Contacts of the helix formed by residues 651 - 658 (chain E) in PDB entry 6V3O
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 PRO 651 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLY* 3.5 27.6 - - - +
136E SER* 5.4 0.4 - - - -
644E THR 4.6 1.1 - - - -
647E ARG* 3.5 42.6 - - + +
650E GLY* 1.3 86.7 - - - +
652E THR* 1.3 61.8 + - - +
653E HIS 3.1 0.8 + - - -
654E LEU* 3.3 4.4 + - - +
655E ALA* 3.0 23.1 + - - +
824E VAL* 5.6 0.9 - - - +
887E LEU* 6.0 0.7 - - + -
1004E FLC 3.3 37.9 - - - +
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Residues in contact with THR 652 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644E THR 4.2 3.4 - - - -
645E VAL 3.1 23.1 + - - +
647E ARG* 2.6 34.9 + - - +
648E GLY* 3.1 9.4 + - - -
650E GLY 2.8 1.9 + - - -
651E PRO* 1.3 75.5 - - - +
653E HIS* 1.3 57.2 + - - +
655E ALA* 4.2 6.3 - - - -
656E ILE* 2.8 44.5 + - + +
693E ARG* 4.5 9.6 - - + +
694E PHE* 3.4 29.2 - - + -
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Residues in contact with HIS 653 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E GLU* 3.1 40.1 + - + +
140E GLU* 2.9 21.9 + - - +
141E SER* 3.3 27.4 - - - -
146E THR* 4.9 1.4 + - - -
650E GLY 2.9 10.3 + - - +
652E THR* 1.3 79.1 - - - +
654E LEU* 1.3 61.7 + - - +
656E ILE 3.4 0.3 + - - -
657E LEU* 3.2 40.0 + - + +
693E ARG* 3.7 17.6 - - + +
696E ALA* 4.3 14.3 - - + +
697E ALA* 3.6 30.1 + - + +
700E GLU* 4.8 4.9 + - - -
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Residues in contact with LEU 654 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E PHE* 3.3 45.1 - - + +
132E ALA* 4.5 7.9 - - - +
134E GLU* 3.2 22.1 + - + +
135E GLY* 3.9 17.0 - - - +
651E PRO 3.3 4.5 + - - +
653E HIS* 1.3 78.8 - - - +
655E ALA* 1.3 63.7 + - - +
657E LEU* 3.2 10.4 + - + -
658E SER* 3.0 21.1 + - - -
820E PRO* 4.6 7.6 - - + -
823E ARG* 4.3 19.5 - - + -
824E VAL* 3.6 22.0 - - + -
827E ASP* 5.7 0.4 - - - +
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Residues in contact with ALA 655 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644E THR* 3.5 45.5 + - - +
645E VAL* 3.7 6.1 - - + +
651E PRO* 3.0 17.0 + - + +
652E THR 3.7 3.6 - - - +
654E LEU* 1.3 77.0 - - - +
656E ILE* 1.3 62.3 + - - +
658E SER* 2.9 22.4 + - - -
659E GLN* 3.6 14.7 + - - +
824E VAL* 4.0 9.1 - - + +
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Residues in contact with ILE 656 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645E VAL* 3.8 18.4 - - + -
652E THR* 2.8 37.8 + - + +
655E ALA* 1.3 75.3 - - - +
657E LEU* 1.3 65.1 + - - +
658E SER 3.2 0.7 + - - -
659E GLN* 3.3 18.6 + - - +
664E ILE* 4.0 11.9 - - + -
668E ILE* 4.8 9.9 - - + -
670E VAL* 5.3 0.2 - - + -
693E ARG 5.0 0.2 - - - +
694E PHE* 3.7 22.2 - - + +
697E ALA* 3.7 26.9 - - + +
698E THR* 3.6 35.2 - - + +
701E HIS* 3.3 11.1 - - + -
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Residues in contact with LEU 657 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E PHE* 6.1 3.6 - - + -
134E GLU* 4.0 21.5 - - + +
653E HIS* 3.2 35.2 + - + +
654E LEU* 3.7 13.5 - - + +
656E ILE* 1.3 76.7 - - - +
658E SER* 1.3 56.2 + - - +
659E GLN 3.5 0.2 + - - -
697E ALA* 3.4 25.4 - - + +
700E GLU* 3.7 35.7 - - + +
701E HIS* 3.6 12.1 - - - +
704E HIS 5.2 4.2 - - - +
706E PRO* 3.4 29.6 - - - +
820E PRO* 5.1 2.0 - - + -
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Residues in contact with SER 658 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618E TYR* 4.2 12.3 - - - -
644E THR* 5.3 0.3 + - - -
654E LEU 3.0 13.9 + - - -
655E ALA 2.9 15.6 + - - -
656E ILE 3.1 1.0 - - - -
657E LEU* 1.3 74.0 - - - +
659E GLN* 1.3 69.3 + - - +
660E PRO* 3.7 0.7 - - - +
706E PRO* 4.2 6.3 - - - +
820E PRO* 3.4 40.2 - - - -
821E PHE* 3.7 9.8 + - - +
824E VAL* 3.7 17.9 - - - +
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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
------------------------------------------------------------
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