Contacts of the helix formed by residues 674 - 683 (chain A) in PDB entry 3M8S
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 SER 674 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672A GLY 3.5 1.5 + - - -
673A MET* 1.3 75.6 - - - +
675A ALA* 1.3 64.8 + - - +
676A HIS* 3.7 7.6 + - - +
677A ARG* 3.2 16.8 + - - +
678A LEU* 3.0 24.4 + - - +
693A ILE* 4.2 1.3 - - - -
202C A 4.3 8.7 + - - -
203C A 4.3 34.3 - - - -
204C A 2.8 25.8 + - - -
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Residues in contact with ALA 675 (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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674A SER* 1.3 73.9 - - - +
676A HIS* 1.3 56.7 + - - +
678A LEU* 3.4 1.0 + - - -
679A SER* 2.9 27.0 + - - -
686A TYR* 3.7 22.9 - - + +
689A ALA* 3.2 10.1 - - - +
690A GLN* 3.3 44.4 - - + +
693A ILE* 3.8 14.7 - - + +
203C A 6.1 0.2 - - - +
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Residues in contact with HIS 676 (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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674A SER* 3.2 7.7 + - - +
675A ALA* 1.3 78.7 - - - +
677A ARG* 1.3 61.7 + - - +
679A SER* 2.9 21.3 + - - -
680A GLN* 3.1 20.5 + - - +
686A TYR* 3.5 27.4 - + + -
201C A 3.5 23.3 + + - -
202C A 3.1 38.5 + + - +
203C A 5.8 2.4 + - - +
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Residues in contact with ARG 677 (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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673A MET* 3.5 24.3 - - + +
674A SER* 3.2 17.1 + - - +
676A HIS* 1.3 77.7 - - - +
678A LEU* 1.3 64.6 + - - +
680A GLN* 2.9 12.3 + - - +
681A GLU* 3.1 38.5 + - - +
202C A 3.4 48.9 + - + -
204C A 3.0 59.2 + - - +
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Residues in contact with LEU 678 (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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665A ILE* 3.9 25.1 - - + -
669A VAL* 4.2 14.4 - - + -
673A MET* 3.8 25.3 - - + -
674A SER 3.0 17.3 + - - +
675A ALA 3.7 2.9 - - - +
677A ARG* 1.3 77.0 - - - +
679A SER* 1.3 61.2 + - - +
681A GLU* 3.3 2.6 + - - -
682A LEU* 3.2 54.6 + - + +
684A ILE* 4.3 0.7 - - + -
689A ALA* 3.3 33.2 - - + +
692A PHE* 4.8 6.5 - - + -
693A ILE* 4.3 10.1 - - + -
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Residues in contact with SER 679 (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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675A ALA 2.9 16.7 + - - -
676A HIS* 2.9 16.6 + - - -
678A LEU* 1.3 76.9 - - - +
680A GLN* 1.3 65.1 + - - +
683A ALA* 2.9 21.7 + - - -
684A ILE* 2.9 33.5 + - - +
686A TYR* 3.7 18.4 + - - +
689A ALA* 3.3 18.1 - - - +
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Residues in contact with GLN 680 (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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521A ALA* 4.9 8.1 - - + +
676A HIS* 3.1 18.1 + - - +
677A ARG 2.9 10.6 + - - +
679A SER* 1.3 92.0 + - - +
681A GLU* 1.3 61.1 + - - +
683A ALA* 3.4 12.6 + - - +
201C A 3.0 40.2 + - + +
202C A 3.9 17.3 - - - +
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Residues in contact with GLU 681 (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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664A THR* 4.7 6.8 + - - -
665A ILE* 4.0 19.3 - - + +
673A MET* 3.7 16.8 - - - +
677A ARG* 3.1 50.2 + - + +
678A LEU* 3.3 4.7 + - - +
680A GLN* 1.3 79.9 - - - +
682A LEU* 1.3 61.4 + - - +
683A ALA* 3.2 2.8 - - - +
202C A 4.4 13.5 + - - +
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Residues in contact with LEU 682 (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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645A TRP* 3.9 23.8 - - + -
646A MET* 4.0 19.1 - - + -
665A ILE* 3.3 41.5 - - + -
678A LEU* 3.2 40.4 + - + +
681A GLU* 1.3 77.1 - - - +
683A ALA* 1.3 70.7 + - - +
684A ILE* 3.4 30.4 + - + +
692A PHE* 5.2 2.2 - - + -
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Residues in contact with ALA 683 (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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679A SER 2.9 10.9 + - - -
680A GLN* 3.4 9.8 + - - +
681A GLU 3.2 4.5 - - - +
682A LEU* 1.3 82.7 - - - +
684A ILE* 1.3 60.6 + - - +
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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