Contacts of the helix formed by residues 1112 - 1123 (chain A) 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 SER1112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1111A GLY* 1.3 73.4 - - - -
1113A TRP* 1.3 65.5 + - - +
1114A GLU* 3.4 18.5 + - - +
1115A ASP* 2.8 43.5 + - - -
1116A TRP* 3.1 21.1 + - - -
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Residues in contact with TRP1113 (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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1023A VAL* 4.1 13.2 - - + -
1027A GLY* 2.9 30.6 + - - -
1029A VAL* 4.2 7.0 - - + -
1054A LEU* 4.2 31.4 - - + -
1056A ILE* 3.6 40.4 - - + +
1060A LYS* 4.4 15.0 - - + +
1097A ILE* 4.4 4.7 - - + -
1098A LEU* 4.6 8.7 - - + -
1101A LEU* 3.5 29.4 - - + -
1112A SER* 1.3 74.3 - - - +
1114A GLU* 1.3 84.3 + - - +
1116A TRP* 3.3 26.8 + + + +
1117A VAL* 3.0 40.4 + - + +
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Residues in contact with GLU1114 (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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1025A THR 5.2 3.2 - - - +
1026A ASP 3.7 23.6 - - - +
1027A GLY* 4.7 2.9 - - - +
1060A LYS* 2.8 36.7 + - - +
1112A SER* 3.1 19.4 + - - +
1113A TRP* 1.3 93.4 + - + +
1115A ASP* 1.3 63.4 + - - +
1117A VAL* 3.4 5.1 + - - +
1118A MET* 3.1 25.3 + - - +
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Residues in contact with ASP1115 (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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1108A ASN* 4.0 18.2 + - - +
1111A GLY* 3.6 6.1 - - - -
1112A SER* 2.8 42.0 + - - +
1114A GLU* 1.3 78.9 - - - +
1116A TRP* 1.3 62.7 + - - +
1118A MET* 3.9 4.1 - - - +
1119A ALA* 3.0 24.4 + - - +
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Residues in contact with TRP1116 (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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1101A LEU* 3.8 19.7 - - + +
1104A PHE* 3.4 28.6 - - + +
1105A LYS* 3.7 46.3 - - + +
1108A ASN* 2.7 28.3 + - + -
1109A PRO 3.7 15.3 - - - -
1111A GLY* 3.1 28.0 - - - -
1112A SER 3.1 10.8 + - - -
1113A TRP* 3.8 30.7 - + + +
1115A ASP* 1.3 77.9 - - - +
1117A VAL* 1.3 57.1 + - - +
1119A ALA* 3.4 6.3 + - + +
1120A ALA* 3.0 29.8 + - - +
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Residues in contact with VAL1117 (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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1023A VAL* 3.8 11.7 - - + -
1024A TYR 3.5 25.6 - - - +
1025A THR* 4.4 6.5 - - - -
1027A GLY* 4.3 7.4 - - - +
1101A LEU* 4.1 16.2 - - + -
1113A TRP* 3.0 49.1 + - + +
1114A GLU 3.8 4.7 - - - +
1116A TRP* 1.3 76.2 - - - +
1118A MET* 1.3 62.8 + - - +
1120A ALA* 3.3 4.2 + - - +
1121A TYR* 3.0 21.0 + - - +
1127A LEU* 3.7 18.9 - - + +
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Residues in contact with MET1118 (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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1025A THR* 3.6 32.1 + - - +
1114A GLU 3.1 16.5 + - - +
1115A ASP* 3.9 4.7 - - - +
1117A VAL* 1.3 77.9 - - - +
1119A ALA* 1.3 54.3 + - - +
1121A TYR* 3.2 26.2 + - - +
1122A GLN* 2.7 58.9 + - + +
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Residues in contact with ALA1119 (chain A).
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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1104A PHE* 3.6 24.9 - - + -
1115A ASP 3.0 18.8 + - - +
1116A TRP* 3.6 5.4 - - + +
1117A VAL 3.3 0.2 - - - -
1118A MET* 1.3 75.2 - - - +
1120A ALA* 1.3 63.0 + - - +
1122A GLN* 3.3 9.3 + - - +
1123A ASP* 3.0 24.9 + - - +
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Residues in contact with ALA1120 (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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1101A LEU* 3.7 19.7 - - + -
1104A PHE* 3.7 23.1 - - + -
1116A TRP 3.0 17.6 + - - +
1117A VAL 3.5 5.2 - - - +
1119A ALA* 1.3 77.9 - - - +
1121A TYR* 1.3 62.6 + - - +
1123A ASP 3.0 8.3 + - - -
1124A ARG 3.1 0.2 + - - -
1125A VAL* 3.0 33.3 + - + +
1127A LEU* 4.0 12.1 - - + -
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Residues in contact with TYR1121 (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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1025A THR* 3.8 24.5 - - + -
1117A VAL 3.0 13.8 + - - +
1118A MET* 3.5 18.8 - - - +
1120A ALA* 1.3 76.7 - - - +
1122A GLN* 1.3 66.9 + - - +
1124A ARG 3.0 15.2 + - - -
1125A VAL 4.5 7.6 - - - +
1127A LEU* 4.2 10.5 - - + +
770B MET* 3.8 22.9 - - + +
1013B PHE* 3.8 24.2 - + - +
1014B LEU* 3.9 22.2 - - - +
1016B GLN* 3.2 39.8 + - - -
1073B ASN* 3.7 34.3 + - + -
1075B SER* 4.7 3.1 + - - -
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Residues in contact with GLN1122 (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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1118A MET* 2.7 53.0 + - + +
1119A ALA* 3.6 8.5 - - - +
1121A TYR* 1.3 77.9 - - - +
1123A ASP* 1.3 57.8 + - - +
1124A ARG* 3.2 1.4 + - - +
1013B PHE* 3.0 62.2 - - + +
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Residues in contact with ASP1123 (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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1104A PHE* 3.6 28.8 - - + -
1119A ALA 3.0 17.2 + - - +
1120A ALA 3.0 3.7 + - - +
1122A GLN* 1.3 75.8 - - - +
1124A ARG* 1.3 69.3 + - - +
1125A VAL* 3.4 4.0 + - + +
1134B ARG* 3.0 28.8 + - - -
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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