Contacts of the helix formed by residues 651 - 658 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D GLY* 3.4 24.9 - - - +
136D SER* 5.2 1.1 - - - -
644D THR 4.7 0.7 - - - +
647D ARG* 3.6 52.9 - - + +
650D GLY* 1.3 87.5 - - - +
652D THR* 1.3 61.9 + - - +
654D LEU* 3.2 7.4 + - - +
655D ALA* 3.0 21.8 + - + +
824D VAL* 5.0 2.1 - - + +
887D LEU* 6.2 1.3 - - + -
1001D PG0 3.5 21.1 - - - +
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Residues in contact with THR 652 (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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644D THR 3.9 0.9 - - - +
645D VAL* 3.1 29.4 - - - +
647D ARG 3.3 9.2 - - - +
648D GLY* 2.9 36.5 - - - +
650D GLY 3.0 1.2 + - - -
651D PRO* 1.3 71.9 - - - +
653D HIS* 1.3 62.1 + - - +
655D ALA* 3.6 9.4 - - - -
656D ILE* 2.8 35.2 + - - +
693D ARG* 4.0 15.4 - - - +
694D PHE* 4.0 21.0 + - + -
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Residues in contact with HIS 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D GLU* 3.3 36.3 + - + +
140D GLU* 3.0 19.6 + - - +
141D SER* 3.3 28.5 - - - -
146D THR* 4.8 1.4 + - - -
650D GLY 3.1 10.6 + - - +
652D THR* 1.3 82.6 + - - +
654D LEU* 1.3 61.7 + - - +
656D ILE* 5.5 0.2 - - - -
657D LEU* 3.2 40.0 + - + +
693D ARG* 3.7 18.2 - - + +
696D ALA* 4.3 14.7 - - + +
697D ALA* 3.5 30.1 + - + +
700D GLU* 4.7 5.1 + - - -
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Residues in contact with LEU 654 (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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131D PHE* 3.5 48.0 - - + +
132D ALA* 4.6 4.7 - - - -
134D GLU* 3.1 22.3 + - + +
135D GLY* 4.0 13.7 - - - -
651D PRO 3.2 7.6 + - - +
653D HIS* 1.3 75.4 - - - +
655D ALA* 1.3 66.1 + - - +
657D LEU* 3.1 9.4 + - + -
658D SER* 2.9 22.3 + - - -
820D PRO* 4.5 10.1 - - + -
823D ARG* 4.3 20.6 - - + -
824D VAL* 3.5 20.0 - - + -
827D ASP* 4.7 6.1 - - - +
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Residues in contact with ALA 655 (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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644D THR* 3.5 46.0 - - - +
645D VAL* 3.8 5.8 - - - +
651D PRO 3.0 14.3 + - - +
652D THR* 3.3 5.1 + - - +
654D LEU* 1.3 76.2 - - - +
656D ILE* 1.3 60.0 + - - +
658D SER* 2.7 24.1 + - - -
659D GLN* 3.3 16.1 + - - -
824D VAL* 3.8 10.4 - - + +
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Residues in contact with ILE 656 (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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645D VAL* 3.8 19.3 - - + -
652D THR* 2.8 22.1 + - - +
655D ALA* 1.3 73.3 - - - +
657D LEU* 1.3 65.5 + - - +
658D SER 3.1 3.0 + - - -
659D GLN* 3.2 23.7 + - - +
664D ILE* 4.1 14.3 - - + +
668D ILE* 4.4 13.2 - - + -
694D PHE* 3.6 37.9 - - + -
697D ALA* 3.7 26.2 - - + +
698D THR* 3.8 28.5 - - - +
701D HIS* 3.5 5.9 - - + -
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Residues in contact with LEU 657 (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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131D PHE* 5.7 3.8 - - + -
134D GLU* 3.9 22.7 - - + -
653D HIS* 3.2 32.5 + - + +
654D LEU* 3.1 15.3 + - + +
656D ILE* 1.3 77.5 - - - +
658D SER* 1.3 55.6 + - - +
659D GLN 3.3 0.4 - - - -
697D ALA* 3.5 26.2 - - + +
700D GLU* 3.6 36.3 - - + +
701D HIS* 3.4 12.3 - - - +
704D HIS 5.2 4.0 - - - +
706D PRO* 3.3 30.4 - - - +
820D PRO* 5.1 1.1 - - + -
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Residues in contact with SER 658 (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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618D TYR* 4.2 6.1 - - - -
644D THR* 5.6 0.5 + - - -
654D LEU 2.9 12.9 + - - -
655D ALA* 2.7 22.3 + - - -
656D ILE 3.1 0.2 - - - -
657D LEU* 1.3 73.9 - - - +
659D GLN* 1.3 70.1 + - - +
706D PRO* 4.1 5.5 - - - +
819D TRP* 5.8 0.2 + - - -
820D PRO* 3.4 42.8 + - - -
821D PHE* 3.7 19.6 + - - +
824D VAL* 4.3 6.3 - - - +
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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