Contacts of the helix formed by residues 363 - 380 (chain B) in PDB entry 3V4K
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 GLY 363 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A LYS* 5.5 7.2 - - - +
361B TRP 3.3 1.0 + - - -
362B ASP* 1.3 72.6 - - - +
364B LEU* 1.3 65.0 + - - +
365B ASP 3.3 2.5 - - - -
366B GLU* 3.1 12.0 + - - +
367B HIS* 2.9 40.1 + - - -
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A SER* 5.1 0.9 - - - +
208B ASN* 3.1 12.8 + - - +
339B THR* 4.3 2.0 - - - -
340B TYR* 3.7 35.9 - - + +
343B PHE* 3.9 20.0 - - + -
358B PHE* 4.0 20.6 - - + -
360B PRO* 4.1 15.9 - - + -
361B TRP* 3.3 54.2 + - + +
362B ASP 3.3 3.0 + - - -
363B GLY* 1.3 76.3 - - - +
365B ASP* 1.3 70.2 + - + +
368B SER* 3.0 17.9 + - - -
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Residues in contact with ASP 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A SER* 3.8 36.9 + - - +
342A GLU* 5.0 5.5 - - - +
339B THR* 4.9 10.7 - - - +
340B TYR 5.4 0.3 + - - -
363B GLY 3.3 0.2 - - - -
364B LEU* 1.3 81.3 - - - +
366B GLU* 1.3 61.8 + - - +
368B SER* 4.3 7.7 + - - -
369B GLN* 2.9 56.6 + - - +
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Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B GLY* 3.1 13.9 + - - +
365B ASP* 1.3 78.2 - - - +
367B HIS* 1.3 69.3 - - + +
369B GLN* 3.4 13.3 + - - +
370B ASP* 3.0 23.4 + - - +
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Residues in contact with HIS 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASN* 3.1 46.3 + - + +
209B GLU* 3.1 17.2 + - + -
210B PRO* 3.4 15.5 - - + +
361B TRP* 5.0 0.4 - + - -
362B ASP 3.6 11.0 - - - -
363B GLY* 2.9 31.5 + - - +
364B LEU 4.1 0.2 + - - -
366B GLU* 1.3 81.3 - - + +
368B SER* 1.3 63.5 + - - +
370B ASP* 3.3 7.1 + - - +
371B LEU* 2.9 30.0 + - + +
381B MG 2.3 31.1 - - - -
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Residues in contact with SER 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASN* 3.6 7.0 - - - +
337B ILE* 3.6 12.0 - - - +
338B MET 2.7 27.2 + - - -
339B THR* 3.3 25.5 - - - +
364B LEU* 3.0 17.5 + - - -
365B ASP* 3.3 10.1 + - - -
367B HIS* 1.3 78.4 - - - +
369B GLN* 1.3 57.8 + - - +
371B LEU* 3.4 2.4 + - - +
372B SER* 2.9 33.0 + - - -
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Residues in contact with GLN 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LYS* 5.9 2.8 - - - +
365B ASP* 2.9 44.4 + - - +
366B GLU* 3.7 12.5 - - - +
368B SER* 1.3 75.1 - - - +
370B ASP* 1.3 65.6 + - - +
372B SER* 3.3 8.1 + - - -
373B GLY* 3.1 17.8 + - - -
376B ARG* 4.9 2.9 + - - -
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Residues in contact with ASP 370 (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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210B PRO* 6.0 2.1 - - - +
366B GLU 3.0 13.8 + - - +
367B HIS* 3.6 11.0 - - - +
369B GLN* 1.3 74.7 - - - +
371B LEU* 1.3 66.0 + - + +
373B GLY* 3.1 4.7 + - - -
374B ARG* 3.0 37.8 + - - +
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASN* 4.4 13.7 - - + +
312B ALA 3.3 26.2 - - - +
313B ARG* 4.2 7.0 - - + -
314B ILE* 3.6 39.1 - - + +
337B ILE* 3.8 17.9 - - + -
367B HIS* 2.9 24.9 + - + +
368B SER* 3.7 4.0 - - - +
370B ASP* 1.3 79.2 - - + +
372B SER* 1.3 56.4 + - - +
374B ARG* 3.1 15.3 + - - +
375B LEU* 2.8 30.0 + - - +
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Residues in contact with SER 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ILE* 3.6 24.4 + - - +
339B THR* 5.4 2.9 - - - +
368B SER* 2.9 25.5 + - - -
369B GLN* 3.6 7.9 - - - -
370B ASP 3.3 0.2 - - - -
371B LEU* 1.3 72.5 - - - +
373B GLY* 1.3 58.0 + - - +
375B LEU* 3.4 3.4 + - - +
376B ARG* 3.0 46.5 + - - +
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Residues in contact with GLY 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B GLN 3.1 8.7 + - - -
370B ASP* 3.1 7.7 + - - -
372B SER* 1.3 77.4 - - - +
374B ARG* 1.3 61.4 + - - +
376B ARG* 3.4 27.4 + - - +
377B ALA* 3.1 21.1 + - - +
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Residues in contact with ARG 374 (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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314B ILE* 3.9 14.2 - - + +
316B ASP* 4.9 11.5 + - - +
322B GLN* 5.8 2.0 - - - +
370B ASP* 3.0 36.1 + - - +
371B LEU* 3.1 19.7 + - - +
373B GLY* 1.3 76.0 - - - +
375B LEU* 1.3 64.0 + - - +
377B ALA* 3.2 8.7 + - - +
378B ILE* 3.1 29.1 + - + +
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Residues in contact with LEU 375 (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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311B THR* 6.3 0.2 - - + -
314B ILE* 3.8 17.2 - - + +
325B LEU* 4.3 19.5 - - + -
335B ILE* 3.6 39.7 - - + +
336B SER* 3.8 15.9 - - - +
337B ILE* 4.0 15.3 - - + -
371B LEU 2.8 15.6 + - - +
372B SER* 3.8 5.2 - - - +
374B ARG* 1.3 75.1 - - - +
376B ARG* 1.3 65.5 + - + +
378B ILE* 3.2 6.6 + - + +
379B LEU* 3.0 45.5 + - + +
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Residues in contact with ARG 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B GLN 4.9 3.0 + - - -
372B SER* 3.0 31.7 + - - +
373B GLY* 3.4 29.4 - - - +
374B ARG 3.4 0.2 - - - -
375B LEU* 1.3 75.1 - - - +
377B ALA* 1.3 62.3 + - - +
379B LEU* 3.8 4.8 - - - -
380B GLN* 3.0 26.3 + - - +
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Residues in contact with ALA 377 (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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326B ARG* 5.1 0.5 + - - -
373B GLY 3.1 12.6 + - - +
374B ARG* 3.5 11.2 - - - +
375B LEU 3.2 0.2 - - - -
376B ARG* 1.3 78.1 - - - +
378B ILE* 1.3 63.0 + - + +
380B GLN* 3.7 14.5 + - - +
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Residues in contact with ILE 378 (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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314B ILE* 4.0 33.9 - - + -
316B ASP* 4.8 4.7 - - + +
322B GLN* 3.7 53.6 - - + +
325B LEU* 4.2 22.9 - - + -
326B ARG* 2.9 38.9 + - - +
374B ARG* 3.1 17.5 + - + +
375B LEU* 3.2 9.2 + - - +
377B ALA* 1.3 78.4 - - + +
379B LEU* 1.3 66.2 + - + +
380B GLN 3.6 1.7 + - - +
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Residues in contact with LEU 379 (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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325B LEU* 3.7 35.2 - - + +
326B ARG* 4.1 10.9 - - - +
329B ALA* 4.0 17.5 - - + -
335B ILE* 4.5 18.8 - - + +
375B LEU* 3.0 43.8 + - + +
376B ARG* 4.2 4.0 - - - +
378B ILE* 1.3 81.7 - - + +
380B GLN* 1.3 66.8 + - - +
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Residues in contact with GLN 380 (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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326B ARG* 4.5 8.0 - - - -
376B ARG 3.0 16.1 + - - +
377B ALA* 3.8 12.4 - - - +
378B ILE 3.4 6.6 - - - +
379B LEU* 1.3 83.8 - - - +
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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