Contacts of the strand formed by residues 428 - 437 (chain A) in PDB entry 4I2C
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 TRP 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A TYR* 3.9 22.7 - + - -
298A ASP* 4.1 6.1 - - - -
376A LEU* 3.8 25.1 - - + -
409A LYS* 3.6 39.6 - - + +
410A LEU 3.2 16.2 - - - +
411A ASP* 3.7 14.1 - - - +
412A HIS* 3.5 13.4 + - - -
426A LYS* 2.7 74.1 + - + +
427A GLY* 1.4 77.9 - - - +
429A LYS* 1.3 62.8 + - - +
430A ALA* 3.9 11.7 - - + -
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Residues in contact with LYS 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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298A ASP* 3.4 25.8 - - - +
301A SER* 3.2 25.5 + - - +
302A CYS 3.0 28.4 + - - -
303A VAL* 4.9 2.2 - - - +
307A GLU* 3.0 32.8 + - - +
408A LEU 3.6 0.2 - - - +
410A LEU* 2.9 40.0 + - + +
412A HIS* 4.0 11.9 + - + +
426A LYS* 4.9 0.2 - - - +
428A TRP* 1.3 79.5 - - - +
430A ALA* 1.3 68.1 + - - +
431A ILE* 3.6 18.3 - - + +
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Residues in contact with ALA 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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295A TYR* 3.7 37.2 - - + -
298A ASP* 2.8 30.7 + - + +
299A LEU* 3.7 10.0 - - + +
376A LEU* 4.0 4.7 - - + -
407A ILE* 3.8 13.5 - - + -
408A LEU 3.5 6.1 - - - -
428A TRP* 3.9 5.2 - - + -
429A LYS* 1.3 77.6 - - - +
431A ILE* 1.4 64.1 + - - +
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Residues in contact with ILE 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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299A LEU* 4.3 2.7 - - - -
303A VAL* 4.0 20.9 - - + -
307A GLU* 4.4 5.2 - - - +
311A VAL* 3.9 22.4 - - + -
344A VAL* 4.0 13.7 - - + -
407A ILE* 3.3 4.2 - - - +
408A LEU* 2.9 37.4 + - + +
410A LEU* 3.7 32.1 - - + -
429A LYS* 3.6 39.7 - - + +
430A ALA* 1.4 81.7 - - - +
432A ARG* 1.3 75.2 + - - +
433A VAL* 3.5 7.2 + - + +
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Residues in contact with ARG 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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256A PHE* 3.2 37.7 - - + -
299A LEU* 3.8 28.3 - - + +
303A VAL* 5.1 1.0 - - - +
342A HIS* 3.9 25.3 + - + +
343A ASP* 3.3 22.1 + - + -
344A VAL 3.0 22.3 + - - -
405A PHE* 3.9 1.6 - - - -
406A LEU 2.9 31.5 + - - +
407A ILE* 3.8 10.3 - - + +
431A ILE* 1.3 76.1 - - - +
433A VAL* 1.3 71.5 + - - +
434A ASP* 2.8 39.7 + - - -
602A APC 4.4 0.8 + - - -
4C A 3.4 21.6 + - - -
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Residues in contact with VAL 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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311A VAL* 3.6 25.6 - - + -
315A VAL* 4.5 3.1 - - + -
344A VAL* 3.2 11.9 - - + +
346A PHE* 4.1 10.1 - - + -
406A LEU* 2.8 53.8 + - + +
408A LEU* 4.1 17.0 - - + -
431A ILE* 3.8 17.9 - - + +
432A ARG* 1.3 77.8 - - - +
434A ASP* 1.3 65.6 + - - +
435A LEU* 3.8 27.8 - - + -
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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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343A ASP* 2.9 3.1 - - - +
344A VAL 3.0 7.8 + - - +
345A ASP* 3.3 11.7 - - - +
346A PHE 2.9 26.7 + - - +
404A CYS 3.3 6.1 - - - +
405A PHE* 3.2 14.5 - - + -
432A ARG* 2.8 32.2 + - - -
433A VAL* 1.3 73.5 - - - +
435A LEU* 1.3 65.4 + - - +
436A VAL* 5.2 0.4 - - - -
450A TRP* 4.4 12.6 - - + -
602A APC 3.1 16.6 + - - -
603A MN 2.1 34.2 + - - +
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Residues in contact with LEU 435 (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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315A VAL* 3.9 15.7 - - + -
346A PHE* 3.6 24.0 - - + -
348A ILE* 4.0 10.5 - - + -
362A LEU* 3.8 20.6 - - + +
365A VAL* 4.5 7.2 - - + -
366A THR* 5.3 1.1 - - + -
369A TRP* 4.0 17.5 - - + -
403A LYS* 3.2 6.6 - - - +
404A CYS* 2.9 56.1 + - - +
406A LEU* 3.8 18.8 - - + -
433A VAL* 3.8 16.6 - - + -
434A ASP* 1.3 79.7 - - - +
436A VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 436 (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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346A PHE 3.0 12.6 + - - +
347A LEU* 3.5 15.1 - - + +
348A ILE* 2.7 36.2 + - - +
362A LEU* 5.0 0.9 - - - -
399A ASP* 4.4 2.2 - - - +
401A PHE* 3.9 23.8 - - + -
402A GLN 3.6 11.4 - - - +
403A LYS* 4.3 4.9 - - + -
434A ASP* 5.2 0.4 - - + -
435A LEU* 1.3 79.2 - - - +
437A MET* 1.3 58.2 + - - +
438A CYS 4.2 0.2 - - - -
450A TRP* 3.2 61.7 - - + +
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Residues in contact with MET 437 (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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323A LEU* 4.2 18.8 - - + -
348A ILE* 3.4 18.4 - - + +
349A THR* 4.2 4.9 - - - -
350A SER* 4.2 19.5 - - - +
358A GLU* 3.4 52.0 - - + +
361A LEU* 3.7 23.8 - - + -
362A LEU* 4.3 10.9 - - + +
401A PHE* 3.5 18.7 - - - +
402A GLN* 3.0 31.2 + - + +
436A VAL* 1.3 72.3 - - - +
438A CYS* 1.3 64.0 + - - +
439A PRO* 4.8 0.2 - - - +
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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