Contacts of the helix formed by residues 1118 - 1127 (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 ASP1118 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1040D VAL* 3.7 30.7 - - - +
1041D PRO* 3.6 10.5 - - + +
1044D LYS* 4.0 24.2 + - + +
1045D ALA 4.1 5.1 + - - -
1047D ILE* 6.0 0.2 - - - +
1116D ALA 3.8 0.4 + - - -
1117D ALA* 1.3 69.9 - - - +
1119D PRO* 1.3 63.4 - - - +
1120D HIS* 3.0 26.7 + - - +
1121D GLU* 2.7 49.2 + - + +
1122D VAL* 3.0 7.6 + - - +
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Residues in contact with PRO1119 (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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1034D GLU 5.9 1.1 - - - +
1035D LEU* 5.4 8.1 - - + +
1038D ALA* 5.2 8.1 - - - -
1039D ARG 4.3 11.2 - - - +
1041D PRO* 4.1 11.2 - - + -
1117D ALA 3.0 12.3 - - - +
1118D ASP* 1.3 87.2 - - - +
1120D HIS* 1.3 63.5 + - + +
1122D VAL* 3.0 28.3 - - + +
1123D LEU* 3.0 11.6 + - - +
1131D VAL* 4.2 1.6 - - + +
1134D HIS* 5.1 3.8 - - + +
1135D LEU* 4.1 24.2 - - + -
1208D LEU* 3.4 27.1 - - + +
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Residues in contact with HIS1120 (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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1038D ALA* 3.0 32.8 + - + +
1040D VAL* 5.0 8.7 - - + -
1118D ASP* 3.0 18.2 + - - +
1119D PRO* 1.3 79.5 - - + +
1121D GLU* 1.3 63.6 + - - +
1123D LEU* 3.6 19.5 + - - +
1124D ARG* 3.6 10.6 + - - +
1208D LEU* 3.0 39.0 + - + +
1209D MET* 5.0 0.9 - - - -
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Residues in contact with GLU1121 (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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1044D LYS* 4.0 20.3 + - - -
1046D PRO* 6.3 1.1 - - + -
1047D ILE* 3.5 25.6 - - + +
1049D ASP* 5.7 0.4 - - - +
1118D ASP* 2.7 37.2 + - + +
1120D HIS* 1.3 71.0 - - - +
1122D VAL* 1.3 62.1 + - - +
1123D LEU 3.2 0.9 + - - -
1124D ARG* 3.4 34.2 + - - +
1125D VAL* 3.2 27.3 + - + +
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Residues in contact with VAL1122 (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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1047D ILE* 3.4 19.7 - - + +
1117D ALA* 5.5 4.3 - - + +
1118D ASP 3.0 5.2 + - - +
1119D PRO* 3.0 31.9 - - + +
1121D GLU* 1.3 75.6 - - - +
1123D LEU* 1.3 55.8 + - - +
1125D VAL* 3.8 2.9 - - - -
1126D GLN* 2.8 61.7 + - + +
1127D GLY 3.6 0.9 + - - -
1130D GLU 4.9 3.1 - - - +
1131D VAL* 3.8 22.6 - - + +
1134D HIS* 4.6 19.7 - - + +
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Residues in contact with LEU1123 (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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1119D PRO 3.0 17.2 + - - +
1120D HIS* 3.6 12.3 - - - +
1121D GLU 3.1 0.6 - - - -
1122D VAL* 1.3 78.0 - - - +
1124D ARG* 1.3 60.5 + - - +
1127D GLY* 2.8 31.7 + - - -
1128D PRO* 3.6 39.4 - - + +
1131D VAL* 3.1 14.8 - - + -
1163D LEU* 4.6 4.5 - - + -
1206D PRO* 3.5 28.9 - - + +
1207D VAL* 3.9 2.2 - - - -
1208D LEU* 3.6 31.6 - - + +
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Residues in contact with ARG1124 (chain D).
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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1049D ASP* 3.2 29.3 + - - -
1120D HIS 3.6 9.0 + - - +
1121D GLU* 3.4 33.5 + - - +
1123D LEU* 1.3 81.9 - - + +
1125D VAL* 1.3 68.6 + - + +
1127D GLY 4.7 0.2 - - - -
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Residues in contact with VAL1125 (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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1047D ILE* 4.4 13.0 - - + -
1048D ALA 4.1 9.0 - - - +
1049D ASP* 4.3 25.1 - - - +
1108D VAL* 3.7 34.2 - - + +
1109D GLY* 5.4 0.2 - - - -
1121D GLU* 3.2 23.3 - - + +
1122D VAL* 4.0 5.2 - - - +
1123D LEU 3.1 1.0 - - - -
1124D ARG* 1.3 96.0 - - + +
1126D GLN* 1.3 68.9 + - + +
1127D GLY 3.5 0.2 - - - -
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Residues in contact with GLN1126 (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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1047D ILE* 5.7 1.8 - - + +
1108D VAL* 4.6 4.2 - - + +
1109D GLY* 3.2 43.9 + - - +
1122D VAL* 2.8 35.9 + - + +
1125D VAL* 1.3 82.7 - - + +
1127D GLY* 1.3 58.9 + - - +
1130D GLU* 2.9 47.5 + - + +
1134D HIS* 6.3 0.2 - - - +
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Residues in contact with GLY1127 (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 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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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