Contacts of the strand formed by residues 402 - 411 (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 GLN 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A GLU 3.3 21.0 - - - +
359A GLN* 2.7 30.5 + - - +
362A LEU* 3.7 27.2 - - + +
363A HIS* 3.8 6.5 + - - -
380A ILE* 4.3 5.1 - - + +
381A LEU 3.4 18.2 - - - +
382A GLU* 3.5 25.9 + - - -
383A SER* 3.6 25.8 - - - +
401A PHE* 1.3 73.0 - - - +
403A LYS* 1.3 60.9 + - - +
436A VAL* 3.6 1.9 - - - +
437A MET* 3.0 37.6 + - + +
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Residues in contact with LYS 403 (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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362A LEU* 3.9 5.6 - - - -
380A ILE* 3.5 2.6 - - - +
381A LEU* 2.7 57.4 + - + +
399A ASP* 2.7 50.4 + - - -
401A PHE 2.8 18.7 + - - +
402A GLN* 1.3 73.7 - - - +
404A CYS* 1.3 60.1 + - - +
405A PHE* 3.6 29.8 - - + -
434A ASP* 6.6 0.4 - - + -
435A LEU 3.2 13.5 - - - +
436A VAL* 4.3 7.9 - - + -
450A TRP* 3.7 21.5 - - + -
602A APC 4.9 4.7 - - + +
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Residues in contact with CYS 404 (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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362A LEU* 4.1 13.9 - - + -
366A THR* 4.5 5.8 - - - -
379A ASP 3.1 12.3 - - - +
380A ILE* 3.8 17.3 - - + -
403A LYS* 1.3 76.9 - - - +
405A PHE* 1.3 64.2 + - - +
406A LEU* 3.8 22.0 - - + -
433A VAL 3.9 0.5 - - - +
434A ASP* 3.3 8.7 - - - +
435A LEU* 2.9 64.6 + - - +
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Residues in contact with PHE 405 (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* 4.9 7.2 - - + -
288A MET* 6.3 0.9 - - + -
377A TYR* 3.7 10.6 - - + -
379A ASP* 2.9 51.4 + - + +
381A LEU* 3.5 28.7 - - + -
403A LYS* 3.6 28.9 - - + -
404A CYS* 1.3 72.2 - - - +
406A LEU* 1.3 60.5 + - - +
432A ARG* 3.9 4.3 - - - +
434A ASP* 3.2 22.7 - - + +
450A TRP* 5.3 0.9 - + - -
602A APC 2.9 30.5 - + - -
4C A 3.2 47.3 - + + +
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Residues in contact with LEU 406 (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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366A THR* 3.8 7.0 - - + -
369A TRP* 3.7 31.9 - - + -
375A LEU* 4.2 2.0 - - + -
377A TYR* 3.4 7.4 - - - +
378A CYS* 3.4 36.6 - - + -
404A CYS* 3.8 18.2 - - + -
405A PHE* 1.3 79.1 - - - +
407A ILE* 1.3 64.1 + - - +
408A LEU* 4.3 12.1 - - + -
432A ARG* 2.9 23.5 + - - +
433A VAL* 2.8 36.9 + - + +
435A LEU* 3.8 22.7 - - + -
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Residues in contact with ILE 407 (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* 3.7 31.4 - - + -
291A ALA* 4.0 12.1 - - + +
295A TYR* 4.2 9.0 - - + -
299A LEU* 3.8 17.0 - - + -
376A LEU* 2.9 38.8 + - + -
377A TYR* 3.0 29.3 + - + +
406A LEU* 1.3 77.2 - - - +
408A LEU* 1.3 65.9 + - - +
430A ALA* 3.8 28.9 - - + -
431A ILE 3.3 8.5 - - - +
432A ARG* 3.8 14.6 - - + -
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Residues in contact with LEU 408 (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* 4.9 9.4 - - + -
314A LEU* 5.1 13.9 - - + -
315A VAL* 5.3 0.9 - - + -
369A TRP* 3.7 53.6 - - + -
374A LEU* 3.3 13.0 - - + +
375A LEU* 4.2 15.0 - - + -
376A LEU* 4.0 3.6 - - - -
406A LEU* 4.3 5.8 - - + -
407A ILE* 1.3 80.5 - - - +
409A LYS* 1.3 66.0 + - - +
410A LEU* 3.5 2.5 + - + -
430A ALA* 3.5 4.5 - - - -
431A ILE* 2.9 37.3 + - + +
433A VAL* 4.1 28.5 - - + -
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Residues in contact with LYS 409 (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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314A LEU* 4.7 5.7 - - - +
373A GLY 3.8 17.3 + - - +
374A LEU* 2.8 49.2 + - + +
376A LEU* 3.9 23.0 - - + +
408A LEU* 1.3 72.1 - - - +
410A LEU* 1.3 60.5 + - - +
411A ASP* 3.7 16.9 + - - +
428A TRP* 3.6 51.2 - - + +
429A LYS 4.1 2.2 - - - -
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Residues in contact with LEU 410 (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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307A GLU* 3.9 30.3 - - + +
310A ALA* 3.8 23.6 - - + -
311A VAL* 4.1 5.6 - - + -
314A LEU* 4.0 23.8 - - + -
408A LEU* 3.5 2.2 + - + +
409A LYS* 1.3 70.1 - - - +
411A ASP* 1.3 72.3 + - - +
412A HIS* 3.6 2.4 + - - -
414A ARG* 4.3 5.6 - - + -
415A VAL* 3.7 23.8 - - + -
428A TRP* 3.2 2.1 - - - -
429A LYS* 2.9 46.2 + - + +
431A ILE* 3.7 24.5 - - + -
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Residues in contact with ASP 411 (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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374A LEU* 4.7 13.6 - - - +
409A LYS* 3.7 18.5 + - - +
410A LEU* 1.3 74.8 - - - +
412A HIS* 1.4 65.1 + - - +
413A GLY* 3.2 4.5 - - - +
414A ARG* 3.1 38.5 + - + +
415A VAL* 3.9 6.2 - - - +
427A GLY 3.8 7.3 - - - +
428A TRP* 3.7 14.8 - - - +
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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