Contacts of the helix formed by residues 376 - 392 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLN* 4.6 3.2 + - - +
347B VAL* 5.9 10.7 - - + +
375B HIS* 1.3 81.5 - - - +
377B ILE* 1.3 62.6 + - + +
378B HIS* 2.8 26.0 + - + +
379B VAL* 2.8 39.3 + - - +
380B MET* 3.4 12.3 + - - +
444B ARG* 4.0 15.5 - - - +
500B ILE* 5.8 0.2 - - - -
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Residues in contact with ILE 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ASN* 1.3 75.0 - - + +
378B HIS* 1.3 78.1 - - + +
380B MET* 3.3 6.0 + - - -
381B ARG* 3.0 15.2 + - - +
443B ASP* 4.2 20.9 - - + +
444B ARG* 5.8 5.1 - - + +
484B ARG* 4.0 24.7 - - - +
495B ALA 3.8 21.8 - - - +
496B ASP* 4.4 9.4 - - - +
498B SER* 2.7 33.0 + - - +
500B ILE* 3.9 25.8 - - + -
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Residues in contact with HIS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ASN* 2.8 23.8 + - + +
377B ILE* 1.3 90.2 - - + +
379B VAL* 1.3 61.5 + - + +
381B ARG* 3.0 35.6 + - - +
382B GLU* 3.0 30.3 + - - +
495B ALA* 3.2 31.5 + - + +
496B ASP* 5.5 1.8 - - - -
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Residues in contact with VAL 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B HIS* 4.1 25.8 - - + -
376B ASN* 2.8 31.0 + - - +
378B HIS* 1.3 77.5 - - + +
380B MET* 1.3 65.3 + - - +
382B GLU* 3.3 5.7 + - - +
383B SER* 3.0 22.2 + - - -
412B TYR* 3.3 41.7 - - + +
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Residues in contact with MET 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ILE* 4.8 7.9 - - + -
375B HIS* 3.6 47.3 - - + +
376B ASN 3.4 8.3 + - - +
377B ILE 3.3 7.5 + - - +
379B VAL* 1.3 77.0 - - - +
381B ARG* 1.3 61.8 + - - +
383B SER* 3.1 15.1 + - - -
384B LEU 3.2 10.4 + - - -
409B TRP* 4.0 3.1 - - + -
412B TYR* 3.8 27.8 - - + -
416B LEU* 6.3 0.4 - - + -
498B SER* 3.7 8.3 - - - +
499B PRO* 4.0 15.1 - - + +
500B ILE* 4.0 14.8 - - + -
503B GLN* 3.2 42.2 - - - +
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Residues in contact with ARG 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ILE* 3.0 11.0 + - - +
378B HIS* 3.0 42.3 + - - +
380B MET* 1.3 75.9 - - - +
382B GLU* 1.3 66.3 + - - +
384B LEU* 3.4 2.8 + - - +
385B ARG* 3.1 22.9 + - + +
493B ALA 6.0 0.2 + - - -
494B ASP 4.7 6.0 + - - -
495B ALA* 2.7 39.2 + - - +
497B ARG* 2.9 31.4 + - - +
498B SER* 4.6 1.4 - - - -
499B PRO* 3.6 16.4 - - + +
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Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B HIS 3.0 18.2 + - - +
379B VAL* 3.9 4.7 - - - +
381B ARG* 1.3 79.5 + - - +
383B SER* 1.3 63.3 + - - +
385B ARG* 3.0 46.6 + - - +
386B LYS* 3.1 39.9 + - + +
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Residues in contact with SER 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B VAL 3.0 13.2 + - - -
380B MET 3.4 9.4 - - - -
382B GLU* 1.3 77.7 - - - +
384B LEU* 1.3 57.8 + - - +
386B LYS* 3.3 7.7 + - - +
387B LEU* 2.9 26.7 + - - +
407B THR* 2.6 31.4 + - - +
409B TRP* 3.3 30.0 + - - +
412B TYR* 3.7 13.5 - - - -
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LYS 5.8 2.9 - - - +
179B MET* 3.6 33.7 - - + -
380B MET 3.2 6.1 + - - +
381B ARG 3.9 6.1 - - - +
382B GLU 3.4 0.2 - - - -
383B SER* 1.3 75.5 - - - +
385B ARG* 1.3 66.1 + - - +
387B LEU* 3.3 17.7 + - + -
388B LYS* 2.9 22.8 + - + +
409B TRP* 4.0 14.5 - - + -
499B PRO* 3.5 32.8 - - + -
502B LEU* 4.1 20.2 - - + -
534B TYR* 5.5 1.8 - - - +
601B TYR* 4.2 9.0 - - + -
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Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG* 3.1 16.4 + - + +
382B GLU* 3.0 44.3 + - - +
383B SER 3.3 0.2 - - - -
384B LEU* 1.3 75.7 - - - +
386B LYS* 1.3 85.4 + - - +
388B LYS* 3.0 19.5 + - + +
389B GLU* 3.2 37.5 + - + +
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Residues in contact with LYS 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU* 3.1 26.0 + - + +
383B SER* 3.7 7.0 - - - +
385B ARG* 1.3 97.7 - - - +
387B LEU* 1.3 62.6 + - - +
389B GLU* 3.0 32.2 - - - +
390B ILE* 3.4 16.2 + - + +
406B GLY* 3.1 31.1 + - - -
407B THR* 3.9 16.2 - - + +
408B HIS* 5.9 0.4 - - - -
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B MET* 4.4 3.4 - - + -
383B SER 2.9 13.8 + - - +
384B LEU* 3.5 18.8 - - + +
385B ARG 3.2 0.4 - - - -
386B LYS* 1.3 78.1 - - - +
388B LYS* 1.3 56.1 + - - +
390B ILE* 3.2 6.2 + - + +
391B VAL* 2.9 44.5 + - + +
404B VAL* 4.7 11.2 - - + -
407B THR* 3.7 23.2 - - + +
409B TRP* 4.3 22.2 - - + -
596B LEU* 4.0 19.3 - - + -
601B TYR* 3.9 37.0 - - + -
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Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 3.6 12.5 - - - +
176B CYS 3.5 17.7 + - - +
179B MET* 3.6 34.9 - - + +
180B ARG* 3.8 22.0 - - - +
181B ASN* 2.9 36.3 + - - +
384B LEU 2.9 12.6 + - - +
385B ARG* 3.0 13.0 + - + +
387B LEU* 1.3 73.6 - - - +
389B GLU* 1.3 63.1 + - - +
390B ILE 3.0 4.9 - - - -
391B VAL* 3.9 0.7 - - - -
392B TYR* 3.0 31.9 + - + +
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Residues in contact with GLU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ARG* 3.2 31.3 + - + +
386B LYS* 3.0 39.1 - - - +
388B LYS* 1.3 75.3 - - - +
390B ILE* 1.3 64.0 + - + +
392B TYR 3.8 10.8 - - - +
393B PRO* 5.2 2.1 - - - +
394B SER 5.3 0.3 - - - +
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Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B LYS* 3.4 16.1 + - + +
387B LEU* 3.2 9.4 + - + +
388B LYS 3.0 0.6 - - - -
389B GLU* 1.3 87.4 - - + +
391B VAL* 1.3 59.9 + - + +
394B SER 3.0 21.0 - - - +
395B ILE* 4.1 5.5 - - - -
396B ASP 4.9 1.4 + - - +
400B TRP* 3.8 27.6 - - + -
403B ASN* 3.1 55.6 - - + +
404B VAL* 4.2 7.4 - - + -
407B THR* 3.9 10.3 - - + -
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Residues in contact with VAL 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B MET* 3.8 17.3 - - + -
387B LEU* 2.9 41.6 + - + +
388B LYS* 3.7 5.4 - - - +
390B ILE* 1.3 77.7 - - + +
392B TYR* 1.3 67.5 + - + +
393B PRO 4.0 2.1 - - - +
394B SER* 3.9 14.2 + - - +
395B ILE* 4.1 10.5 - - - +
400B TRP* 3.9 22.7 - - + -
596B LEU* 4.8 0.4 - - + -
601B TYR* 3.4 26.7 - - + +
602B VAL* 4.0 25.2 - - + +
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Residues in contact with TYR 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B TYR* 4.4 6.2 + - - -
118B PRO* 4.3 21.6 - - + +
179B MET 3.6 27.8 - - - +
180B ARG* 3.7 12.9 - - + +
181B ASN* 3.2 50.1 + - + -
388B LYS* 3.0 22.7 + - + +
389B GLU* 3.8 12.1 - - - +
391B VAL* 1.3 82.9 - - + +
393B PRO* 1.3 83.6 - - + +
394B SER 3.5 2.5 - - - -
604B TRP* 3.3 32.1 - - + -
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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