Contacts of the helix formed by residues 1072 - 1081 (chain C) 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 ALA1072 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067C MET* 3.5 14.3 + - - +
1070C TYR* 3.3 4.0 + - + -
1071C GLY* 1.3 72.3 - - - +
1073C ALA* 1.3 66.2 + - - +
1074C TYR 3.3 0.2 - - - -
1075C THR* 4.0 8.1 - - - -
1076C LEU* 3.2 21.7 + - - +
554D GLU* 3.0 39.2 - - + +
558D LEU* 4.2 6.5 - - + -
559D MET* 4.0 18.4 - - + -
1259D ILE* 5.1 0.9 - - - -
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Residues in contact with ALA1073 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071C GLY 2.9 8.5 + - - -
1072C ALA* 1.3 71.9 - - - +
1074C TYR* 1.3 57.9 - - - +
1076C LEU* 3.4 2.9 + - - +
1077C GLN* 3.0 29.8 + - - +
1258D LEU* 3.8 13.8 - - + +
1259D ILE* 3.5 36.2 + - + +
1261D ALA 3.9 1.6 - - - +
1263D THR* 3.1 12.5 + - - +
1264D GLY* 3.7 21.3 - - - +
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Residues in contact with TYR1074 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073C ALA* 1.3 74.1 - - - +
1075C THR* 1.3 60.5 + - - +
1077C GLN* 3.3 9.7 + - - +
1078C GLU* 2.8 32.0 + - - +
548D SER* 5.1 4.2 + - - +
550D GLU* 3.5 42.6 + - + -
551D ALA* 4.5 4.3 - - - +
554D GLU* 3.1 12.8 + - - +
1258D LEU* 3.2 35.6 - - + +
1263D THR* 3.4 26.9 - - - -
1269D ARG* 3.8 18.5 + - - +
51E VAL* 5.9 0.2 - - + -
52E ILE* 3.4 26.4 - - + +
56E LYS* 5.8 2.3 - - - -
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Residues in contact with THR1075 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067C MET* 3.6 22.0 - - + -
1072C ALA* 4.0 8.7 - - - -
1074C TYR* 1.3 72.6 - - - +
1076C LEU* 1.3 62.7 + - - +
1078C GLU* 3.3 10.2 + - - +
1079C LEU* 3.1 31.3 + - + +
1083C LYS* 6.3 0.7 - - - +
497D LEU* 4.0 21.1 - - + -
546D PRO* 5.1 3.0 - - + +
551D ALA* 3.4 29.7 + - + +
554D GLU* 2.6 28.3 + - - +
559D MET* 4.2 4.1 - - + +
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Residues in contact with LEU1076 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059C PHE* 3.9 15.3 - - + -
1064C CYS* 3.8 31.0 - - + +
1067C MET* 3.6 20.6 - - + +
1068C GLN* 3.7 25.6 - - + -
1072C ALA 3.2 12.9 + - - +
1073C ALA 3.7 4.3 - - - +
1075C THR* 1.3 74.8 - - - +
1077C GLN* 1.3 66.1 + - - +
1079C LEU* 3.0 15.8 + - - +
1080C LEU* 3.1 20.2 + - + +
1253D VAL* 3.7 28.7 - - + -
1259D ILE* 4.1 13.7 - - + -
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Residues in contact with GLN1077 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073C ALA 3.0 18.0 + - - +
1074C TYR* 3.7 12.8 - - - +
1076C LEU* 1.3 77.9 - - - +
1078C GLU* 1.3 55.8 + - - +
1080C LEU* 3.3 2.9 + - - +
1081C THR* 2.5 40.2 + - + +
1105C GLU* 5.6 3.2 + - - +
1106C PRO* 3.4 37.2 + - + +
5D ASN* 6.3 0.6 - - - +
6D PHE* 6.3 1.4 - - - -
1256D GLY* 3.0 30.9 + - - +
1257D LYS* 4.2 6.8 - - - +
1258D LEU* 3.1 33.9 - - + +
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Residues in contact with GLU1078 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074C TYR 2.8 21.7 + - - +
1075C THR* 3.5 8.7 - - - +
1076C LEU 3.2 0.2 - - - -
1077C GLN* 1.3 75.1 + - - +
1079C LEU* 1.3 61.8 + - - +
1081C THR* 3.9 3.4 - - - -
1082C ILE* 3.4 27.4 + - + +
1083C LYS* 3.2 47.6 + - - +
1106C PRO* 5.2 3.1 - - + -
546D PRO* 3.8 2.3 - - - +
547D LEU* 3.2 25.9 + - - +
548D SER* 2.8 40.1 + - - +
551D ALA* 3.6 13.1 - - - +
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Residues in contact with LEU1079 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059C PHE* 3.2 44.2 - - + -
1067C MET* 4.7 1.1 - - + -
1075C THR* 3.1 29.8 + - + +
1076C LEU* 3.0 7.9 + - - +
1078C GLU* 1.3 80.1 - - + +
1080C LEU* 1.3 67.1 + - + +
1081C THR 3.3 1.3 + - - -
1083C LYS* 3.5 41.2 - - + +
1084C SER* 3.8 6.1 - - - -
422D VAL* 3.2 44.3 - - + +
497D LEU* 5.6 2.5 - - + -
544D HIS* 4.0 13.0 - - + +
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Residues in contact with LEU1080 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059C PHE* 4.3 14.6 - - + -
1064C CYS* 4.1 18.6 - - - -
1076C LEU* 3.1 25.1 + - + +
1077C GLN* 4.3 2.9 - - - +
1079C LEU* 1.3 78.8 - - + +
1081C THR* 1.3 66.7 + - + +
1084C SER* 4.6 0.7 - - - -
1085C ASP* 4.4 0.7 - - - +
1109C PRO* 3.6 6.6 - - + +
417D LEU 5.5 0.4 - - - +
418D LEU* 3.8 18.2 - - - +
420D LYS* 3.3 54.2 + - + +
1253D VAL* 3.6 42.4 - - + +
1256D GLY* 5.9 0.4 - - - -
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Residues in contact with THR1081 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077C GLN* 2.5 28.6 + - + +
1078C GLU 3.8 0.7 + - - -
1079C LEU 3.3 2.2 - - - -
1080C LEU* 1.3 85.9 - - + +
1082C ILE* 1.3 68.7 + - - +
1083C LYS 3.1 0.7 - - - -
1084C SER 2.9 18.9 + - - -
1085C ASP 3.1 0.7 + - - -
1086C ASP* 2.9 29.8 + - - +
1106C PRO* 3.3 24.8 - - + +
1107C GLY 4.6 2.9 - - - +
1109C PRO* 4.3 13.2 - - + -
1256D GLY* 3.9 32.8 - - - +
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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