Contacts of the strand formed by residues 392 - 405 (chain A) in PDB entry 2W77
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 GLU 392 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A ASP* 2.6 31.7 - - - +
355A ASN 3.3 10.1 - - - +
356A ASP* 3.9 13.9 - - - +
357A PRO* 3.5 12.3 - - + -
390A SER* 3.3 8.7 + - - +
391A TRP* 1.3 76.6 - - - +
393A GLN* 1.3 59.9 + - - +
394A TYR* 3.5 25.6 - - - -
423A TYR* 3.3 6.1 - - - +
424A HIS* 3.0 63.9 + - + +
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Residues in contact with GLN 393 (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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203A ASP* 3.2 25.1 + - - +
204A ARG* 4.5 3.6 + - - -
233A ALA* 3.9 11.2 - - + -
234A GLY* 2.8 39.6 + - - +
236A THR* 3.8 14.2 - - - +
237A LEU* 3.9 8.4 - - - +
355A ASN* 2.8 47.6 + - + +
391A TRP* 3.2 53.7 + - + +
392A GLU* 1.3 72.2 - - - +
394A TYR* 1.3 60.7 + - - +
422A GLY 3.5 4.7 - - - +
423A TYR* 4.5 0.4 - - + -
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Residues in contact with TYR 394 (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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233A ALA 4.0 1.6 - - - +
352A TYR* 5.6 8.3 - + + +
353A GLN 3.3 7.9 - - - +
354A ASP* 3.4 20.0 - - + +
355A ASN* 5.1 0.2 - - - -
392A GLU* 3.5 14.1 - - - -
393A GLN* 1.3 74.7 - - - +
395A THR* 1.3 75.6 + - - +
396A ARG* 4.1 20.5 + - + -
420A ILE* 3.6 22.2 - - + -
421A ASN* 3.7 0.5 - - - -
422A GLY* 2.6 60.5 + - - +
423A TYR* 3.8 5.2 - - - -
424A HIS* 6.1 0.7 - - + -
450A GLY 4.7 2.0 + - - -
451A GLU* 3.1 33.6 + - - +
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Residues in contact with THR 395 (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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233A ALA 3.3 21.1 - - - +
234A GLY* 4.2 15.7 - - - +
235A ASN* 4.7 0.7 - - - +
351A ASP* 5.0 2.2 + - - -
352A TYR* 3.4 3.9 - - - -
353A GLN* 2.8 51.2 + - - +
355A ASN* 5.2 1.6 + - - +
394A TYR* 1.3 86.6 - - - +
396A ARG* 1.3 65.6 + - - +
419A LYS* 4.4 15.5 - - - +
420A ILE 3.1 8.7 - - - -
421A ASN* 3.8 11.7 - - - +
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Residues in contact with ARG 396 (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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351A ASP* 3.2 17.3 - - - +
352A TYR* 4.1 24.2 - - + -
394A TYR* 4.1 21.4 - - + -
395A THR* 1.3 76.2 - - - +
397A THR* 1.3 65.4 + - - +
398A VAL* 6.1 5.2 - - + +
418A HIS 3.9 0.3 - - - +
419A LYS* 3.5 4.2 - - - +
420A ILE* 2.8 60.1 + - + +
451A GLU* 4.8 4.2 + - - -
1821A PO4 3.3 28.3 + - - -
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Residues in contact with THR 397 (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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270A ARG* 4.1 8.8 + - - +
350A ALA* 3.1 6.9 - - - +
351A ASP* 2.8 54.7 + - - +
396A ARG* 1.3 75.8 + - - +
398A VAL* 1.3 74.2 + - - +
399A PHE* 4.1 13.9 - - + -
417A ASP* 3.8 22.7 - - - +
418A HIS 3.3 12.1 - - - +
419A LYS* 3.9 20.8 - - + -
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Residues in contact with VAL 398 (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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349A GLY 3.5 8.7 - - - +
350A ALA* 4.3 8.7 - - + -
396A ARG* 5.8 5.8 - - + +
397A THR* 1.3 82.1 - - - +
399A PHE* 1.3 70.1 + - - +
416A LEU 4.0 0.2 - - - +
417A ASP* 3.7 0.3 - - - -
418A HIS* 2.8 51.5 + - + +
1816A N8E 4.0 29.6 - - + -
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Residues in contact with PHE 399 (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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220A ASP* 4.8 5.2 - - - -
270A ARG* 3.6 39.5 - - - -
333A TYR* 4.4 4.9 - + - -
335A ILE* 4.1 24.5 - - + -
347A THR* 4.7 2.2 - - + -
348A VAL* 3.3 5.7 - - - +
349A GLY* 2.8 67.4 + - - +
350A ALA* 4.0 4.7 - - - -
351A ASP* 4.9 0.4 - - - -
397A THR* 4.1 14.6 - - + -
398A VAL* 1.3 81.1 - - - +
400A ALA* 1.3 61.8 + - - +
401A ASN* 3.8 25.8 - - - +
416A LEU 3.2 12.8 - - - +
417A ASP* 3.8 16.4 - - - +
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Residues in contact with ALA 400 (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 LEU* 5.1 6.3 - - + -
347A THR 3.2 11.0 - - - +
348A VAL* 4.4 12.3 - - + -
399A PHE* 1.3 75.6 - - - +
401A ASN* 1.3 66.0 + - - +
414A VAL 4.0 0.3 - - - +
416A LEU* 2.8 47.1 + - + +
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Residues in contact with ASN 401 (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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345A MET 4.0 0.6 - - - +
346A LEU* 3.6 8.4 - - - +
347A THR* 2.9 52.1 + - - +
399A PHE* 3.8 24.0 - - - +
400A ALA* 1.3 90.1 + - - +
402A LEU* 1.3 61.0 + - - +
403A GLU* 6.0 0.9 - - + -
413A LYS* 4.5 13.6 - - - -
414A VAL 3.1 13.0 - - - +
415A GLN* 3.3 33.2 + - + +
416A LEU 4.4 1.0 - - - +
417A ASP* 4.9 1.8 + - - -
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Residues in contact with LEU 402 (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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340A LEU* 4.1 22.7 - - + -
344A THR* 4.3 15.0 - - + -
345A MET 3.4 22.0 - - - +
346A LEU* 4.2 14.4 - - + -
401A ASN* 1.3 73.9 - - - +
403A GLU* 1.3 63.1 + - - +
404A HIS* 6.0 2.0 - - + -
412A GLY 4.0 0.2 - - - +
413A LYS* 3.4 4.1 - - - +
414A VAL* 2.9 47.3 + - + +
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Residues in contact with GLU 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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64A ARG* 4.4 17.6 + - - +
134A SER 4.8 7.8 - - - +
136A GLN* 3.7 19.9 + - - +
343A ASP 4.0 0.5 - - - +
344A THR* 3.3 5.0 - - - +
345A MET* 2.8 57.4 + - + +
347A THR* 6.2 0.2 - - - +
401A ASN* 5.7 1.1 - - + -
402A LEU* 1.3 78.1 - - - +
404A HIS* 1.3 62.4 + - - +
405A ASN* 4.9 3.1 - - - +
411A VAL* 4.2 12.3 - - + +
412A GLY 3.3 11.9 - - - +
413A LYS* 4.0 29.0 + - + -
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Residues in contact with HIS 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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343A ASP* 3.4 12.5 + - - -
344A THR* 3.0 36.7 + - + +
402A LEU* 6.0 2.2 - - + -
403A GLU* 1.3 74.6 - - - +
405A ASN* 1.3 84.8 + - - +
406A PHE* 3.8 38.6 + + + -
407A ALA 5.4 0.2 + - - -
411A VAL* 3.2 5.1 - - - +
412A GLY 2.7 39.5 + - - +
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Residues in contact with ASN 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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57A SER* 6.0 1.0 - - - +
60A GLN* 3.3 41.2 + - + +
61A GLU* 6.1 0.2 - - - +
64A ARG* 4.2 16.6 + - - +
342A PRO 4.6 2.6 + - - -
343A ASP* 2.9 42.4 + - + +
403A GLU* 4.9 3.6 - - - +
404A HIS* 1.3 90.7 + - - +
406A PHE* 1.3 66.7 + - - +
407A ALA 3.6 1.6 + - - -
410A TRP 3.8 6.1 - - - +
411A VAL* 4.3 11.6 - - + +
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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