Contacts of the helix formed by residues 613 - 617 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278C TRP* 5.5 3.3 - + - -
609D THR* 3.6 32.9 - - + +
610D TYR 3.5 5.0 - - - +
611D ARG 3.1 3.4 + - - -
612D HIS* 1.3 104.5 - + - +
614D LYS* 1.3 64.7 + - - +
615D ALA 3.2 2.5 - - - +
616D MET* 3.1 30.4 + - + +
617D HIS* 3.7 2.5 - - - -
651D ILE* 5.1 9.1 - - + +
678D ILE* 4.0 25.7 - - + +
724D VAL* 4.1 26.4 - - + +
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Residues in contact with LYS 614 (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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277C LYS* 6.0 2.2 - - - +
612D HIS* 3.2 17.7 + - - +
613D HIS* 1.3 70.0 - - - +
615D ALA* 1.3 56.9 + - - +
616D MET 3.1 0.5 + - - -
617D HIS* 3.1 16.7 + - + -
618D GLU* 2.8 65.9 + - + +
645D ASP* 3.8 15.0 - - + +
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Residues in contact with ALA 615 (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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613D HIS 3.2 1.6 + - - -
614D LYS* 1.3 77.6 - - - +
616D MET* 1.3 59.4 + - + +
617D HIS 3.5 0.5 + - - -
618D GLU 4.6 1.0 + - - -
619D LEU 5.2 0.7 + - - -
643D ARG* 2.9 55.5 + - + +
644D ARG 3.9 5.2 + - - +
645D ASP* 3.6 16.0 + - + +
649D ASN* 3.7 14.4 - - + +
651D ILE* 3.7 24.2 - - + -
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Residues in contact with MET 616 (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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558D TRP 4.1 4.2 - - - +
559D ALA* 3.6 38.8 - - + +
564D LYS* 5.0 0.3 - - - -
609D THR 4.5 0.7 - - - +
610D TYR* 3.1 42.8 - - + +
613D HIS* 3.4 28.0 - - + +
614D LYS 3.1 0.6 - - - -
615D ALA* 1.3 78.1 - - - +
617D HIS* 1.3 56.6 + - - +
620D ASP* 3.9 1.6 - - - +
643D ARG* 3.5 32.6 + - + +
651D ILE* 3.1 41.3 - - + -
653D VAL* 4.2 0.4 - - + -
678D ILE* 5.6 0.9 - - + -
722D TRP* 4.3 16.4 - - + -
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Residues in contact with HIS 617 (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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239D PHE 4.0 1.0 - - - +
240D ASP 3.4 21.7 + - - +
241D ALA 4.1 1.1 - - - +
242D PRO* 3.4 42.3 - - + +
563D LYS* 3.3 18.9 + - - +
610D TYR* 2.8 47.0 + - + +
612D HIS 4.2 9.3 + - - -
613D HIS 3.7 11.9 + - - -
614D LYS* 3.1 22.7 + - + +
615D ALA 3.3 0.6 + - - -
616D MET* 1.3 78.6 - - - +
618D GLU* 1.3 69.6 + - + +
619D LEU 3.5 2.7 - - - -
620D ASP* 3.6 13.5 + - - +
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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