Contacts of the helix formed by residues 914 - 919 (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 HIS 914 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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912D ASP* 3.3 15.9 + - - +
913D ALA* 1.3 99.9 - - + +
915D VAL* 1.3 61.9 + - - +
916D GLU* 3.1 3.8 - - - +
917D THR* 3.2 24.7 + - + +
918D SER* 3.1 17.9 + - - +
1144D ARG* 2.9 58.8 + - + +
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Residues in contact with VAL 915 (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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898D VAL* 5.8 0.7 - - + -
900D LEU* 3.7 18.2 - - + +
901D ALA* 3.5 13.5 - - + +
911D ARG* 4.0 26.0 - - + +
912D ASP* 3.1 45.3 - - + +
913D ALA 3.6 0.6 - - - -
914D HIS* 1.3 77.9 - - - +
916D GLU* 1.3 68.2 + - + +
917D THR 3.3 0.2 - - - -
918D SER* 4.2 2.5 - - - -
919D ALA* 2.9 34.0 + - + +
920D PHE* 3.0 10.2 + - - +
948D ILE* 5.3 8.3 - - + -
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Residues in contact with GLU 916 (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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570D SER 5.5 3.8 - - - +
911D ARG* 4.9 5.5 + - - -
913D ALA 5.1 2.9 + - - +
914D HIS* 3.1 2.3 - - - -
915D VAL* 1.3 93.4 - - + +
917D THR* 1.3 63.6 + - + +
920D PHE* 3.4 42.7 - - + +
945D ASP* 3.1 25.8 - - - +
1151D HIS* 3.8 8.3 - - - -
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Residues in contact with THR 917 (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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914D HIS* 3.2 27.2 + - + +
915D VAL 3.3 0.2 - - - -
916D GLU* 1.3 85.1 - - + +
918D SER* 1.3 62.2 + - - +
1140D GLN* 4.3 14.8 + - - +
1144D ARG* 4.9 3.5 + - + -
1149D SER* 4.9 11.7 - - - +
1150D ILE 3.5 27.6 - - - +
1151D HIS* 3.1 19.6 + - - +
1152D ASP* 2.9 32.6 + - - -
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Residues in contact with SER 918 (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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898D VAL* 3.9 23.9 - - - +
912D ASP* 5.4 1.4 + - - -
914D HIS* 3.1 17.8 + - - +
915D VAL* 4.2 1.4 - - - -
917D THR* 1.3 80.7 + - - +
919D ALA* 1.3 57.4 + - - +
922D ARG* 2.5 35.0 + - - +
1151D HIS* 4.7 0.4 - - - -
1152D ASP* 3.2 26.2 - - - -
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Residues in contact with ALA 919 (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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898D VAL* 4.0 22.4 - - + -
900D LEU* 4.1 22.0 - - + -
915D VAL* 2.9 21.9 + - + +
918D SER* 1.3 78.3 + - - +
920D PHE* 1.3 66.3 + - - +
921D ALA 3.5 0.5 + - - -
922D ARG* 3.1 19.6 + - - +
943D LEU* 3.9 13.4 - - + +
948D ILE* 4.4 8.7 - - + +
961D VAL* 5.8 0.4 - - - -
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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