Contacts of the helix formed by residues 613 - 617 (chain A) in PDB entry 1M7X
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 613 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609A THR* 3.7 32.5 - - + +
610A TYR 3.4 2.3 - - - +
611A ARG 2.8 9.3 + - - -
612A HIS* 1.3 101.0 + + - +
614A LYS* 1.3 66.8 + - - +
615A ALA* 3.0 2.8 + - + -
616A MET* 3.0 13.2 + - + -
617A HIS* 3.3 12.4 - - - -
651A ILE* 3.7 25.0 - - + +
678A ILE* 4.1 19.4 - - + +
724A VAL* 4.1 25.0 - - + +
278B TRP* 5.7 1.5 - + - -
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Residues in contact with LYS 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A HIS* 3.8 19.3 - - - +
613A HIS* 1.3 70.7 - - - +
615A ALA* 1.3 62.4 + - - +
617A HIS* 3.1 22.8 + - + -
618A GLU* 2.9 49.1 + - + +
645A ASP* 3.7 22.9 + - + +
277B LYS* 5.4 5.8 - - - +
327B ALA 5.7 2.6 + - - -
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Residues in contact with ALA 615 (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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613A HIS* 3.0 1.4 + - + -
614A LYS* 1.3 78.0 - - - +
616A MET* 1.3 59.3 + - - +
617A HIS 3.4 1.0 + - - -
618A GLU 4.6 0.7 + - - -
643A ARG* 3.4 43.7 + - - +
644A ARG 3.8 7.8 + - - +
645A ASP* 3.6 17.5 + - + +
649A ASN* 3.9 16.4 - - + +
651A ILE* 4.0 27.4 - - + -
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Residues in contact with MET 616 (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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558A TRP 4.1 2.5 - - - +
559A ALA* 3.3 46.9 - - + +
564A LYS* 4.9 0.2 - - - -
609A THR 4.6 0.4 - - - +
610A TYR* 3.0 36.2 - - + +
613A HIS* 3.0 16.8 + - + +
615A ALA* 1.3 75.8 - - - +
617A HIS* 1.3 59.2 + - - +
643A ARG* 3.8 33.4 + - + +
651A ILE* 3.8 37.2 - - + -
653A VAL* 4.3 2.9 - - + -
722A TRP* 4.0 28.9 - - + -
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Residues in contact with HIS 617 (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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239A PHE 4.0 0.2 - - - +
240A ASP 3.7 13.0 + - - +
241A ALA 4.3 0.4 - - - +
242A PRO* 3.4 46.2 - - + +
563A LYS* 3.1 22.7 + - - +
610A TYR* 2.8 45.4 + - + +
611A ARG* 4.0 6.1 - - - -
612A HIS 4.2 4.2 + - - -
613A HIS 3.3 19.1 + - - -
614A LYS* 3.1 31.8 + - + +
615A ALA 3.3 1.6 + - - -
616A MET* 1.3 79.6 - - - +
618A GLU* 1.3 64.7 + - - +
619A LEU 3.6 2.2 - - - +
620A ASP* 3.9 11.8 - - - +
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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