Contacts of the helix formed by residues 424 - 433 (chain B) in PDB entry 3IW4
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 424 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B GLY* 1.3 76.5 - - - -
425B LEU* 1.3 65.9 + - - +
426B MET* 3.4 8.2 + - - +
427B TYR* 2.8 40.3 + - - +
428B HIS* 3.1 18.0 + - - -
466B LEU 4.0 6.3 - - - +
467B ASP* 4.2 17.9 - - - +
469B VAL 3.1 13.7 - - - +
470B MET* 3.7 13.1 - - + +
901B LW4 3.7 20.4 - - - -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ASP* 1.3 69.4 - - - +
426B MET* 1.3 70.5 + - - +
428B HIS* 3.1 3.0 + - + +
429B ILE* 3.0 24.9 + - - +
435B PHE* 4.4 10.5 - - + -
443B TYR* 4.2 22.0 - - + -
447B ILE* 5.0 5.2 - - + -
466B LEU* 3.7 26.0 + - + +
469B VAL* 2.6 39.8 + - + +
471B LEU* 4.0 31.2 - - + -
477B ILE* 4.3 4.7 - - + -
527B LEU* 5.2 1.8 - - + -
531B MET* 4.0 26.7 - - - -
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Residues in contact with MET 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LEU* 3.8 11.7 - - + +
644A VAL* 3.3 37.7 - - + +
647A ASN* 4.1 23.6 - - + +
424B ASP* 3.3 9.8 + - - +
425B LEU* 1.3 78.4 - - - +
427B TYR* 1.3 64.8 + - - +
429B ILE* 3.3 3.7 - - - +
430B GLN* 2.9 53.5 + - + +
466B LEU* 3.6 31.5 + - + +
467B ASP* 3.9 15.9 - - - +
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Residues in contact with TYR 427 (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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423B GLY* 4.8 6.5 - - - -
424B ASP* 2.8 31.3 + - - +
426B MET* 1.3 75.3 - - - +
428B HIS* 1.3 99.0 + + - +
430B GLN* 3.1 22.5 + - - +
431B GLN* 3.1 37.5 + - + +
617B LYS* 5.5 8.1 - - - +
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Residues in contact with HIS 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B GLY 2.3 33.2 + - - -
423B GLY* 3.8 1.8 + - - -
424B ASP 3.1 10.9 + - - +
425B LEU* 3.1 9.6 + - + +
427B TYR* 1.3 104.2 - + - +
429B ILE* 1.3 57.3 + - - +
431B GLN* 2.5 40.4 + - - +
432B VAL* 3.8 3.2 + - - +
435B PHE* 4.2 14.9 - - + -
471B LEU* 2.9 36.6 - - + +
614B PHE* 4.0 17.9 - + + -
616B PRO* 3.6 15.8 - - + +
617B LYS 5.5 1.6 - - - -
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Residues in contact with ILE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A LEU* 3.7 26.9 - - + -
425B LEU 3.0 11.0 + - - +
426B MET* 3.3 14.8 - - - +
428B HIS* 1.3 75.8 - - - +
430B GLN* 1.3 60.4 + - - +
431B GLN 2.8 3.1 + - - -
432B VAL* 3.0 2.8 + - - +
433B GLY* 2.8 32.4 + - - +
434B LYS* 4.5 8.3 - - - -
435B PHE* 3.3 39.9 - - + -
466B LEU* 4.6 15.7 - - + -
530B GLU* 3.8 8.5 - - + +
531B MET* 3.4 37.7 - - + +
534B GLY* 5.0 2.2 - - - -
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Residues in contact with GLN 430 (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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373A ASP* 5.4 1.8 + - - -
377A GLN* 5.8 1.2 + - - -
641A ASP* 4.9 7.2 - - - +
643A LEU* 4.9 7.4 - - + -
644A VAL* 3.2 19.4 - - - +
426B MET* 2.9 49.1 + - + +
427B TYR* 3.1 16.3 - - - +
428B HIS 2.7 4.4 + - - -
429B ILE* 1.3 80.8 - - + +
431B GLN* 1.3 67.7 + - - +
433B GLY* 4.3 4.7 - - - +
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Residues in contact with GLN 431 (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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427B TYR* 3.1 53.7 + - + +
428B HIS* 2.5 23.8 + - - +
430B GLN* 1.3 91.0 - - - +
432B VAL* 1.3 66.5 + - + +
433B GLY 3.5 0.2 - - - -
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Residues in contact with VAL 432 (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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428B HIS 4.7 4.3 - - - +
429B ILE 3.0 4.1 + - - +
431B GLN* 1.3 84.8 - - + +
433B GLY* 1.3 54.5 + - - +
434B LYS* 2.8 30.8 + - + +
435B PHE* 4.7 15.3 - - + -
436B LYS* 5.7 6.1 - - + +
439B GLN* 5.7 2.5 - - - +
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Residues in contact with GLY 433 (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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643A LEU* 4.9 4.9 - - - +
429B ILE* 2.8 15.0 + - - +
430B GLN* 4.3 3.7 - - - -
431B GLN 3.5 2.0 - - - -
432B VAL* 1.3 75.8 - - - +
434B LYS* 1.3 55.6 + - - -
534B GLY* 3.1 25.5 - - - +
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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