
1130B THR* 4.1 17.5 - - + -
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Residues in contact with ILE1021 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019B ALA* 5.1 2.0 - - + -
1020B LEU* 1.3 82.5 - - - +
1022B HIS* 1.3 69.5 + - - +
1023B VAL* 4.8 6.1 - - + -
1029B VAL* 3.5 27.1 - - + -
1030B LEU 3.5 4.0 - - - +
1031B VAL* 4.0 22.4 - - + -
1054B LEU* 5.7 2.2 - - + -
1090B VAL* 3.9 11.2 - - + +
1093B ALA* 3.6 27.4 - - + -
1094B CYS* 3.8 27.4 - - - +
1097B ILE* 4.8 8.1 - - + +
1127B LEU 3.9 0.7 - - - +
1128B SER* 3.3 4.0 - - - -
1129B THR* 2.9 39.5 + - + +
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Residues in contact with HIS1022 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068A THR 4.4 1.6 - - - -
1069A ASN* 3.0 32.5 + - - -
1070A THR 3.4 17.9 - - - -
1072A PRO* 3.4 25.3 - - + +
1020B LEU* 3.6 25.3 - - + +
1021B ILE* 1.3 75.6 + - - +
1023B VAL* 1.3 62.6 + - - +
1024B TYR* 3.9 24.9 - - + -
1028B SER 4.0 0.2 - - - +
1029B VAL* 3.3 5.4 - - - +
1030B LEU* 2.8 44.4 + - + +
1032B SER* 6.5 0.9 - - - -
1127B LEU 3.5 3.1 - - - -
1128B SER* 2.8 29.5 + - - -
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Residues in contact with VAL1023 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A ASN* 3.0 20.8 + - - -
1021B ILE* 4.8 1.6 - - + -
1022B HIS* 1.3 78.2 - - - +
1024B TYR* 1.3 71.4 + - - +
1027B GLY 4.1 5.8 - - - +
1028B SER 3.5 8.3 - - - +
1029B VAL* 4.2 15.3 - - + +
1054B LEU* 5.8 1.1 - - + -
1097B ILE* 4.1 31.4 - - + -
1101B LEU* 6.1 0.2 - - + -
1113B TRP* 4.0 13.2 - - + -
1117B VAL* 3.9 27.6 - - + -
1127B LEU* 3.0 30.1 + - + +
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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