Contacts of the strand formed by residues 339 - 354 (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 GLN 339 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A ASN* 3.8 4.9 - - - +
335A LEU* 3.2 56.7 + - + +
336A PRO* 3.1 25.8 + - - +
337A ALA* 4.9 3.0 - - - +
338A ASN* 1.3 79.4 - - - +
340A ARG* 1.3 66.3 + - - +
341A LEU* 5.6 0.4 - - + -
388A TYR* 3.2 30.5 + - + +
389A SER 3.1 6.1 - - - +
390A LEU* 3.6 23.6 - - + +
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Residues in contact with ARG 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 6.3 1.2 - - - -
233A ALA* 5.5 2.6 - - - +
272A ASP* 3.1 32.5 + - - -
332A GLY* 3.8 14.7 - - - -
333A TRP 3.2 8.5 - - - +
334A ASN* 3.0 29.3 + - - +
335A LEU* 5.6 0.4 - - - -
338A ASN* 5.2 0.9 - - - +
339A GLN* 1.3 79.5 - - - +
341A LEU* 1.3 69.6 + - - +
342A GLN* 2.6 33.4 + - + +
387A ASP 3.3 6.4 - - - +
388A TYR* 3.4 1.2 - - - -
389A SER* 3.0 42.0 + - - +
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLY* 3.4 1.0 - - - -
333A TRP* 2.8 56.3 + - + +
335A LEU* 4.8 22.4 - - + +
339A GLN* 5.4 0.2 - - - +
340A ARG* 1.3 80.6 - - - +
342A GLN* 1.3 63.9 + - - +
386A PHE* 4.0 23.1 - - + -
387A ASP 3.2 2.7 - - - -
388A TYR* 3.3 39.0 - - + -
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Residues in contact with GLN 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 5.6 4.5 + - - -
330A LYS* 3.9 33.7 - - - +
331A VAL 3.2 16.4 - - - +
332A GLY* 4.3 1.7 - - - -
333A TRP* 4.6 1.1 - - - -
340A ARG* 2.6 36.7 + - + +
341A LEU* 1.3 77.3 - - - +
343A LEU* 1.3 72.8 + - - +
344A SER* 4.2 8.3 - - - -
385A ALA 3.6 1.4 - - - +
386A PHE* 3.3 7.7 - - - -
387A ASP* 2.8 61.6 + - + +
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LYS* 3.3 3.3 - - - -
331A VAL* 2.9 42.4 + - + +
333A TRP* 4.2 26.0 - - + -
342A GLN* 1.3 75.9 - - - +
344A SER* 1.3 61.1 + - - +
385A ALA 3.5 3.6 - - - +
386A PHE* 3.6 35.9 - - + -
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Residues in contact with SER 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A MET* 5.2 2.6 - - - -
328A LEU* 5.6 1.1 - - - -
329A ALA 3.2 6.1 - - - -
330A LYS* 3.8 23.8 - - - -
342A GLN* 4.2 11.4 + - - -
343A LEU* 1.3 76.6 - - - +
345A TYR* 1.3 61.9 + - - +
383A ASN 3.7 1.1 - - - +
384A ALA* 3.4 4.7 - - - +
385A ALA* 2.9 51.5 + - - +
387A ASP* 4.7 4.0 + - - -
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Residues in contact with TYR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ARG* 4.5 6.3 - - + -
328A LEU* 3.5 7.1 - - - +
329A ALA* 2.8 44.8 + - + +
344A SER* 1.3 75.7 - - - +
346A LEU* 1.3 61.6 + - - +
347A GLN* 2.9 46.4 + - + -
382A ARG* 3.2 35.8 - - + +
383A ASN 3.2 11.7 - - - -
384A ALA* 4.3 15.0 - - + -
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 3.7 44.9 - - + -
198A ILE* 4.1 8.7 - - + -
202A LEU* 4.4 18.2 - - + -
230A THR* 4.1 12.6 - - + -
326A SER* 4.8 0.2 - - - -
327A ARG 3.4 10.5 - - - +
328A LEU* 4.0 17.5 - - + -
345A TYR* 1.3 77.8 - - - +
347A GLN* 1.3 69.4 + - - +
348A THR* 4.3 12.3 - - + -
381A ALA 3.7 1.0 - - - +
382A ARG* 3.5 0.9 - - - -
383A ASN* 2.6 55.5 + - + +
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Residues in contact with GLN 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A HIS 3.7 4.5 + - - +
326A SER* 3.2 5.4 - - - -
327A ARG* 3.0 61.2 + - + +
345A TYR* 2.9 34.9 + - + +
346A LEU* 1.3 74.7 - - - +
348A THR* 1.3 64.5 + - - +
349A GLN* 5.2 6.3 + - - +
380A MET* 3.8 24.4 - - + +
381A ALA 3.1 9.9 - - - +
382A ARG* 4.2 5.5 - - + -
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Residues in contact with THR 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 3.3 39.2 + - - +
198A ILE* 4.3 7.0 - - + -
199A ASP 4.7 1.1 - - - +
324A MET* 4.7 7.2 - - - -
325A HIS 3.7 3.6 - - - -
326A SER* 3.4 22.0 - - - +
346A LEU* 4.3 17.7 - - + -
347A GLN* 1.3 74.6 - - - +
349A GLN* 1.3 61.1 + - - +
350A THR* 3.8 2.5 + - - -
379A VAL* 3.4 5.9 - - - +
380A MET* 4.4 1.3 - - - -
381A ALA* 2.9 44.2 + - - +
383A ASN* 5.9 1.8 - - - +
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Residues in contact with GLN 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ARG* 4.0 21.4 - - - +
324A MET* 3.1 6.2 - - - +
325A HIS* 2.8 60.8 + - + +
347A GLN* 4.1 8.2 + - - +
348A THR* 1.3 72.5 - - - +
350A THR* 1.3 62.5 + - - +
351A ALA* 6.0 0.4 - - + +
378A ASP* 4.7 14.1 + - - +
379A VAL 3.5 4.0 - - - +
380A MET* 3.7 27.3 - - + +
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Residues in contact with THR 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASP* 5.8 0.4 - - - +
158A PRO* 3.6 31.4 - - + -
197A TYR* 3.9 27.6 - - + +
323A ARG* 3.6 7.6 - - - +
324A MET* 3.8 23.4 - - + +
348A THR 4.1 5.2 + - - -
349A GLN* 1.3 78.3 + - - +
351A ALA* 1.3 65.6 + - - +
352A SER* 5.1 1.1 - - - +
377A THR* 3.9 1.3 - - + +
378A ASP* 3.4 6.3 - - - +
379A VAL* 2.7 46.4 + - + +
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A TYR* 3.5 2.3 - - - +
323A ARG* 2.9 73.1 + - + +
349A GLN* 4.4 0.9 - - - +
350A THR* 1.3 76.0 - - - +
352A SER* 1.3 62.7 + - - +
353A PRO* 4.8 0.3 - - - +
376A TYR* 3.9 16.1 + - + +
377A THR 3.3 8.5 - - - +
378A ASP* 4.9 8.1 - - - +
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLN 3.5 12.7 + - - -
157A ASP* 4.8 4.0 - - - -
158A PRO* 3.6 18.3 - - - +
319A ASP 4.8 0.5 + - - -
320A THR 5.2 0.5 + - - -
321A HIS 3.6 7.1 + - - -
322A TYR* 3.5 15.0 - - - +
350A THR* 4.3 1.8 - - - -
351A ALA* 1.3 76.1 - - - +
353A PRO* 1.3 76.4 + - - +
376A TYR* 4.0 5.0 - - - -
377A THR* 2.5 49.1 + - - -
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Residues in contact with PRO 353 (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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156A GLN 3.3 20.1 - - - +
319A ASP* 3.6 27.6 - - + +
321A HIS* 3.2 52.7 - - + +
351A ALA 4.8 0.2 - - - +
352A SER* 1.3 92.7 + - - +
354A ILE* 1.3 62.6 + - - +
373A ARG* 3.9 6.5 - - - +
375A GLY 3.6 6.3 - - - +
376A TYR* 3.6 28.9 - - + -
377A THR* 4.9 0.5 + - - -
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Residues in contact with ILE 354 (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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156A GLN 5.1 2.0 - - - -
319A ASP* 3.6 12.1 - - - +
353A PRO* 1.3 75.9 - - - +
355A ALA* 1.3 68.5 + - - +
373A ARG* 3.7 0.5 - - - +
374A THR* 3.1 26.8 + - - +
375A GLY* 3.0 16.0 + - - +
376A TYR 3.4 24.5 - - - +
377A THR* 3.2 28.0 - - - +
413A SER* 4.4 10.8 - - - +
414A ASP 4.3 4.9 - - - +
415A THR* 5.7 4.0 - - + -
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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
------------------------------------------------------------
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