Contacts of the helix formed by residues 425 - 433 (chain A) 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 LEU 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A GLY 4.0 0.6 + - - -
424A ASP* 1.3 70.3 - - - +
426A MET* 1.3 66.6 + - - +
428A HIS* 2.7 16.4 + - + +
429A ILE* 2.7 20.1 + - + +
435A PHE* 4.3 8.1 - - + -
443A TYR* 4.2 22.2 - - + -
447A ILE* 4.5 10.5 - - + -
466A LEU* 3.5 29.6 - - + +
469A VAL* 2.9 41.3 + - + +
470A MET* 4.6 0.4 - - - +
471A LEU* 4.0 28.3 - - + -
477A ILE* 4.8 1.3 - - + -
527A LEU* 4.5 0.9 - - + -
531A MET* 4.1 22.4 - - + -
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Residues in contact with MET 426 (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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424A ASP* 3.8 12.7 - - + +
425A LEU* 1.3 79.0 - - - +
427A TYR* 1.3 62.8 + - - +
429A ILE* 3.4 3.8 + - - +
430A GLN* 3.1 48.8 + - + +
466A LEU* 4.1 43.5 + - + +
467A ASP* 4.6 13.7 - - - +
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Residues in contact with TYR 427 (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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422A GLY 5.1 1.1 - - - -
423A GLY* 5.2 3.4 - - - -
424A ASP* 2.9 27.9 + - - +
426A MET* 1.3 78.4 - - - +
428A HIS* 1.3 96.1 + + - +
430A GLN* 3.1 21.3 + - - +
431A GLN* 3.1 51.1 + - + +
617A LYS* 4.8 12.3 + - - +
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Residues in contact with HIS 428 (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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422A GLY 2.5 28.9 + - - -
423A GLY 4.1 1.1 - - - -
424A ASP 2.9 16.6 + - - +
425A LEU* 2.7 13.6 + - - +
427A TYR* 1.3 96.9 - + - +
429A ILE* 1.3 58.7 + - - +
431A GLN* 3.1 26.7 - - + +
432A VAL* 3.6 11.1 - - - +
435A PHE* 3.9 17.7 - - + -
471A LEU* 3.2 34.3 - - + +
614A PHE* 3.8 24.5 - + + -
616A PRO* 3.9 8.9 - - + +
617A LYS* 5.5 2.2 - - + -
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Residues in contact with ILE 429 (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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425A LEU* 2.7 17.8 + - + +
426A MET* 3.8 4.7 - - - +
428A HIS* 1.3 69.4 - - - +
430A GLN* 1.3 62.2 + - + +
431A GLN 3.1 0.2 - - - -
432A VAL* 3.2 2.4 + - - -
433A GLY* 2.8 47.8 + - - +
434A LYS* 4.2 6.3 - - - -
435A PHE* 3.3 36.3 - - + -
466A LEU* 3.8 34.3 - - + -
530A GLU* 4.4 9.2 - - + +
531A MET* 3.9 23.1 - - + -
534A GLY* 4.7 3.6 - - - +
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Residues in contact with GLN 430 (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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426A MET* 3.1 41.2 + - + +
427A TYR* 3.1 21.8 + - + +
429A ILE* 1.3 78.2 - - + +
431A GLN* 1.3 63.2 + - - +
432A VAL 3.4 0.5 + - - -
433A GLY* 3.8 6.8 + - - +
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Residues in contact with GLN 431 (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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427A TYR* 3.1 60.3 + - + +
428A HIS* 3.1 19.7 - - - +
429A ILE 3.1 0.4 - - - -
430A GLN* 1.3 79.7 - - - +
432A VAL* 1.3 65.0 + - + +
617A LYS* 5.1 10.3 - - - +
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Residues in contact with VAL 432 (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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428A HIS 3.6 14.8 - - - +
429A ILE 3.2 2.0 + - - +
431A GLN* 1.3 86.3 - - + +
433A GLY* 1.3 53.1 + - - +
434A LYS* 2.8 42.6 + - - +
435A PHE* 3.9 15.7 - - + -
439A GLN* 5.3 2.5 - - - +
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Residues in contact with GLY 433 (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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429A ILE* 2.8 19.9 + - - +
430A GLN* 3.8 5.8 + - - -
431A GLN 3.7 1.4 - - - -
432A VAL* 1.3 72.0 - - - +
434A LYS* 1.3 64.7 + - - +
534A GLY* 3.3 20.8 - - - +
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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