Contacts of the strand formed by residues 400 - 414 (chain A) in PDB entry 5C58
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 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A TYR* 3.9 25.8 - + - -
389A SER* 3.6 3.8 + - - -
390A LEU* 2.7 43.5 + - + +
391A ALA* 4.6 0.2 - - - +
398A LEU* 4.2 8.7 - - + -
399A ASP* 1.3 77.4 - - - +
401A GLN* 1.3 76.0 + - - +
402A ALA* 3.6 33.0 - - + -
439A ALA* 4.3 11.4 - - + -
440A GLN 3.3 33.4 - - - -
441A ASN* 3.6 17.7 - - + +
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Residues in contact with GLN 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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388A TYR 3.2 11.2 - - - +
389A SER* 4.5 9.3 + - - +
399A ASP* 5.3 4.0 - - - +
400A PHE* 1.3 84.1 - - - +
402A ALA* 1.3 61.8 + - - +
438A GLN 4.8 0.3 - - - -
439A ALA* 3.7 1.0 - - - -
440A GLN* 2.9 61.0 + - + +
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Residues in contact with ALA 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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386A PHE* 6.4 0.2 - - - -
387A ASP* 3.5 5.4 - - - +
388A TYR* 2.8 37.5 + - + +
400A PHE* 3.6 23.8 - - + -
401A GLN* 1.3 75.0 - - - +
403A LYS* 1.3 65.5 + - - +
404A LEU* 5.5 6.1 - - + -
438A GLN 3.3 14.8 - - - +
439A ALA* 4.5 2.0 - - + -
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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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178A ASP 2.2 36.0 + - - +
179A GLY* 3.3 11.1 - - - -
180A MET* 4.4 9.0 - - + -
385A ALA* 4.7 3.6 - - + -
386A PHE* 3.3 9.2 - - - +
387A ASP* 3.2 25.6 - - - +
402A ALA* 1.3 77.6 - - - +
404A LEU* 1.3 78.6 + - - +
405A TYR* 3.8 22.2 - - + -
436A GLY 4.6 0.2 - - - -
437A ALA* 3.4 4.3 - - - +
438A GLN* 2.8 58.0 + - + +
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Residues in contact with LEU 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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385A ALA* 3.3 1.7 - - - +
386A PHE* 2.8 59.7 + - + +
402A ALA* 5.5 5.4 - - + -
403A LYS* 1.3 83.7 - - - +
405A TYR* 1.3 61.8 + - - +
436A GLY 3.5 7.2 - - - +
437A ALA* 5.0 7.6 - - + -
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Residues in contact with TYR 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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180A MET* 3.6 26.5 - - + -
181A ARG* 3.5 48.7 - - - +
384A ALA 3.2 13.0 - - - +
385A ALA* 3.7 8.3 - - + -
403A LYS* 3.8 18.8 - - + -
404A LEU* 1.3 75.2 - - - +
406A TYR* 1.3 66.7 + - - +
407A VAL* 3.8 11.9 - - + -
434A THR* 4.2 8.2 - - + +
435A TYR* 3.9 3.3 - - - -
436A GLY* 2.9 58.3 + - - +
437A ALA 4.2 1.1 - - - -
438A GLN* 3.8 23.6 + - + -
460A GLU* 4.4 1.8 + - + +
461A PHE 5.2 0.2 + - - -
462A TYR* 3.9 10.7 - - - +
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Residues in contact with TYR 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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180A MET* 3.7 0.4 - - - +
382A ARG* 3.7 6.6 - - + +
383A ASN* 3.6 2.8 - - - -
384A ALA* 2.7 50.3 + - + +
405A TYR* 1.3 77.2 - - - +
407A VAL* 1.3 67.2 + - - +
408A ASP* 2.7 42.1 + - + -
431A ARG* 3.8 3.1 + - - -
433A ARG* 3.4 15.1 - - + -
434A THR 3.2 9.4 - - - -
435A TYR* 3.4 43.2 + + + -
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Residues in contact with VAL 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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180A MET* 3.9 3.8 - - + -
181A ARG 3.5 20.6 - - - +
182A GLN* 3.9 15.9 - - - +
183A ASN 5.7 0.9 - - - +
382A ARG 3.3 4.7 - - - +
383A ASN* 3.2 26.0 - - - +
405A TYR* 3.8 20.9 - - + -
406A TYR* 1.3 79.9 - - - +
408A ASP* 1.3 64.2 + - - +
409A THR* 3.8 18.6 - - - +
432A LEU 4.5 1.6 - - - +
433A ARG* 3.2 6.9 - - - +
434A THR* 2.8 42.7 + - - +
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Residues in contact with ASP 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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380A MET 3.3 4.0 - - - +
381A ALA* 3.3 2.3 - - - -
382A ARG* 2.7 63.9 + - + +
406A TYR* 2.7 35.3 + - + -
407A VAL* 1.3 74.9 - - - +
409A THR* 1.3 63.0 + - - +
410A GLN* 4.2 4.7 + - - +
431A ARG* 2.7 43.3 + - - +
432A LEU 3.9 2.2 - - - -
433A ARG* 3.7 4.3 - - - -
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Residues in contact with THR 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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182A GLN* 4.4 5.5 + - - -
183A ASN 5.9 0.3 + - - -
184A PHE* 3.6 45.9 + - + +
195A THR 5.5 0.2 - - - +
196A MET* 6.2 0.7 - - - -
197A TYR* 4.3 6.7 - - + -
379A VAL* 4.0 22.7 - - + -
380A MET 3.6 2.0 - - - -
381A ALA* 4.0 16.2 - - + +
407A VAL* 3.8 16.6 - - - +
408A ASP* 1.3 72.9 + - - +
410A GLN* 1.3 61.5 + - - +
431A ARG* 3.5 1.9 - - - -
432A LEU 3.0 34.1 + - - -
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Residues in contact with GLN 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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378A ASP 3.9 1.2 - - - +
379A VAL* 3.4 4.9 - - - +
380A MET* 2.9 40.7 + - + +
382A ARG* 4.7 9.6 + - - +
408A ASP* 3.9 5.2 + - - +
409A THR* 1.3 74.3 - - - +
411A ASP* 1.3 63.3 + - - +
412A ASP* 3.8 16.2 + - - +
429A ARG* 3.2 45.0 - - + +
430A THR 3.5 3.6 - - - +
431A ARG* 3.5 45.5 + - + +
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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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184A PHE* 3.9 12.8 - - + -
186A LYS* 3.1 28.9 - - - +
197A TYR* 5.3 0.7 + - - -
377A THR* 3.2 24.4 - - - +
378A ASP 3.3 3.1 - - - +
379A VAL* 3.2 20.5 - - + +
410A GLN* 1.3 75.1 - - - +
412A ASP* 1.3 78.5 + - - +
413A SER* 3.3 13.7 + - - -
428A THR 3.8 0.7 - - - +
429A ARG* 3.3 6.9 - - - +
430A THR* 2.7 45.8 + - - +
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Residues in contact with ASP 412 (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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376A TYR 3.8 1.0 - - - +
377A THR* 3.7 0.5 - - - -
378A ASP* 2.8 51.8 + - + +
410A GLN* 3.8 18.1 + - - +
411A ASP* 1.3 79.3 + - - +
413A SER* 1.3 61.4 + - - +
414A ASP* 4.8 4.6 - - - +
428A THR 3.7 4.0 - - - +
429A ARG* 3.3 33.6 + - - +
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Residues in contact with SER 413 (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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186A LYS* 4.1 8.9 - - - -
354A ILE* 4.4 13.1 - - - +
376A TYR 3.3 8.1 - - - -
377A THR* 3.7 12.5 + - - +
411A ASP* 3.3 26.0 + - - -
412A ASP* 1.3 71.9 + - - +
414A ASP* 1.3 65.7 + - - +
415A THR* 5.2 1.5 - - - +
426A TYR 3.8 0.3 - - - +
427A ALA* 3.4 2.6 - - - -
428A THR* 3.0 49.5 + - - +
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Residues in contact with ASP 414 (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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354A ILE* 4.3 2.6 - - - +
375A GLY* 3.1 23.8 - - - -
376A TYR* 3.1 19.8 + - + +
412A ASP* 4.8 2.9 - - - +
413A SER* 1.3 82.6 + - - +
415A THR* 1.3 68.1 + - - +
416A TYR* 4.1 10.5 - - + -
426A TYR 3.8 4.9 - - - +
427A ALA* 3.9 18.0 - - - +
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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