Contacts of the strand formed by residues 365 - 369 (chain A) in PDB entry 1IAX
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 PHE 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 4.1 6.1 - - + -
208A SER 3.9 10.1 - - - -
209A ASN* 3.7 21.5 - - + -
210A PRO* 3.3 29.6 - - + -
212A GLY* 3.6 20.0 - - - -
240A TYR* 3.7 26.7 - + - -
360A ASN* 3.6 12.5 + - - -
362A ALA 4.0 3.3 - - - +
363A GLY* 4.1 10.5 - - - -
364A LEU* 1.3 91.0 - - - +
366A CYS* 1.3 60.3 + - - +
412A ARG* 3.9 22.0 - - + -
413A VAL 3.3 18.2 - - - +
414A CYS* 3.8 17.7 - - - -
415A PHE* 3.2 22.0 - - - -
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Residues in contact with CYS 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PRO 4.5 4.0 - - - -
211A LEU 5.7 0.4 - - - -
343A HIS* 4.7 4.7 - - + +
346A PHE* 3.8 22.0 - - - -
347A THR* 5.0 2.0 - - - +
350A LEU* 4.5 0.9 - - - -
357A CYS* 3.5 31.6 - - + -
360A ASN* 3.9 17.7 - - - +
365A PHE* 1.3 78.9 - - - +
367A TRP* 1.3 59.3 + - - +
368A MET* 3.2 7.8 + - - -
411A PHE 3.3 1.4 - - - +
412A ARG* 3.5 2.9 - - - -
413A VAL* 3.2 29.4 + - - -
415A PHE* 3.6 18.8 - - + -
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Residues in contact with TRP 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PRO* 3.7 23.6 - - + -
178A PHE* 3.1 33.8 - + - -
210A PRO* 3.2 46.9 + - + +
211A LEU* 3.7 20.3 + - + +
357A CYS* 4.0 3.6 - - - +
358A LEU* 3.0 33.5 + - + +
360A ASN* 4.8 2.6 + - - -
366A CYS* 1.3 69.6 - - - +
368A MET* 1.3 59.0 + - - +
400A GLY* 3.9 22.0 - - - -
403A PHE* 4.4 7.2 - + + -
405A CYS* 3.9 9.6 - - - -
410A TRP* 3.0 53.2 - + + -
411A PHE 3.7 11.7 - - - -
412A ARG* 3.9 17.7 - - + -
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Residues in contact with MET 368 (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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350A LEU* 4.0 25.8 - - - -
355A ILE* 4.0 16.2 - - + -
357A CYS* 4.0 14.1 - - - -
366A CYS* 3.2 3.2 + - - +
367A TRP* 1.3 71.8 - - - +
369A ASP* 1.3 61.3 + - - +
370A LEU* 3.2 48.0 + - + -
389A ILE* 5.3 4.7 - - + -
397A VAL* 5.6 3.1 - - + -
410A TRP* 3.3 6.9 - - - -
411A PHE* 2.8 49.1 + - + +
413A VAL* 3.8 27.1 - - + -
430A ILE* 5.2 11.4 - - + -
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Residues in contact with ASP 369 (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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355A ILE* 4.7 4.9 - - - +
356A LYS* 3.1 27.3 + - + +
367A TRP 3.6 1.6 + - - -
368A MET* 1.3 70.2 - - - +
370A LEU* 1.3 65.6 + - - +
371A ARG* 2.5 64.8 + - - +
372A PRO* 4.0 14.2 - - - +
409A GLY 4.0 0.8 - - - +
410A TRP* 3.2 25.0 - - + -
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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