Contacts of the helix formed by residues 376 - 392 (chain A) in PDB entry 5C16
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 ASN 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A GLN* 4.8 2.4 + - - -
347A VAL* 5.6 14.2 - - + +
375A HIS* 1.3 79.1 - - - +
377A ILE* 1.3 64.1 + - + +
378A HIS* 3.0 32.9 + - + +
379A VAL* 3.1 28.4 + - - +
380A MET* 3.7 8.9 - - - +
444A ARG* 3.9 18.5 - - - +
500A ILE* 5.7 0.2 - - - -
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Residues in contact with ILE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASN* 1.3 74.6 - - + +
378A HIS* 1.3 82.6 - - + +
380A MET* 3.4 2.7 + - - +
381A ARG* 3.2 11.1 + - - +
443A ASP* 3.9 26.9 - - + +
444A ARG* 5.5 5.3 - - + +
484A ARG* 3.7 29.4 - - - +
495A ALA 4.1 17.5 - - - +
496A ASP* 4.4 7.2 - - - +
498A SER* 2.9 32.8 + - - +
500A ILE* 3.9 25.8 - - + -
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Residues in contact with HIS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ASN* 3.0 23.6 + - + +
377A ILE* 1.3 90.6 - - + +
379A VAL* 1.3 65.7 + - - +
381A ARG* 3.3 36.5 + - - +
382A GLU* 3.1 22.7 + - - +
495A ALA* 3.3 29.8 + - + +
496A ASP* 5.6 1.8 - - - -
576B PHE* 6.4 2.0 - + - -
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Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A HIS* 3.6 23.1 - - + -
376A ASN* 3.1 27.8 + - - +
378A HIS* 1.3 74.4 - - - +
380A MET* 1.3 73.8 + - + +
382A GLU* 3.5 6.7 + - - +
383A SER* 2.8 28.1 + - - -
412A TYR* 3.5 36.0 - - + +
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Residues in contact with MET 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE* 4.4 9.2 - - + -
375A HIS* 3.5 47.3 - - + +
376A ASN 3.7 8.1 - - - +
377A ILE* 3.6 7.2 - - - +
378A HIS 3.2 0.4 - - - -
379A VAL* 1.3 80.7 - - + +
381A ARG* 1.3 64.1 + - - +
383A SER* 3.3 5.2 + - - -
384A LEU* 3.1 24.1 + - - +
409A TRP* 3.8 4.7 - - + -
412A TYR* 3.8 26.9 - - + -
498A SER* 3.9 8.1 - - - +
499A PRO* 3.8 9.2 - - + +
500A ILE* 4.3 11.7 - - + -
503A GLN* 3.1 40.6 - - - +
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Residues in contact with ARG 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ILE* 3.2 7.8 + - - +
378A HIS* 3.3 40.7 + - - +
380A MET* 1.3 79.1 - - - +
382A GLU* 1.3 63.6 + - - +
384A LEU* 3.3 4.6 + - - +
385A ARG* 3.0 24.2 + - + +
494A ASP 4.5 8.6 + - - -
495A ALA* 2.9 38.4 + - - +
497A ARG* 2.9 30.5 + - - +
498A SER* 4.8 0.6 - - - -
499A PRO* 3.7 15.3 - - + +
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Residues in contact with GLU 382 (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 HIS 3.1 14.7 + - - +
379A VAL* 3.7 7.9 - - - +
381A ARG* 1.3 82.9 + - - +
383A SER* 1.3 62.6 + - - +
385A ARG* 2.4 48.8 + - - +
386A LYS* 3.0 32.6 + - + +
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Residues in contact with SER 383 (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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379A VAL 2.8 19.1 + - - -
380A MET 3.5 6.1 - - - -
381A ARG 3.2 0.2 - - - -
382A GLU* 1.3 76.7 - - - +
384A LEU* 1.3 62.4 + - - +
386A LYS* 3.1 8.6 + - - +
387A LEU* 3.0 21.5 + - - +
407A THR* 2.9 28.5 + - - -
409A TRP* 3.2 32.0 + - - +
412A TYR* 3.8 14.2 - - - -
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Residues in contact with LEU 384 (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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177A LYS 5.7 2.9 - - - +
179A MET* 4.1 28.3 - - + -
380A MET 3.1 13.5 + - - +
381A ARG 3.9 3.6 - - - +
383A SER* 1.3 79.8 - - - +
385A ARG* 1.3 57.9 + - - +
387A LEU* 3.3 12.6 + - + +
388A LYS* 2.9 28.1 + - + +
409A TRP* 3.8 16.8 - - + -
499A PRO* 3.6 29.6 - - + -
502A LEU* 4.3 14.4 - - + -
534A TYR* 5.3 2.9 - - - +
601A TYR* 4.1 20.9 - - + -
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Residues in contact with ARG 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ARG* 3.0 17.2 + - + +
382A GLU* 2.4 46.3 + - - +
383A SER 3.2 0.2 - - - -
384A LEU* 1.3 77.6 - - - +
386A LYS* 1.3 79.1 + - - +
388A LYS* 3.4 8.6 + - + +
389A GLU* 3.3 52.2 + - + +
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Residues in contact with LYS 386 (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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382A GLU* 3.0 26.4 + - + +
383A SER* 3.6 7.0 - - - +
385A ARG* 1.3 96.5 - - - +
387A LEU* 1.3 63.0 + - - +
389A GLU* 3.3 29.4 + - - +
390A ILE* 3.5 13.7 + - - +
403A ASN 5.8 0.4 - - - -
406A GLY* 3.0 31.9 + - - +
407A THR* 3.8 16.2 - - + +
408A HIS* 5.4 2.0 - - + -
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Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A MET* 4.5 4.3 - - + -
383A SER 3.0 13.3 + - - +
384A LEU* 3.6 17.0 - - + +
385A ARG 3.2 0.4 - - - -
386A LYS* 1.3 74.9 - - - +
388A LYS* 1.3 62.9 + - - +
390A ILE* 3.3 20.3 - - + +
391A VAL* 3.2 38.6 + - + +
404A VAL* 4.8 4.7 - - + -
407A THR* 3.6 15.6 - - + +
409A TRP* 4.1 28.3 - - + -
596A LEU* 4.2 19.1 - - + -
601A TYR* 4.1 28.5 - - + -
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Residues in contact with LYS 388 (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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175A VAL* 3.5 11.3 - - - +
176A CYS 3.0 25.6 + - - +
179A MET* 3.5 33.6 - - + +
180A ARG* 3.2 20.0 + - - +
181A ASN* 2.8 35.1 + - - +
384A LEU* 2.9 14.6 + - + +
385A ARG* 3.7 8.7 - - + +
386A LYS 3.3 0.4 - - - -
387A LEU* 1.3 75.0 - - - +
389A GLU* 1.3 66.8 + - + +
391A VAL* 3.7 1.6 - - - -
392A TYR* 3.2 29.8 + - + +
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Residues in contact with GLU 389 (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 ARG* 3.3 35.2 + - + +
386A LYS* 3.3 20.1 + - - +
388A LYS* 1.3 79.1 - - - +
390A ILE* 1.3 62.3 + - + +
392A TYR 3.3 16.8 - - - +
393A PRO* 5.3 0.2 - - - +
394A SER 5.1 1.2 - - - +
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Residues in contact with ILE 390 (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 LYS* 3.6 9.9 - - + +
387A LEU* 3.3 27.4 - - + +
389A GLU* 1.3 81.5 - - + +
391A VAL* 1.3 63.0 + - + +
394A SER 3.3 16.3 - - - +
395A ILE* 3.6 15.1 - - - +
396A ASP 4.6 1.6 + - - -
400A TRP* 4.5 6.6 - - + -
403A ASN* 3.8 35.2 - - + +
404A VAL* 3.7 41.1 - - + +
407A THR* 3.9 7.6 - - + -
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Residues in contact with VAL 391 (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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179A MET* 3.9 10.8 - - + +
387A LEU* 3.2 37.0 - - + +
388A LYS* 3.5 13.5 - - - +
390A ILE* 1.3 82.7 - - + +
392A TYR* 1.3 67.1 + - + +
393A PRO 3.9 3.3 - - - +
394A SER* 3.8 15.0 + - - -
395A ILE* 4.1 8.5 + - + +
400A TRP* 4.3 10.8 - - + -
596A LEU* 5.1 0.7 - - + -
601A TYR* 3.6 25.4 - - + +
602A VAL* 3.9 33.2 - - + +
605A ASN* 5.8 1.7 - - - +
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Residues in contact with TYR 392 (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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115A TYR* 4.5 6.8 + - - -
118A PRO* 4.4 19.4 - - + +
179A MET 3.8 22.7 - - - +
180A ARG* 3.8 13.6 - - + +
181A ASN* 2.7 55.9 + - + -
182A LEU* 5.2 0.2 - - - +
388A LYS* 3.2 17.8 + - + +
389A GLU* 3.3 18.4 - - - +
390A ILE 3.5 0.4 - - - -
391A VAL* 1.3 83.1 - - + +
393A PRO* 1.3 89.1 - - + +
394A SER 3.3 2.9 - - - -
604A TRP* 4.4 21.1 - - + -
605A ASN* 5.5 2.5 - - + -
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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
------------------------------------------------------------
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