Contacts of the helix formed by residues 683 - 693 (chain A) in PDB entry 5M7R
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 GLY 683 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A LYS* 6.2 1.1 - - - -
682A ARG* 1.3 73.0 - - - +
684A GLY* 1.3 66.5 + - - +
686A ALA* 3.9 6.9 + - - +
687A GLY* 3.1 18.8 + - - -
287B ASP* 3.0 15.1 + - - -
289B LYS* 3.9 36.2 - - - +
290B ARG* 4.2 5.8 - - - -
690B GLN* 5.4 2.0 - - - -
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Residues in contact with GLY 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A PHE 3.0 13.7 + - - +
682A ARG 4.1 1.6 - - - +
683A GLY* 1.3 76.6 - - - +
685A LEU* 1.3 67.7 + - - -
686A ALA 3.2 0.4 - - - -
687A GLY* 3.0 8.7 + - - -
688A GLU* 3.2 15.0 + - - +
289B LYS 5.5 0.7 - - - -
290B ARG* 3.4 28.6 - - - +
565B PHE* 6.3 2.9 - - - -
571B HIS* 4.1 6.5 - - - -
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Residues in contact with LEU 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684A GLY* 1.3 70.9 - - - -
686A ALA* 1.3 65.4 + - - +
688A GLU* 2.9 14.6 + - - +
689A PHE* 3.1 45.4 + - + -
563B ASP 4.9 0.7 - - - +
564B LEU* 3.4 57.4 + - + +
565B PHE* 6.1 1.6 - - + -
571B HIS* 3.6 38.1 + - + +
575B GLY* 3.9 24.9 - - - +
579B LEU* 4.2 13.0 - - + -
647B ILE* 4.5 6.5 - - + -
651B MET* 4.5 0.7 - - + -
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Residues in contact with ALA 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683A GLY 4.0 7.0 - - - +
684A GLY 3.2 0.4 - - - -
685A LEU* 1.3 77.9 - - - +
687A GLY* 1.3 57.5 + - - +
689A PHE* 3.3 3.7 + - - +
690A GLN* 2.9 30.4 + - - +
289B LYS* 4.5 3.8 - - + +
565B PHE* 5.9 6.8 - - + -
646B ASP* 3.3 26.9 - - - +
647B ILE* 3.8 24.9 - - + +
650B ILE* 4.1 18.5 - - + +
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Residues in contact with GLY 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682A ARG 4.4 0.2 - - - -
683A GLY* 3.1 20.3 + - - -
684A GLY 3.0 8.6 + - - -
686A ALA* 1.3 77.2 - - - +
688A GLU* 1.3 57.0 + - - +
690A GLN* 3.5 13.8 + - - +
691A ARG* 3.0 44.6 + - - +
289B LYS* 5.4 2.4 - - - +
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Residues in contact with GLU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A ALA 5.2 4.4 - - - +
681A PHE* 4.1 17.5 - - - +
682A ARG 5.4 0.2 - - - +
684A GLY 3.2 8.4 + - - +
685A LEU* 2.9 9.1 + - - +
687A GLY* 1.3 74.5 - - - +
689A PHE* 1.3 63.4 + - - +
691A ARG* 3.6 29.9 + - - +
692A LEU* 3.3 28.7 + - + +
571B HIS* 2.8 33.3 + - - -
579B LEU* 3.2 29.9 - - + +
583B GLN* 5.1 2.4 + - - -
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Residues in contact with PHE 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A LEU* 3.1 48.5 + - + -
686A ALA* 3.8 6.5 - - - +
688A GLU* 1.3 72.2 - - - +
690A GLN* 1.3 67.7 + - - +
692A LEU* 2.9 18.0 + - - +
693A LEU* 3.3 14.9 + - - +
578B MET* 3.7 18.4 - - + -
579B LEU* 3.6 30.3 - - + -
582B PHE* 3.7 31.5 - + + -
614B PHE* 4.3 5.8 - + - -
650B ILE* 3.9 7.9 - - + -
651B MET* 3.2 36.8 - - + -
654B VAL* 3.8 22.0 - - + -
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Residues in contact with GLN 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A ALA 2.9 16.9 + - - +
687A GLY* 3.6 11.1 + - - +
689A PHE* 1.3 77.8 - - - +
691A ARG* 1.3 65.4 + - - +
693A LEU* 3.4 26.9 + - + +
289B LYS* 4.0 19.2 - - - -
650B ILE* 4.5 13.5 - - + +
679B TRP* 4.2 19.7 - - + +
682B ARG* 3.5 47.8 + - + +
683B GLY* 5.4 0.5 + - - -
691B ARG* 5.0 12.3 - - - +
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Residues in contact with ARG 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A ALA 5.0 4.6 + - - -
681A PHE 4.9 0.8 - - - -
682A ARG* 2.9 31.3 + - - +
687A GLY* 3.0 33.0 + - - +
688A GLU* 3.6 32.6 - - - +
689A PHE 3.0 0.6 + - - -
690A GLN* 1.3 80.6 - - - +
692A LEU* 1.3 64.5 + - + +
693A LEU 3.4 5.4 + - - +
690B GLN* 5.6 4.0 - - - +
691B ARG* 5.9 7.2 - - + -
695B ILE* 4.0 38.5 - - - +
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Residues in contact with LEU 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688A GLU* 3.3 17.5 - - + +
689A PHE* 2.9 7.4 + - - +
691A ARG* 1.3 79.9 - - + +
693A LEU* 1.3 62.3 + - - +
694A PRO* 4.6 0.5 - - - +
579B LEU* 3.8 17.3 - - + -
582B PHE* 3.8 24.5 - - + -
583B GLN* 3.8 34.8 - - + +
586B ARG* 3.4 48.8 + - - +
657B PHE* 4.9 0.3 - - - -
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Residues in contact with LEU 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A PHE 3.3 6.8 + - - +
690A GLN* 3.7 25.4 - - + +
691A ARG 3.4 8.8 - - - +
692A LEU* 1.3 81.1 - - - +
694A PRO* 1.3 71.8 - - + +
695A ILE 3.6 2.4 + - - -
582B PHE* 4.3 3.1 - - + -
586B ARG* 5.4 0.7 - - - -
650B ILE* 5.1 6.3 - - + +
653B MET* 3.9 29.6 - - + +
654B VAL* 4.0 30.3 - - + +
657B PHE* 3.9 37.7 - - + -
671B PHE* 5.1 0.4 - - + -
679B TRP* 4.2 19.2 - - + +
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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