Contacts of the helix formed by residues 1060 - 1071 (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 GLY1060 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1058C ARG* 3.4 19.5 + - - +
1059C PHE* 1.3 83.8 - - - +
1061C GLU* 1.3 65.8 + - - -
1062C MET 3.3 2.9 + - - -
1063C GLU* 3.0 18.6 + - - -
1064C CYS* 3.3 17.5 + - - -
415D GLN* 3.7 12.1 - - - -
419D GLY* 4.1 4.0 - - - -
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Residues in contact with GLU1061 (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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1060C GLY* 1.3 72.0 - - - -
1062C MET* 1.3 65.9 + - + +
1064C CYS* 3.1 21.1 + - + +
1065C TRP* 3.2 40.7 + - + +
414D ARG* 3.1 45.6 + - - +
415D GLN* 3.0 28.6 - - + +
418D LEU* 4.4 12.4 - - + +
419D GLY* 4.3 3.3 - - - +
874D ARG* 3.9 17.6 + - - -
1250D LYS* 4.3 15.6 + - - -
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Residues in contact with MET1062 (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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1060C GLY 3.3 0.4 - - - -
1061C GLU* 1.3 79.7 - - + +
1063C GLU* 1.3 70.7 + - - +
1065C TRP* 3.0 44.2 + - + +
1066C ALA* 3.1 11.1 + - - +
415D GLN* 5.7 2.5 - - - +
501D ALA* 5.7 0.9 - - + -
502D PRO* 3.7 31.4 - - + -
503D THR* 3.6 33.0 - - - +
504D LEU* 5.3 3.1 - - - -
870D GLY* 6.1 4.5 - - - -
1000D GLN* 4.8 0.5 + - - -
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Residues in contact with GLU1063 (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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1058C ARG 5.1 4.0 - - - +
1059C PHE* 3.7 32.4 - - + -
1060C GLY* 3.0 31.1 + - - +
1061C GLU 3.3 0.2 - - - -
1062C MET* 1.3 83.6 + - - +
1064C CYS* 1.3 57.9 + - - +
1066C ALA* 3.0 5.0 + - - +
1067C MET* 2.9 27.0 + - - +
499D ASN* 3.8 25.1 - - - +
501D ALA* 4.5 10.2 - - - +
503D THR* 2.5 38.3 + - - +
509D ILE* 4.1 5.5 - - + +
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Residues in contact with CYS1064 (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* 3.6 24.9 - - - -
1060C GLY 3.3 14.1 + - - -
1061C GLU* 3.1 13.5 + - + +
1063C GLU* 1.3 78.3 - - - +
1065C TRP* 1.3 58.1 + - + +
1067C MET* 3.0 3.2 + - - +
1068C GLN* 2.8 41.7 + - - +
1076C LEU* 3.8 18.2 - - + -
1080C LEU* 4.1 16.4 - - - -
418D LEU* 4.1 13.7 - - + -
1253D VAL* 5.3 5.4 - - + -
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Residues in contact with TRP1065 (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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1061C GLU* 3.2 40.3 + - + +
1062C MET* 3.0 38.4 + - + +
1064C CYS* 1.3 77.9 - - + +
1066C ALA* 1.3 56.4 + - - +
1068C GLN* 3.2 19.9 + - - +
1069C ALA* 2.8 25.3 + - - +
503D THR 5.5 2.2 - - - -
504D LEU 6.1 0.7 - - - -
870D GLY 5.2 2.5 - - - -
873D THR* 4.4 13.9 - - + -
874D ARG* 3.5 49.1 - - + -
877D VAL* 3.6 38.0 - - + +
881D GLN* 5.4 3.1 + - - -
996D ILE* 3.7 8.6 - - + +
1000D GLN* 3.3 21.3 + - + +
1250D LYS* 5.7 4.6 - - - +
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Residues in contact with ALA1066 (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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1062C MET 3.1 4.2 + - - -
1063C GLU 3.0 9.4 + - - +
1065C TRP* 1.3 75.8 - - - +
1067C MET* 1.3 62.3 + - - +
1069C ALA* 3.3 2.8 + - - +
1070C TYR* 3.2 29.3 + - - -
503D THR* 3.5 29.2 - - + -
505D HIS 4.0 0.4 - - - +
506D ARG* 3.8 23.2 - - - +
509D ILE* 4.2 10.5 - - + -
1000D GLN* 3.3 10.4 - - - +
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Residues in contact with MET1067 (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* 3.4 26.2 - - + -
1063C GLU 2.9 9.7 + - - +
1064C CYS 3.0 7.6 + - - +
1066C ALA* 1.3 77.3 - - - +
1068C GLN* 1.3 61.8 + - - +
1070C TYR* 3.3 12.2 + - + +
1071C GLY 3.3 7.6 + - - -
1072C ALA* 3.5 16.3 + - - +
1075C THR* 3.6 25.8 - - + -
1076C LEU* 3.6 42.6 - - + +
1079C LEU* 4.7 0.9 - - + -
497D LEU* 4.8 3.1 - - + -
509D ILE* 3.7 32.1 - - + -
559D MET* 3.7 20.9 - - - +
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Residues in contact with GLN1068 (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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1064C CYS* 2.8 29.4 + - - +
1065C TRP* 3.3 27.2 - - - +
1067C MET* 1.3 69.0 - - - +
1069C ALA* 1.3 66.0 + - - +
1071C GLY* 3.0 13.3 + - - -
1076C LEU* 3.7 19.5 - - + -
881D GLN* 4.4 3.2 + - - +
993D ALA* 4.0 13.7 - - - +
996D ILE* 3.4 22.4 - - + +
1249D LEU* 3.1 36.4 + - + +
1250D LYS* 4.7 1.6 - - - +
1253D VAL* 4.1 15.9 - - - +
1259D ILE* 4.0 19.7 - - + +
1261D ALA* 5.4 0.3 - - - +
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Residues in contact with ALA1069 (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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1065C TRP 2.8 13.8 + - - +
1066C ALA 3.4 9.9 - - - +
1067C MET 3.2 0.2 - - - -
1068C GLN* 1.3 77.6 - - - +
1070C TYR* 1.3 60.7 + - - +
1071C GLY 3.3 0.7 + - - -
506D ARG* 3.4 36.8 + - + -
992D GLU* 3.9 8.8 - - - +
993D ALA 4.7 4.7 + - - +
996D ILE* 4.6 7.6 - - + +
997D VAL* 3.9 23.0 - - + +
1000D GLN* 3.6 15.0 - - - +
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Residues in contact with TYR1070 (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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1066C ALA 3.2 18.6 + - - -
1067C MET* 3.3 8.5 + - - +
1068C GLN 3.3 0.2 - - - -
1069C ALA* 1.3 78.5 - - - +
1071C GLY* 1.3 59.2 + - - +
1072C ALA* 3.6 5.7 + - + +
506D ARG* 2.9 51.7 + - + +
507D LEU* 3.3 15.1 - - - +
509D ILE* 2.7 29.9 + - + -
510D GLN* 4.0 5.7 - - - +
558D LEU* 3.7 26.4 - - + +
559D MET* 3.3 37.7 - - + -
564D ASN* 3.8 25.7 + - - -
47E LYS* 5.3 1.4 + - - -
48E TYR* 3.3 20.3 + - - -
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Residues in contact with GLY1071 (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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1067C MET 3.3 0.8 + - - -
1068C GLN* 3.0 17.9 + - - -
1069C ALA 3.2 1.0 + - - -
1070C TYR* 1.3 78.3 - - - +
1072C ALA* 1.3 59.5 + - - +
1073C ALA* 2.9 9.3 + - - -
558D LEU* 4.3 3.1 - - - -
993D ALA* 6.0 2.5 - - - -
1259D ILE* 5.2 2.9 - - - -
1261D ALA* 3.8 4.1 - - - +
1262D GLY* 3.3 19.4 - - - -
1263D THR* 3.0 26.7 + - - +
48E TYR* 3.9 3.4 - - - -
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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