Contacts of the strand formed by residues 430 - 434 (chain A) in PDB entry 2IUK
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 430 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A ARG* 3.3 13.2 - - - +
386A LEU* 3.3 40.0 + - + +
389A PHE* 4.6 0.9 - - + -
412A LEU* 4.0 9.9 - - + -
416A MET* 4.2 6.3 - - + -
421A VAL* 3.7 34.8 - - + +
424A ALA* 3.5 10.7 + - + +
425A LEU* 3.7 23.6 - - + +
428A GLN* 4.5 0.2 - - - +
429A ARG* 1.3 76.9 - - - +
431A PHE* 1.4 58.9 - - - +
460A ILE* 3.7 22.0 - - + -
461A LEU 3.8 3.6 - - - +
462A PHE* 4.1 12.3 - - + -
472A LEU* 3.8 18.2 - - + -
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Residues in contact with PHE 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ILE* 3.8 15.7 - - + -
384A ARG 3.5 14.1 - - - +
385A ARG* 3.4 25.1 - - + -
386A LEU* 4.1 7.4 - - - +
428A GLN 3.0 28.3 - - - -
429A ARG 3.3 18.2 - - - -
430A LEU* 1.4 70.1 - - - +
432A ILE* 1.4 63.9 + - - +
460A ILE* 3.6 9.0 - - - +
461A LEU* 3.0 36.2 + - + +
463A LEU* 3.7 14.8 - - + -
469A LEU* 4.1 11.9 - - + -
616A LEU* 3.7 12.3 - - + -
630A VAL* 3.6 14.8 - - + -
631A ILE* 3.3 31.9 - - + -
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Residues in contact with ILE 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ILE* 3.3 9.9 - - - +
384A ARG* 3.1 68.8 + - + +
386A LEU* 4.2 11.2 - - + +
391A PRO* 3.8 30.1 - - + -
431A PHE* 1.4 80.4 - - - +
433A LEU* 1.3 65.8 + - - +
434A ASP* 3.4 27.9 + - + +
458A ARG* 4.4 8.7 - - + -
459A THR 3.4 14.1 - - - +
460A ILE* 4.1 7.9 - - + -
461A LEU* 4.6 2.7 - - - +
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Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 5.6 1.1 - - + -
374A VAL* 4.0 25.1 - - + -
379A ASN 5.6 0.7 - - - +
382A VAL* 3.4 42.2 - - + +
383A ILE* 4.8 1.1 - - - +
432A ILE* 1.3 71.8 - - - +
434A ASP* 1.4 57.7 + - - +
435A TYR* 3.9 14.4 - - + -
457A THR* 3.8 3.3 + - - +
458A ARG* 3.5 4.2 - - - -
459A THR* 3.0 41.1 + - + +
461A LEU* 4.7 7.6 - - + -
512A VAL* 4.0 26.6 - - + +
513A ILE* 5.5 2.7 - - + -
516A ASP* 3.6 26.2 - - - +
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Residues in contact with ASP 434 (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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382A VAL* 5.5 5.5 - - - +
384A ARG* 4.3 24.5 + - - +
391A PRO* 4.5 0.9 - - - +
392A LYS 4.1 8.5 - - - +
432A ILE* 3.4 20.8 + - + +
433A LEU* 1.4 70.9 - - - +
435A TYR* 1.3 67.1 - - - +
436A GLN* 3.4 18.2 + - - +
437A ASP* 4.2 13.0 + - - +
438A ALA* 5.5 2.1 + - - +
457A THR 4.1 1.3 - - - -
458A ARG* 3.1 32.9 + - - -
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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