Contacts of the helix formed by residues 1127 - 1146 (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 GLY1127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1122D VAL 3.6 0.2 + - - -
1123D LEU* 2.8 25.7 + - - -
1124D ARG 4.7 0.2 - - - -
1125D VAL 3.5 1.2 - - - -
1126D GLN* 1.3 74.7 - - - +
1128D PRO* 1.3 76.7 - - - +
1129D ARG 3.4 2.0 - - - -
1130D GLU 3.4 2.1 + - - -
1131D VAL* 2.9 23.4 + - - +
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Residues in contact with PRO1128 (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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1123D LEU* 3.6 12.1 - - + -
1127D GLY* 1.3 83.3 - - - +
1129D ARG* 1.3 64.1 + - - +
1131D VAL* 3.1 10.8 + - + +
1132D GLN* 3.2 11.7 + - - +
1163D LEU* 3.2 29.0 - - + +
1206D PRO* 3.5 38.6 - - + -
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Residues in contact with ARG1129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894D ARG* 3.6 34.5 - - - +
895D GLY 3.1 22.0 + - - -
896D ILE* 4.1 18.5 - - + +
897D ASN* 4.5 12.1 + - - +
965D LEU* 5.3 2.1 - - + +
966D THR* 4.8 6.5 - - + -
1127D GLY 3.4 0.6 - - - -
1128D PRO* 1.3 80.5 - - - +
1130D GLU* 1.3 71.1 + - - +
1132D GLN* 3.4 13.5 + - - +
1133D ILE* 3.1 34.0 + - + +
2004D SO4 2.8 42.2 + - - -
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Residues in contact with GLU1130 (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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1122D VAL* 4.9 3.1 - - - +
1126D GLN* 2.9 57.8 + - + +
1127D GLY 3.4 2.0 + - - +
1128D PRO 3.2 0.6 - - - -
1129D ARG* 1.3 87.9 + - - +
1131D VAL* 1.3 65.7 + - - +
1133D ILE* 3.4 18.6 + - - +
1134D HIS* 3.0 22.5 + - - +
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Residues in contact with VAL1131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119D PRO* 4.2 7.4 - - + +
1122D VAL* 3.8 11.9 - - + +
1123D LEU* 3.1 39.7 - - + +
1127D GLY 2.9 18.8 + - - +
1128D PRO 3.1 6.2 + - - +
1130D GLU* 1.3 76.3 - - - +
1132D GLN* 1.3 58.8 + - - +
1134D HIS* 2.8 22.8 + - + +
1135D LEU* 2.9 25.5 + - + +
1163D LEU* 4.3 5.8 - - + -
1208D LEU* 3.8 32.3 - - + -
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Residues in contact with GLN1132 (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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965D LEU* 3.1 50.3 + - + +
1128D PRO* 3.2 6.9 + - - +
1129D ARG* 3.8 10.3 - - - +
1131D VAL* 1.3 77.1 - - + +
1133D ILE* 1.3 63.5 + - - +
1135D LEU* 4.7 0.4 - - - -
1136D VAL* 3.1 31.8 + - - +
1159D VAL* 3.5 32.6 + - + +
1160D ARG* 4.2 10.5 + - - +
1163D LEU* 3.2 44.4 - - + +
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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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896D ILE* 3.9 31.2 - - + -
965D LEU* 3.7 23.1 - - + -
1129D ARG* 3.1 21.8 - - + +
1130D GLU* 3.7 24.9 - - - +
1131D VAL 3.2 0.6 - - - -
1132D GLN* 1.3 76.8 - - - +
1134D HIS* 1.3 57.8 + - - +
1136D VAL* 4.0 4.9 - - + +
1137D LYS* 3.0 42.3 + - - +
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Residues in contact with HIS1134 (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 LEU* 5.5 2.6 - - - +
1111D GLN* 5.9 3.6 - - - -
1116D ALA* 6.1 0.7 - - - -
1117D ALA* 4.1 34.5 + - + +
1119D PRO* 5.1 3.0 - - + +
1122D VAL* 4.6 24.0 - - + +
1126D GLN* 6.3 0.2 - - - +
1130D GLU 3.0 13.5 + - - +
1131D VAL* 2.8 11.2 + - - +
1133D ILE* 1.3 74.7 - - - +
1135D LEU* 1.3 78.5 + - + +
1137D LYS* 2.8 25.1 + - - +
1138D GLU* 2.8 48.5 + - + +
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Residues in contact with LEU1135 (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 LEU* 4.4 28.5 - - + +
1038D ALA* 6.2 0.2 - - - -
1119D PRO* 4.1 26.9 - - + -
1131D VAL* 2.9 38.7 + - + +
1132D GLN* 4.1 3.1 - - - +
1134D HIS* 1.3 78.7 - - + +
1136D VAL* 1.3 57.1 + - - +
1138D GLU* 3.3 3.2 + - - +
1139D VAL* 2.8 40.0 + - + +
1159D VAL* 4.1 22.0 - - + -
1162D MET* 4.1 25.8 - - + -
1163D LEU* 6.2 0.4 - - + -
1208D LEU* 4.3 10.8 - - + -
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Residues in contact with VAL1136 (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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965D LEU* 5.0 2.9 - - + -
1132D GLN 3.1 19.1 + - - +
1133D ILE* 4.0 4.9 - - - +
1135D LEU* 1.3 76.8 - - - +
1137D LYS* 1.3 59.1 + - - +
1140D GLN* 2.9 29.2 + - + +
1152D ASP* 4.0 34.8 - - + +
1155D ILE* 3.7 24.5 - - + -
1156D GLU* 4.0 22.2 - - + +
1159D VAL* 3.7 21.8 - - + -
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Residues in contact with LYS1137 (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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1133D ILE* 3.0 29.4 + - - +
1134D HIS* 2.8 18.3 + - - +
1136D VAL* 1.3 77.9 - - - +
1138D GLU* 1.3 68.7 + - - +
1140D GLN* 4.9 0.2 - - - -
1141D GLU* 3.1 31.2 + - - +
1144D ARG* 3.5 18.7 + - - +
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Residues in contact with GLU1138 (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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1031D ARG* 2.9 32.4 + - - +
1035D LEU* 3.7 17.0 - - + -
1111D GLN* 5.3 4.0 - - - +
1116D ALA* 6.2 1.3 - - - -
1134D HIS* 2.8 53.0 + - + +
1135D LEU* 4.0 2.0 - - - +
1137D LYS* 1.3 77.5 - - - +
1139D VAL* 1.3 67.0 + - - +
1141D GLU* 3.0 26.6 + - - +
1142D VAL* 3.1 17.3 + - - +
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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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1002D ILE* 5.6 0.2 - - + -
1032D VAL* 4.9 2.5 - - + -
1035D LEU* 3.4 33.0 - - + -
1036D PHE* 3.5 40.4 - - + -
1135D LEU* 2.8 30.8 + - + +
1138D GLU* 1.3 71.7 - - - +
1140D GLN* 1.3 62.8 + - - +
1142D VAL* 3.2 14.4 + - - +
1143D TYR* 3.2 30.9 + - + -
1155D ILE* 3.6 24.7 - - + -
1159D VAL* 5.8 0.4 - - + -
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Residues in contact with GLN1140 (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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917D THR* 4.3 7.6 - - - +
1136D VAL* 2.9 21.7 + - + +
1139D VAL* 1.3 77.1 - - - +
1141D GLU* 1.3 57.2 + - - +
1143D TYR* 3.4 5.0 + - - +
1144D ARG* 2.8 77.1 + - - +
1148D VAL 3.9 4.5 - - - +
1150D ILE* 3.2 44.3 + - - +
1152D ASP* 4.2 16.9 + - - +
1155D ILE* 3.0 27.7 - - + +
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Residues in contact with GLU1141 (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 LYS* 3.1 27.0 + - - +
1138D GLU* 3.0 22.1 + - - +
1140D GLN* 1.3 75.0 - - - +
1142D VAL* 1.3 64.7 + - + +
1144D ARG* 3.6 17.2 + - + +
1145D ALA* 3.0 22.9 + - + +
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Residues in contact with VAL1142 (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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1009D LEU* 5.0 6.3 - - + -
1027D GLY* 4.5 7.1 - - - +
1028D GLY* 3.9 23.6 - - - +
1031D ARG* 3.4 32.8 - - + +
1032D VAL* 3.5 28.3 - - + -
1035D LEU* 4.7 2.9 - - + -
1138D GLU 3.1 15.2 + - - +
1139D VAL 3.2 7.3 + - - +
1141D GLU* 1.3 75.6 - - + +
1143D TYR* 1.3 67.5 + - + +
1145D ALA* 3.0 21.5 + - - +
1146D GLN* 3.4 9.3 + - + +
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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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872D LEU* 4.5 5.9 - - - +
1002D ILE* 3.0 46.9 + - + +
1005D PRO* 3.7 20.2 - - + -
1006D GLY* 4.7 1.4 - - - -
1009D LEU* 4.3 24.6 - - + +
1032D VAL* 3.8 29.1 - - + +
1139D VAL* 3.2 41.4 + - + -
1140D GLN* 4.0 8.7 - - - +
1142D VAL* 1.3 81.5 - - + +
1144D ARG* 1.3 63.9 + - - +
1146D GLN* 2.9 17.9 + - - +
1147D GLY 3.2 0.2 + - - -
1148D VAL* 3.1 38.0 + - + +
1150D ILE* 4.6 10.5 - - + -
1155D ILE* 5.3 3.8 - - + -
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Residues in contact with ARG1144 (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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914D HIS* 2.9 64.4 + - + +
917D THR* 4.9 7.2 + - + -
1137D LYS* 3.5 35.8 + - - +
1140D GLN* 2.8 57.8 + - - +
1141D GLU* 3.6 17.0 + - + +
1143D TYR* 1.3 73.4 - - - +
1145D ALA* 1.3 59.6 + - - +
1147D GLY* 2.8 20.0 + - - +
1148D VAL 4.0 10.1 - - - +
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Residues in contact with ALA1145 (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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1027D GLY 5.7 3.4 - - - +
1141D GLU* 3.0 13.9 + - + +
1142D VAL* 3.0 15.9 + - - +
1144D ARG* 1.3 77.6 - - - +
1146D GLN* 1.3 66.8 + - - +
1147D GLY 3.6 0.3 + - - -
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Residues in contact with GLN1146 (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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1008D GLN* 3.2 33.7 + - + +
1009D LEU* 4.3 14.6 - - + -
1010D THR* 3.3 40.5 + - - +
1027D GLY 4.0 9.6 - - - +
1028D GLY* 5.3 0.4 - - - -
1142D VAL* 3.8 12.1 - - + +
1143D TYR 2.9 9.1 + - - +
1145D ALA* 1.3 82.6 + - - +
1147D GLY* 1.3 63.3 + - - +
1148D VAL* 3.4 13.7 + - + +
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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