Contacts of the helix formed by residues 1028 - 1037 (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 GLY1028 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009D LEU* 4.2 10.5 - - - -
1010D THR 4.4 10.5 - - - -
1027D GLY* 1.3 78.5 - - - +
1029D LEU* 1.3 67.6 + - - -
1030D PRO* 3.3 8.0 - - - +
1031D ARG* 3.0 15.9 + - - +
1032D VAL* 3.0 19.3 + - - +
1142D VAL* 3.9 8.0 - - - +
1146D GLN* 5.3 0.9 - - - -
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Residues in contact with LEU1029 (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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864D LEU 4.7 3.1 - - - +
865D ARG* 4.2 13.7 - - + +
868D ASP* 3.2 35.0 - - + +
869D SER* 3.7 16.6 - - - +
872D LEU* 3.7 34.5 - - + -
1006D GLY 4.9 3.4 - - - +
1009D LEU* 3.6 34.1 - - + +
1010D THR 4.9 1.2 - - - -
1028D GLY* 1.3 70.7 - - - -
1030D PRO* 1.3 69.7 - - + +
1032D VAL* 3.2 2.4 + - + +
1033D GLN* 3.1 26.8 + - + +
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Residues in contact with PRO1030 (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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1010D THR 5.5 5.2 - - - -
1027D GLY 5.3 3.6 - - - +
1028D GLY* 3.3 9.0 - - - +
1029D LEU* 1.3 93.9 - - + +
1031D ARG* 1.3 57.1 + - - +
1033D GLN* 3.4 7.6 + - + +
1034D GLU* 2.9 28.6 + - - +
1042D ARG* 5.4 13.5 - - - +
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Residues in contact with ARG1031 (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* 4.1 12.1 - - - +
1028D GLY 3.0 20.5 + - - +
1030D PRO* 1.3 80.4 - - - +
1032D VAL* 1.3 62.3 + - - +
1034D GLU* 3.1 27.2 + - - +
1035D LEU* 3.1 42.7 + - + +
1042D ARG* 5.9 8.9 - - - +
1115D GLY 4.9 2.8 + - - -
1116D ALA* 3.0 38.2 - - - +
1138D GLU* 2.9 38.8 + - - +
1142D VAL* 3.4 26.7 - - + +
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Residues in contact with VAL1032 (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* 4.1 11.7 - - + -
1009D LEU* 4.4 8.3 - - + -
1028D GLY 3.0 17.4 + - - +
1029D LEU* 3.6 9.6 - - + +
1031D ARG* 1.3 76.0 - - - +
1033D GLN* 1.3 58.7 + - - +
1035D LEU* 2.9 25.3 + - + +
1036D PHE* 3.0 43.0 + - + -
1139D VAL* 4.9 2.5 - - + +
1142D VAL* 3.5 27.1 - - + -
1143D TYR* 3.8 26.0 - - + +
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Residues in contact with GLN1033 (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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868D ASP* 5.5 5.7 - - - +
871D TYR* 4.7 6.7 - - - -
872D LEU* 4.9 10.7 - - + +
875D ARG* 3.0 38.8 + - - +
1029D LEU* 3.1 22.2 + - + +
1030D PRO* 3.9 6.8 - - + +
1032D VAL* 1.3 77.3 - - - +
1034D GLU* 1.3 62.6 + - - +
1036D PHE* 4.6 4.9 - - - +
1037D GLU* 3.0 33.6 + - + +
1039D ARG* 3.2 35.1 - - - +
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Residues in contact with GLU1034 (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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1030D PRO 2.9 15.1 + - - +
1031D ARG* 3.1 43.5 + - - +
1033D GLN* 1.3 76.3 - - - +
1035D LEU* 1.3 63.0 + - + +
1037D GLU* 5.0 0.4 - - - -
1038D ALA* 3.5 0.9 + - - -
1039D ARG* 3.4 48.5 + - + +
1040D VAL 3.9 2.8 - - - +
1041D PRO* 2.9 10.5 - - + +
1042D ARG* 2.4 52.8 + - - +
1119D PRO* 5.9 0.9 - - - +
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Residues in contact with LEU1035 (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* 3.3 49.4 - - + +
1032D VAL* 2.9 11.1 + - - +
1034D GLU* 1.3 76.2 - - + +
1036D PHE* 1.3 65.1 + - - +
1037D GLU 3.1 1.3 - - - -
1038D ALA* 3.0 16.1 + - - +
1119D PRO* 5.4 7.9 - - + -
1134D HIS* 5.5 2.7 - - - +
1135D LEU* 4.4 29.0 - - + +
1138D GLU* 3.7 19.3 - - + +
1139D VAL* 3.4 48.5 - - + +
1142D VAL* 4.7 0.9 - - + -
1162D MET* 4.4 4.7 - - - +
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Residues in contact with PHE1036 (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* 4.8 2.9 - - + -
876D LEU* 4.4 11.4 - - + -
1002D ILE* 4.2 23.3 - - + -
1032D VAL* 3.0 48.4 + - + +
1033D GLN* 4.6 2.9 - - - +
1035D LEU* 1.3 76.4 - - - +
1037D GLU* 1.3 58.0 + - - +
1038D ALA 3.4 0.4 + - - -
1139D VAL* 3.5 33.7 - - + -
1155D ILE* 4.2 13.2 - - + -
1158D ILE* 3.3 41.1 - - + -
1159D VAL* 4.9 3.1 - - + -
1162D MET* 3.3 23.5 - - + +
1210D GLY* 3.6 0.9 - - - -
1211D ILE* 3.1 40.3 + - + +
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Residues in contact with GLU1037 (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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875D ARG* 2.8 25.7 + - - -
1033D GLN* 3.0 22.1 + - + +
1036D PHE* 1.3 77.1 - - - +
1038D ALA* 1.3 71.1 + - - +
1039D ARG* 3.2 37.7 + - + +
1210D GLY* 3.1 14.7 + - - -
1211D ILE* 3.5 15.8 + - - +
1212D THR* 2.8 44.7 + - - -
1213D LYS 4.2 0.5 + - - -
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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