Contacts of the helix formed by residues 605 - 612 (chain A) in PDB entry 4IQJ
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 ASP 605 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A GLU* 5.1 12.4 - - - +
58A LYS* 4.9 3.6 + - - -
492A ILE* 3.8 4.7 - - - -
493A GLY 3.8 14.8 - - - +
494A THR* 5.5 0.7 - - - -
495A PHE* 5.1 23.2 - - + +
603A GLN 4.1 0.6 + - - -
604A TYR* 1.3 72.1 - - - +
606A MET* 1.3 66.9 + - - +
607A GLY* 3.5 13.5 + - - -
608A ALA* 3.1 24.3 + - - +
609A VAL* 3.0 25.5 + - - +
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Residues in contact with MET 606 (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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492A ILE* 3.7 16.2 - - + +
493A GLY 4.4 0.8 + - - -
575A HIS* 3.2 45.5 - - + +
578A GLY* 4.3 7.2 - - - -
605A ASP* 1.3 79.2 - - - +
607A GLY* 1.3 61.5 + - - +
609A VAL* 3.9 2.1 - - - +
610A GLU* 3.2 30.2 + - - +
616A LYS* 3.2 44.7 - - + +
618A ASP* 3.6 11.7 - - - +
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Residues in contact with GLY 607 (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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58A LYS* 4.8 8.0 - - - -
605A ASP* 3.4 10.2 + - - -
606A MET* 1.3 77.4 - - - +
608A ALA* 1.3 60.5 + - - +
610A GLU* 3.5 7.4 + - - +
611A ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 608 (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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51A PHE 6.1 0.2 - - - +
54A VAL* 3.4 36.9 - - + +
55A GLU* 5.1 2.2 - - + +
58A LYS* 4.5 6.1 - - - +
604A TYR* 3.7 17.9 - - + -
605A ASP* 3.1 20.4 + - - +
606A MET 3.4 0.2 - - - -
607A GLY* 1.3 76.6 - - - +
609A VAL* 1.3 63.2 + - - +
611A ALA* 3.2 15.2 + - - +
612A LEU* 3.4 16.4 + - - +
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Residues in contact with VAL 609 (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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492A ILE* 4.3 14.4 - - + -
580A VAL* 3.9 32.5 - - + -
590A VAL* 5.2 2.0 - - + -
602A THR* 3.7 30.3 - - + -
604A TYR* 3.8 10.5 - - + +
605A ASP 3.0 23.7 + - - +
606A MET 3.9 3.1 - - - +
608A ALA* 1.3 76.2 - - - +
610A GLU* 1.3 60.8 + - - +
612A LEU* 3.4 21.2 + - - +
614A LEU* 3.8 25.9 + - + +
616A LYS* 5.1 5.6 - - + -
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Residues in contact with GLU 610 (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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291A MET* 3.3 17.1 - - + +
293A TYR* 5.5 0.3 - - - -
461A MET* 5.0 11.0 - - + +
463A ASP* 5.1 9.2 - - - +
606A MET* 3.2 19.1 + - - +
607A GLY* 4.0 5.9 - - - +
609A VAL* 1.3 72.4 - - - +
611A ALA* 1.3 60.2 + - - +
612A LEU 3.1 2.2 - - - -
613A GLY* 3.0 19.0 + - - +
614A LEU 4.6 8.1 - - - +
616A LYS* 3.4 42.2 - - + +
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Residues in contact with ALA 611 (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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54A VAL* 4.7 1.8 - - + -
58A LYS* 5.3 6.3 - - + -
286A PRO 3.0 14.5 - - - +
287A ILE* 3.7 30.4 - - + -
291A MET* 3.3 24.3 - - - +
607A GLY 2.9 19.6 + - - +
608A ALA* 3.2 10.5 + - - +
610A GLU* 1.3 77.9 - - - +
612A LEU* 1.3 58.9 + - - +
613A GLY 3.2 0.4 - - - -
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Residues in contact with LEU 612 (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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54A VAL* 4.6 6.7 - - + -
106A TYR* 4.7 4.0 - - + +
285A LEU* 4.6 6.3 - - + -
286A PRO* 3.4 44.1 - - + +
287A ILE* 4.2 13.0 - - + -
291A MET* 4.6 2.4 - - - -
292A VAL 4.2 6.6 - - - +
294A ARG* 4.6 6.8 + - - +
589A LEU* 4.1 25.6 - - + +
590A VAL* 3.7 30.3 - - + -
604A TYR* 4.0 18.2 - - + -
608A ALA 3.4 16.1 + - - +
609A VAL* 3.7 7.9 - - - +
610A GLU 3.1 0.4 - - - -
611A ALA* 1.3 77.0 - - - +
613A GLY* 1.3 61.7 + - - +
614A LEU* 4.3 8.6 - - + +
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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