Contacts of the helix formed by residues 975 - 979 (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 ALA 975 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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885D VAL* 3.4 8.3 - - + +
887D GLU 2.9 9.4 + - - +
888D HIS* 3.4 23.3 + - - +
974D CYS* 1.3 72.2 - - - +
976D MET* 1.3 59.2 + - - +
978D TYR* 3.2 3.1 + - - +
979D GLY 2.8 26.5 + - - -
987D LEU* 3.6 17.5 - - + +
988D VAL* 3.5 34.3 - - + +
990D ILE* 4.7 4.7 - - + -
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Residues in contact with MET 976 (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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888D HIS* 3.0 46.3 + - - +
889D ASP* 3.7 20.2 - - + +
923D THR* 2.9 43.6 + - + +
940D GLY* 4.0 32.1 - - - +
962D ARG* 3.5 22.7 - - - +
974D CYS* 3.4 0.4 - - - -
975D ALA* 1.3 76.5 - - - +
977D CYS* 1.3 64.2 + - - +
979D GLY 3.4 1.2 + - - -
987D LEU* 4.2 14.4 - - + -
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Residues in contact with CYS 977 (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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890D CYS* 3.6 3.6 - - - -
892D THR* 4.3 4.9 - - - -
922D ARG* 5.5 0.7 + - - -
923D THR* 4.5 0.9 + - - -
962D ARG* 2.8 55.3 - - - +
963D SER* 3.7 21.1 - - - +
964D VAL* 4.1 2.6 + - + +
966D THR* 4.9 1.6 - - - -
967D CYS* 3.6 19.3 - - + -
974D CYS* 3.3 6.3 - - - +
975D ALA 3.4 0.4 - - - -
976D MET* 1.3 79.4 - - - +
978D TYR* 1.3 64.5 + - - +
2001D ZN 2.2 36.1 - - - -
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Residues in contact with TYR 978 (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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885D VAL* 5.0 1.1 - - + -
921D ALA 4.5 0.7 - - - +
922D ARG* 5.4 5.0 + - - -
964D VAL* 4.1 24.3 - - + +
973D VAL* 4.6 5.4 - - + -
974D CYS 3.2 17.9 + - - +
975D ALA 3.6 2.0 - - - +
977D CYS* 1.3 81.4 - - - +
979D GLY* 1.3 53.0 + - - +
980D ARG 4.3 6.5 + - - -
981D SER* 4.6 4.0 - - - -
982D MET* 5.1 4.9 + - - +
988D VAL* 3.5 40.6 - - + -
994D VAL* 3.1 42.3 - - + +
997D VAL* 5.4 1.9 - - - +
1153D LYS* 2.7 72.0 + - + +
1154D HIS* 3.9 15.4 - - - -
1157D VAL* 4.4 4.0 - - + -
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Residues in contact with GLY 979 (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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921D ALA 4.4 2.5 - - - -
922D ARG* 5.2 0.7 - - - -
923D THR* 3.9 16.6 - - - -
975D ALA 2.8 15.1 + - - -
976D MET 3.4 8.8 + - - -
978D TYR* 1.3 75.5 - - - +
980D ARG* 1.3 67.1 + - - +
987D LEU* 3.7 8.2 - - - +
988D VAL* 3.2 26.9 + - - +
1153D LYS* 3.6 2.0 - - - -
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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