Contacts of the helix formed by residues 369 - 383 (chain A) in PDB entry 4X61
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 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A ALA 3.0 10.9 + - - -
367A GLY 3.3 0.6 - - - -
368A ARG* 1.3 79.3 - - - +
370A PRO* 1.3 68.4 - - - +
371A LEU 3.3 2.5 - - - -
372A VAL* 3.0 23.4 + - - +
373A ASN* 3.2 19.3 + - - -
401A LEU* 3.5 14.1 - - - +
409A TRP* 4.0 5.6 - - - -
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Residues in contact with PRO 370 (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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328A GLU* 4.1 16.4 - - + +
334A TYR* 3.5 31.1 - - + +
366A ALA 3.7 8.3 - - - +
368A ARG 3.6 6.0 - - - +
369A GLY* 1.3 91.6 - - - +
371A LEU* 1.3 59.0 + - - +
373A ASN* 3.4 11.0 + - + +
374A ALA* 2.9 27.4 + - - +
377A ARG* 4.6 3.5 + - - -
701A SAM 3.3 28.5 - - - +
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LYS* 5.1 0.7 - - - -
334A TYR* 3.7 23.6 - - + -
337A TYR* 3.7 44.9 - - + -
341A ILE* 4.8 1.6 - - - +
363A VAL* 4.0 22.1 - - + +
365A GLY 5.3 0.4 - - - +
366A ALA 5.0 0.4 + - - +
369A GLY 3.3 0.6 - - - -
370A PRO* 1.3 75.7 - - - +
372A VAL* 1.3 59.7 + - - +
374A ALA* 3.7 8.2 - - + +
375A SER* 2.9 30.0 + - - -
433A VAL* 4.1 14.0 - - + +
434A SER* 4.4 0.4 - - - -
435A GLU* 4.1 25.4 - - + +
701A SAM 3.8 27.1 - - - +
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Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL* 4.0 18.8 - - + -
366A ALA* 4.4 5.8 - - + -
369A GLY* 3.0 22.6 + - - +
371A LEU* 1.3 75.4 - - - +
373A ASN* 1.3 61.2 + - - +
375A SER* 3.1 7.4 + - - -
376A LEU* 3.0 27.9 + - + +
388A LEU* 4.0 9.2 - - + -
390A ALA* 4.0 24.0 - - + -
409A TRP* 3.8 30.1 - - + -
413A VAL* 3.9 24.5 - - + -
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Residues in contact with ASN 373 (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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369A GLY 3.2 14.3 + - - -
370A PRO* 3.4 9.4 + - + +
372A VAL* 1.3 73.3 - - - +
374A ALA* 1.3 59.2 + - - +
376A LEU* 3.2 9.9 + - - +
377A ARG* 2.8 52.8 + - + +
404A TRP* 3.8 32.4 - - - -
409A TRP* 2.7 32.1 + - - +
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Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A TYR* 4.4 16.6 - - + +
338A GLN* 3.5 17.5 - - + +
341A ILE* 4.4 5.2 - - + -
370A PRO 2.9 17.9 + - - +
371A LEU* 3.7 18.6 - - + +
372A VAL 3.2 0.2 - - - -
373A ASN* 1.3 76.5 - - - +
375A SER* 1.3 56.8 + - - +
377A ARG* 3.6 21.0 - - - +
378A ALA* 3.1 29.1 + - - +
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Residues in contact with SER 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ILE* 3.4 24.4 - - - +
345A LEU* 5.3 0.2 - - - +
361A LEU* 4.0 14.4 - - - +
363A VAL* 4.3 5.5 - - - +
371A LEU 2.9 16.8 + - - -
372A VAL 3.1 10.6 + - - -
374A ALA* 1.3 77.3 - - - +
376A LEU* 1.3 57.5 + - - +
378A ALA* 3.5 3.4 + - - +
379A ALA* 3.2 20.4 + - - +
386A ILE* 3.5 12.4 - - - +
388A LEU* 3.9 25.1 - - - +
433A VAL* 4.5 3.5 - - - +
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Residues in contact with LEU 376 (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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372A VAL* 3.0 21.6 + - + +
373A ASN* 3.2 15.4 + - - +
375A SER* 1.3 75.1 - - - +
377A ARG* 1.3 64.6 + - + +
379A ALA* 3.4 3.9 + - + +
380A LYS* 3.3 44.3 + - - +
386A ILE* 4.5 4.7 - - + -
388A LEU* 3.7 19.3 - - + -
409A TRP* 3.6 35.4 - - + +
412A GLN* 3.4 32.5 - - + +
413A VAL* 4.8 2.7 - - + -
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Residues in contact with ARG 377 (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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334A TYR* 4.9 14.1 + - - +
335A SER 5.6 0.4 - - - +
338A GLN* 3.1 36.1 + - - +
370A PRO 4.6 3.0 + - - -
373A ASN* 2.8 39.0 + - - +
374A ALA* 3.6 23.2 - - - +
376A LEU* 1.3 77.0 - - + +
378A ALA* 1.3 57.2 + - - +
379A ALA 3.4 0.2 - - - -
380A LYS* 3.8 6.4 + - - +
381A GLN* 3.2 27.0 + - - +
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Residues in contact with ALA 378 (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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338A GLN* 3.4 27.6 - - + +
341A ILE* 3.9 12.8 - - + -
342A TYR* 3.8 14.1 - - - +
345A LEU* 3.7 3.9 - - - +
374A ALA 3.1 18.7 + - - +
375A SER 3.8 4.9 - - - +
376A LEU 3.2 0.2 - - - -
377A ARG* 1.3 76.3 - - - +
379A ALA* 1.3 59.7 + - - +
381A GLN* 3.6 7.8 - - - +
382A ALA* 3.1 30.0 + - - +
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 4.0 9.8 - - - +
375A SER 3.2 16.4 + - - +
376A LEU* 3.7 7.2 - - + +
377A ARG 3.4 0.4 - - - -
378A ALA* 1.3 77.7 - - - +
380A LYS* 1.3 58.4 + - + +
382A ALA 3.5 0.5 + - - -
383A ASP* 3.0 23.2 + - - -
384A ARG 3.0 29.6 + - - +
386A ILE* 3.7 26.7 - - + -
412A GLN* 5.7 1.3 - - - +
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Residues in contact with LYS 380 (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 LEU* 3.3 40.2 + - - +
377A ARG* 4.2 6.1 - - - +
378A ALA 3.4 0.2 - - - -
379A ALA* 1.3 79.8 - - + +
381A GLN* 1.3 61.2 + - - +
383A ASP* 3.9 8.7 + - - +
412A GLN* 5.1 4.9 + - - +
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Residues in contact with GLN 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLN* 3.1 29.0 + - - +
339A GLN* 4.1 16.9 + - - +
342A TYR* 3.5 44.7 - - + +
377A ARG 3.2 16.9 + - - +
378A ALA 3.6 3.8 - - - +
379A ALA 3.2 0.2 - - - -
380A LYS* 1.3 77.9 - - - +
382A ALA* 1.3 57.8 + - - +
383A ASP* 3.3 3.6 + - - +
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Residues in contact with ALA 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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342A TYR* 3.9 20.2 - - + +
345A LEU* 4.2 13.5 - - + -
346A LEU* 3.6 26.9 - - + +
378A ALA 3.1 17.2 + - - +
379A ALA 4.3 0.7 - - - +
381A GLN* 1.3 75.7 - - - +
383A ASP* 1.3 63.0 + - - +
384A ARG* 2.8 32.1 + - + +
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Residues in contact with ASP 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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351A GLU* 5.1 0.7 - - - +
354A LYS* 3.2 44.9 + - + +
379A ALA 3.0 7.4 + - - -
380A LYS* 3.9 7.9 + - - +
381A GLN 3.3 4.7 - - - +
382A ALA* 1.3 81.9 - - - +
384A ARG* 1.3 71.8 + - - +
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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