Contacts of the helix formed by residues 1131 - 1148 (chain D) in PDB entry 2VE7
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 VAL1131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1148B LYS* 6.1 1.6 - - - +
1127D GLU* 3.6 36.3 - - + +
1129D THR 3.4 2.0 - - - +
1130D THR* 1.3 97.2 - - + +
1132D THR* 1.3 70.1 + - + +
1133D ILE 3.3 1.8 - - - -
1134D PRO* 3.2 5.2 - - - +
1135D SER* 3.0 32.9 + - - -
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Residues in contact with THR1132 (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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1128B LEU* 3.4 15.1 - - - +
1127D GLU* 2.9 24.9 + - - +
1128D ASP* 2.6 30.5 - - + +
1131D VAL* 1.3 83.0 - - + +
1133D ILE* 1.3 57.7 + - - +
1135D SER* 3.6 8.9 - - - -
1136D ALA* 2.9 28.8 + - - +
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Residues in contact with ILE1133 (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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1124B ASN* 3.4 51.8 - - + +
1127B ARG* 4.4 26.2 - - + +
1128B LEU* 4.2 23.3 - - + +
1131B LEU* 5.6 3.1 - - + -
1128D ASP 4.1 12.3 - - - +
1129D THR* 4.5 10.3 - - + +
1132D THR* 1.3 75.1 + - - +
1134D PRO* 1.4 70.9 - - + +
1135D SER 3.0 1.1 - - - -
1136D ALA* 2.9 5.6 + - + +
1137D VAL* 2.7 47.3 + - + +
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Residues in contact with PRO1134 (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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1129D THR 3.2 21.8 - - - +
1130D THR 3.4 20.6 - - - +
1131D VAL 3.2 14.1 - - - +
1133D ILE* 1.4 92.3 - - + +
1135D SER* 1.3 53.6 + - - -
1137D VAL* 3.8 10.1 - - + +
1138D TYR* 3.1 28.8 + - - +
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Residues in contact with SER1135 (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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1148B LYS* 3.3 42.2 + - - +
1131D VAL* 3.0 23.9 + - - -
1132D THR* 3.6 11.0 - - - -
1133D ILE 3.0 0.6 - - - -
1134D PRO* 1.3 78.0 - - - +
1136D ALA* 1.3 60.2 + - - +
1138D TYR* 3.7 5.9 + - - +
1139D VAL* 3.3 25.8 + - - +
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Residues in contact with ALA1136 (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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1128B LEU* 5.1 14.1 - - + +
1131B LEU* 3.6 21.5 - - + +
1132B GLN* 6.2 0.2 - - - +
1132D THR 2.9 18.8 + - - +
1133D ILE* 2.9 5.6 + - + +
1135D SER* 1.3 74.0 - - - +
1137D VAL* 1.3 59.9 + - - +
1138D TYR 3.3 0.4 - - - -
1139D VAL* 3.6 8.4 + - - +
1140D ALA* 3.1 27.5 + - - +
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Residues in contact with VAL1137 (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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1127B ARG* 4.4 15.9 - - - +
1131B LEU* 4.0 17.7 - - + -
1133D ILE* 2.7 39.7 + - + +
1134D PRO* 3.8 9.2 - - + +
1136D ALA* 1.3 73.4 - - - +
1138D TYR* 1.3 56.9 + - - +
1140D ALA* 3.5 4.0 + - - +
1141D GLN* 3.0 43.7 + - - +
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Residues in contact with TYR1138 (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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1148B LYS* 4.0 32.8 - - + -
1154B LEU* 3.8 29.2 - - + +
1207B PHE* 5.0 6.1 - - - -
1134D PRO 3.1 18.0 + - - +
1135D SER* 3.9 4.0 - - - +
1136D ALA 3.3 0.2 - - - -
1137D VAL* 1.3 76.5 - - - +
1139D VAL* 1.3 60.0 + - + +
1141D GLN* 3.3 21.0 - - - +
1142D LEU* 3.0 58.1 + - + +
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Residues in contact with VAL1139 (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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1135B ALA* 5.0 9.0 - - + -
1146B ILE* 3.5 39.0 - - + +
1148B LYS* 3.5 34.1 - - + +
1154B LEU* 5.1 4.3 - - + -
1135D SER 3.3 11.0 + - - +
1136D ALA* 4.0 7.2 - - - +
1137D VAL 3.4 0.2 - - - -
1138D TYR* 1.3 77.5 - - + +
1140D ALA* 1.3 66.9 + - - +
1142D LEU* 3.6 5.1 + - + -
1143D TYR* 3.3 33.8 + - + -
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Residues in contact with ALA1140 (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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1131B LEU* 4.6 21.1 - - + +
1134B SER* 5.3 6.3 - - - +
1135B ALA* 6.0 2.7 - - + +
1138B TYR* 5.3 3.5 - - + -
1136D ALA 3.1 18.6 + - - +
1137D VAL* 3.8 7.2 - - - +
1138D TYR 3.3 0.2 - - - -
1139D VAL* 1.3 76.1 - - + +
1141D GLN* 1.3 64.6 + - - +
1143D TYR* 3.6 10.3 + - - +
1144D HIS* 3.4 21.3 + - - +
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Residues in contact with GLN1141 (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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1137D VAL* 3.0 36.9 + - - +
1138D TYR* 3.3 24.4 - - + +
1140D ALA* 1.3 76.2 - - - +
1142D LEU* 1.3 54.4 + - + +
1144D HIS* 3.3 7.9 + - - +
1145D GLN* 2.8 40.2 + - - +
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Residues in contact with LEU1142 (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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1146B ILE* 3.8 20.0 - - + -
1154B LEU* 4.5 13.0 - - + -
1156B PHE* 4.3 22.0 - - + -
1207B PHE* 4.3 20.4 - - + -
1138D TYR* 3.0 55.8 + - + +
1139D VAL* 3.8 3.4 - - + +
1140D ALA 3.4 0.2 - - - -
1141D GLN* 1.3 76.8 - - + +
1143D TYR* 1.3 57.8 + - - +
1145D GLN* 3.9 19.3 - - - +
1146D VAL* 2.6 47.8 + - + +
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Residues in contact with TYR1143 (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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1135B ALA* 3.9 24.1 + - + -
1138B TYR* 3.4 46.9 - + + -
1139B LYS* 4.0 7.1 - - - +
1142B LEU* 4.2 8.7 - - + -
1144B LEU* 2.8 40.8 + - + -
1145B GLU* 3.5 2.8 - - - +
1146B ILE* 3.1 41.8 + - + -
1139D VAL* 3.3 29.4 + - + -
1140D ALA* 3.8 9.2 - - - +
1141D GLN 3.4 0.6 - - - -
1142D LEU* 1.3 76.0 - - - +
1144D HIS* 1.3 57.5 + - - +
1146D VAL* 4.2 3.3 - - + +
1147D SER* 2.8 39.4 + - - -
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Residues in contact with HIS1144 (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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1138B TYR* 4.2 7.1 + - + +
1140D ALA 3.4 9.4 + - - +
1141D GLN* 3.3 10.2 + - - +
1143D TYR* 1.3 78.4 - - - +
1145D GLN* 1.3 58.8 + - - +
1148D LYS* 3.0 28.8 + - + +
1149D ILE 4.1 19.8 + - - -
1150D GLU* 4.1 30.3 - - + +
1165D HIS* 5.1 8.3 - - - +
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Residues in contact with GLN1145 (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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1205B ASN* 3.8 23.4 + - - +
1207B PHE* 3.8 28.1 - - + +
1208B SER* 3.2 13.4 + - - +
1141D GLN* 2.8 21.9 + - - +
1142D LEU* 3.0 21.2 + - - +
1144D HIS* 1.3 80.0 - - - +
1146D VAL* 1.3 62.9 + - + +
1147D SER 3.4 0.3 + - - -
1148D LYS* 3.2 31.8 - - - +
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Residues in contact with VAL1146 (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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1142B LEU* 6.0 1.1 - - + -
1144B LEU* 5.2 4.3 - - + -
1146B ILE* 5.9 1.3 - - + -
1156B PHE* 5.1 2.7 - - + -
1207B PHE* 3.6 31.2 - - + +
1208B SER* 2.9 26.4 + - - +
1211B LEU* 3.6 46.4 - - + -
1142D LEU* 2.6 31.8 + - + +
1143D TYR* 4.2 3.8 - - + +
1145D GLN* 1.3 72.1 - - + +
1147D SER* 1.3 58.2 + - - +
1190D TRP* 3.7 13.8 - - + -
1193D VAL* 3.8 8.7 - - - +
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Residues in contact with SER1147 (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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1138B TYR* 3.4 7.1 - - - -
1142B LEU* 3.8 30.5 - - - -
1143D TYR 2.8 22.1 + - - -
1146D VAL* 1.3 77.5 - - - +
1148D LYS* 1.3 70.7 + - - +
1149D ILE* 3.0 42.0 + - - +
1164D HIS* 3.5 7.8 + - - -
1190D TRP* 5.5 1.1 - - - -
1193D VAL* 4.0 13.3 - - - +
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Residues in contact with LYS1148 (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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1206B ASN* 5.0 5.7 - - - +
1208B SER* 3.3 25.4 - - - +
1144D HIS* 3.0 21.5 + - + +
1145D GLN* 3.2 34.3 + - - +
1147D SER* 1.3 77.1 - - - +
1149D ILE* 1.3 58.9 + - - +
1164D HIS* 3.7 13.8 - - + +
1165D HIS* 2.7 54.5 + - - +
1166D GLY* 5.6 1.3 - - - -
1193D VAL* 5.7 1.3 - - + -
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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
------------------------------------------------------------
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