Contacts of the helix formed by residues 610 - 623 (chain B) in PDB entry 5IWM
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 610 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR* 4.8 1.6 + - - -
608B LEU* 4.3 3.1 - - - -
609B GLU* 1.3 79.5 - - + +
611B ALA* 1.3 60.7 + - - +
612B ILE* 3.4 18.3 + - - +
613B GLU* 3.4 37.2 + - - +
614B ALA* 3.0 29.1 + - - +
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Residues in contact with ALA 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B TYR* 3.3 8.2 + - - +
529B ARG* 3.4 31.2 - - - +
608B LEU* 4.2 10.6 - - + +
609B GLU 4.0 2.4 + - - -
610B ASP* 1.3 74.0 + - - +
612B ILE* 1.3 60.6 + - + +
614B ALA 3.3 0.5 + - - -
615B ASP* 2.9 39.9 + - - +
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Residues in contact with ILE 612 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B ASP* 3.3 14.7 + - - +
611B ALA* 1.3 79.2 - - + +
613B GLU* 1.3 62.0 + - - +
615B ASP* 3.4 14.2 + - - +
616B GLN* 3.2 49.6 + - - +
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Residues in contact with GLU 613 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASN* 5.2 5.0 + - - -
15A THR* 4.1 21.7 + - + +
19A ARG* 4.5 11.9 + - - +
609B GLU* 5.6 1.2 - - - +
610B ASP* 3.4 31.6 + - - +
611B ALA 3.3 0.4 - - - -
612B ILE* 1.3 75.6 - - - +
614B ALA* 1.3 56.6 - - - +
616B GLN* 3.4 12.2 + - - +
617B THR* 2.7 44.1 + - - +
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Residues in contact with ALA 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 4.6 4.7 - - + -
15A THR* 3.7 17.0 + - - +
525B TYR* 3.3 26.2 - - + +
608B LEU* 3.8 14.6 - - + -
610B ASP 3.0 17.3 + - - +
611B ALA 3.5 0.2 - - - +
613B GLU* 1.3 74.9 - - - +
615B ASP* 1.3 63.6 + - - +
617B THR* 3.3 2.9 + - - -
618B PHE* 3.0 36.2 + - + -
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Residues in contact with ASP 615 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B TYR* 2.8 31.6 + - - -
526B ARG* 3.4 25.7 + - - +
529B ARG* 4.5 9.8 + - - -
611B ALA* 2.9 29.9 + - - +
612B ILE* 3.6 15.0 - - - +
614B ALA* 1.3 75.0 - - - +
616B GLN* 1.3 64.3 + - + +
619B GLU* 3.3 22.3 + - - +
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Residues in contact with GLN 616 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B ILE* 3.2 37.9 + - + +
613B GLU* 3.7 9.9 - - + +
614B ALA 3.2 0.6 - - - -
615B ASP* 1.3 77.8 - - + +
617B THR* 1.3 58.9 + - - +
619B GLU* 3.2 6.4 + - - +
620B MET* 2.9 32.8 + - - +
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Residues in contact with THR 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR* 3.4 28.2 - - + +
18A MET* 4.3 9.2 - - + -
19A ARG* 3.4 32.3 + - + +
613B GLU 2.7 21.5 + - - -
614B ALA* 3.8 5.6 - - - -
616B GLN* 1.3 76.7 - - - +
618B PHE* 1.3 62.1 + - + +
620B MET* 4.4 7.9 - - + -
621B LEU* 3.2 46.1 + - + +
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Residues in contact with PHE 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.7 29.4 - - + -
15A THR* 6.0 1.3 - - - -
18A MET* 3.6 35.9 - - + -
465B GLU* 3.6 7.5 - - - +
521B LEU 4.1 1.8 - - - -
522B THR* 3.5 42.2 - - + -
525B TYR* 3.6 40.4 - + + -
526B ARG* 3.5 22.9 - - - +
614B ALA* 3.0 33.0 + - + +
617B THR* 1.3 77.3 - - - +
619B GLU* 1.3 57.2 + - - +
622B MET* 3.2 32.0 + - + +
623B GLY 3.6 1.9 + - - -
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Residues in contact with GLU 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B GLU* 3.2 20.4 - - - +
526B ARG* 4.3 5.6 + - - +
615B ASP 3.3 19.8 + - - +
616B GLN* 3.2 7.9 + - - +
618B PHE* 1.3 74.9 - - - +
620B MET* 1.3 61.4 + - - +
623B GLY* 2.9 33.8 + - - -
624B ASP* 5.3 4.5 - - - +
625B VAL* 5.5 5.2 + - - +
628B ASN* 5.8 1.1 + - - -
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Residues in contact with MET 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG* 4.2 22.7 - - - +
616B GLN 2.9 14.7 + - - +
617B THR* 4.0 9.0 - - + +
619B GLU* 1.3 78.9 - - - +
621B LEU* 1.3 76.9 + - + +
625B VAL 4.5 2.9 - - - +
628B ASN* 3.9 32.5 - - + +
629B ARG* 3.5 24.4 + - - +
632B PHE* 3.8 37.9 - - + -
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Residues in contact with LEU 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 3.7 34.3 - - + +
19A ARG* 4.1 5.4 - - + +
22A PHE* 3.5 27.6 - - + -
466B LYS* 5.6 0.2 - - - -
617B THR* 3.2 33.2 + - + +
620B MET* 1.3 93.2 - - + +
622B MET* 1.3 72.3 + - + +
629B ARG* 2.9 29.5 + - + +
632B PHE* 3.7 36.1 - - + -
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Residues in contact with MET 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 3.8 19.7 - - + -
22A PHE* 3.6 34.8 - - + -
463B ASN* 3.0 43.6 + - - +
465B GLU* 3.5 18.5 - - + +
466B LYS* 3.3 12.2 - - - +
515B HIS* 4.9 2.0 - - - +
518B THR* 3.9 13.5 - - - +
519B LEU* 3.8 22.0 - - + -
522B THR* 3.3 24.2 - - + +
618B PHE* 3.2 17.8 + - + +
621B LEU* 1.3 79.7 - - + +
623B GLY* 1.3 65.6 + - - +
629B ARG* 4.0 0.7 - - - -
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Residues in contact with GLY 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B GLU* 4.3 15.5 - - - -
466B LYS* 3.6 4.1 - - - -
618B PHE 3.6 2.4 + - - -
619B GLU* 2.9 29.2 + - - -
621B LEU 3.6 0.4 - - - -
622B MET* 1.3 79.3 - - - +
624B ASP* 1.3 60.8 + - - -
625B VAL 3.4 3.5 + - - -
629B ARG* 2.7 33.6 + - - -
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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