Contacts of the helix formed by residues 357 - 376 (chain A) in PDB entry 4GDF
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 ARG 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A LEU 3.8 0.4 - - - -
356A THR* 1.3 81.9 - - + +
358A GLU* 1.3 65.6 - - - +
359A GLN 3.0 3.3 - - - +
360A MET* 3.4 28.5 + - - +
361A LEU* 3.2 17.5 + - - +
412A MET 3.1 25.2 + - - -
413A VAL* 3.4 21.4 - - + +
415A ASN* 3.4 23.4 + - - +
468A PHE* 3.1 62.1 + - + +
523A PRO* 3.4 21.6 - - - +
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Residues in contact with GLU 358 (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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356A THR* 3.6 12.1 - - + +
357A ARG* 1.3 78.5 - - - +
359A GLN* 1.3 60.7 + - + +
361A LEU* 3.4 14.0 + - - +
362A THR* 2.9 40.6 + - - +
410A LYS* 2.8 31.8 + - - +
413A VAL* 3.8 25.0 - - + +
587A GLU 6.2 0.2 - - - -
589A ALA* 4.7 13.9 + - + +
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Residues in contact with GLN 359 (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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354A GLN 4.0 4.3 - - - +
355A LEU* 3.4 26.0 - - + +
356A THR* 2.7 48.7 + - - +
358A GLU* 1.3 78.7 - - + +
360A MET* 1.3 60.1 + - - +
362A THR* 3.0 8.3 + - - -
363A ASN* 2.8 37.7 + - - +
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Residues in contact with MET 360 (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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352A SER* 4.8 17.5 - - - +
355A LEU* 4.0 28.3 - - + +
356A THR 4.5 5.2 - - - +
357A ARG* 3.4 34.0 + - - +
358A GLU 3.4 0.2 - - - -
359A GLN* 1.3 76.2 - - - +
361A LEU* 1.3 58.2 + - - +
363A ASN* 3.2 11.4 + - - +
364A ARG* 3.0 27.3 + - - +
466A ASP 6.2 0.2 - - - +
467A GLN 6.1 0.4 - - - -
468A PHE* 3.9 30.7 - - + -
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Residues in contact with LEU 361 (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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357A ARG 3.2 10.6 + - - +
358A GLU* 3.6 18.6 - - - +
359A GLN 3.2 0.4 - - - -
360A MET* 1.3 75.4 - - - +
362A THR* 1.3 62.0 + - - +
364A ARG* 3.3 4.3 + - + +
365A PHE* 2.8 67.3 + - + -
409A LEU* 4.3 20.6 - - + +
410A LYS* 5.1 2.7 - - - +
413A VAL* 3.5 28.0 - - + -
443A CYS* 3.7 33.9 - - + -
468A PHE* 4.1 11.6 - - + -
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Residues in contact with THR 362 (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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358A GLU* 2.9 27.4 + - - +
359A GLN* 3.0 11.0 + - - -
361A LEU* 1.3 73.4 - - - +
363A ASN* 1.3 70.3 + - - +
365A PHE* 3.2 7.5 + - - +
366A ASN* 2.9 23.5 + - - +
589A ALA* 3.2 25.6 - - + +
591A SER* 3.5 15.0 - - - +
592A ILE* 3.5 33.8 - - + +
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Residues in contact with ASN 363 (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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348A LYS* 6.2 0.2 - - - +
355A LEU* 3.8 31.4 - - - +
359A GLN* 2.8 22.6 + - - +
360A MET* 3.2 10.0 + - - +
362A THR* 1.3 80.7 - - - +
364A ARG* 1.3 56.9 + - - +
366A ASN* 2.9 33.2 + - - +
367A ASP* 3.0 17.4 + - - +
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Residues in contact with ARG 364 (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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360A MET 3.0 13.7 + - - +
361A LEU* 3.5 11.0 - - - +
363A ASN* 1.3 73.6 - - - +
365A PHE* 1.3 67.7 + - + +
366A ASN 3.1 0.2 + - - -
367A ASP* 3.2 16.6 + - - +
368A LEU* 3.0 51.9 + - - +
371A ARG* 4.0 16.5 - - - +
441A GLU* 2.6 37.3 + - - +
442A LEU 3.0 19.5 + - - +
443A CYS* 3.7 22.0 - - - +
444A GLY* 4.0 10.0 - - - +
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Residues in contact with PHE 365 (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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361A LEU* 2.8 59.4 + - + +
362A THR* 3.5 7.2 - - - +
364A ARG* 1.3 77.8 - - - +
366A ASN* 1.3 56.4 + - - +
368A LEU* 3.5 7.9 + - + +
369A LEU* 2.9 32.2 + - + +
409A LEU* 4.0 15.3 - - + -
442A LEU* 4.3 22.9 - - + -
576A LEU* 3.4 25.7 - - + +
579A LEU* 3.4 33.7 - - + -
588A PHE* 4.2 17.9 - + - -
592A ILE* 4.1 16.4 - - + -
596A ILE* 5.6 0.7 - - + -
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Residues in contact with ASN 366 (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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362A THR* 2.9 23.7 + - - +
363A ASN* 2.9 17.6 + - - +
365A PHE* 1.3 75.1 - - - +
367A ASP* 1.3 56.2 + - - +
369A LEU* 2.8 5.7 + - - +
370A ASP* 2.7 41.4 + - - +
592A ILE* 3.3 32.5 - - - +
595A ARG* 2.7 31.1 + - - +
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Residues in contact with ASP 367 (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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281A LYS* 5.8 3.9 + - - -
363A ASN* 3.0 18.4 + - - +
364A ARG* 3.9 21.0 + - - +
366A ASN* 1.3 77.2 - - - +
368A LEU* 1.3 61.5 + - - +
370A ASP* 3.2 14.6 + - - +
371A ARG* 3.0 31.0 + - + +
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Residues in contact with LEU 368 (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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364A ARG* 3.0 46.1 + - + +
365A PHE* 3.7 6.5 - - + +
367A ASP* 1.3 77.3 - - - +
369A LEU* 1.3 62.2 + - - +
371A ARG* 3.2 21.6 + - - +
372A MET* 3.0 28.3 + - - +
441A GLU* 3.9 4.7 - - + +
442A LEU* 3.2 44.6 - - + +
572A GLY 5.1 1.1 - - - -
573A ILE* 3.5 33.4 - - + +
576A LEU* 3.9 12.6 - - + -
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Residues in contact with LEU 369 (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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365A PHE* 2.9 13.1 + - + +
366A ASN 2.8 11.1 + - - +
368A LEU* 1.3 79.3 - - - +
370A ASP* 1.3 54.5 + - - +
372A MET* 3.2 29.5 + - + +
373A ASP* 3.0 31.4 + - - +
576A LEU* 3.8 16.4 - - + -
580A ILE* 5.4 5.4 - - + -
592A ILE* 4.8 7.9 - - + -
595A ARG* 3.7 45.1 - - + +
596A ILE* 4.4 15.5 - - + -
599A TRP* 3.6 29.2 - - + +
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Residues in contact with ASP 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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366A ASN* 2.7 18.1 + - - +
367A ASP* 3.2 16.1 + - - +
369A LEU* 1.3 74.2 - - - +
371A ARG* 1.3 66.3 + - + +
373A ASP* 3.6 10.2 + - - +
374A ILE* 3.2 26.2 + - + +
595A ARG* 2.7 37.4 + - - +
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Residues in contact with ARG 371 (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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364A ARG* 4.0 21.4 - - - +
367A ASP* 3.0 21.8 + - + +
368A LEU* 3.2 34.8 + - - +
370A ASP* 1.3 76.5 - - + +
372A MET* 1.3 58.6 + - - +
374A ILE* 3.4 13.5 + - + +
375A MET* 3.0 32.8 + - + +
441A GLU* 3.6 22.8 + - - -
573A ILE* 4.1 17.5 - - + +
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Residues in contact with MET 372 (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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368A LEU 3.0 17.3 + - - +
369A LEU* 3.4 36.3 - - + +
370A ASP 3.2 0.4 - - - -
371A ARG* 1.3 75.1 - - - +
373A ASP* 1.3 66.0 + - - +
375A MET* 3.1 7.3 + - - -
376A PHE* 3.0 42.4 + - + +
573A ILE* 3.5 30.1 - - + +
576A LEU* 4.0 16.4 - - + -
577A LEU* 3.5 38.6 - - + -
580A ILE* 5.7 1.6 - - + -
599A TRP* 3.8 17.7 - - + -
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Residues in contact with ASP 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 LEU 3.0 13.0 + - - +
370A ASP* 3.8 9.4 - - - +
371A ARG 3.4 0.4 - - - -
372A MET* 1.3 75.2 - - - +
374A ILE* 1.3 62.7 + - + +
376A PHE 3.9 0.9 - - - -
377A GLY* 3.2 22.0 + - - -
595A ARG* 3.2 26.8 + - - -
599A TRP* 3.4 26.7 + - - -
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Residues in contact with ILE 374 (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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311A PRO* 6.2 4.7 - - + -
370A ASP* 3.2 22.2 - - + +
371A ARG* 3.6 9.6 - - + +
372A MET 3.2 0.4 - - - -
373A ASP* 1.3 76.4 - - + +
375A MET* 1.3 68.8 + - + +
377A GLY* 3.2 7.9 + - - -
379A THR 3.4 19.4 - - - +
380A GLY* 4.3 1.4 - - - -
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Residues in contact with MET 375 (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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371A ARG* 3.0 22.9 + - + +
372A MET* 3.1 11.2 + - - +
374A ILE* 1.3 73.9 - - - +
376A PHE* 1.3 75.6 + - + +
377A GLY 2.8 10.3 + - - +
380A GLY* 3.7 17.8 - - - +
381A SER 5.3 0.7 - - - +
382A ALA* 3.4 27.9 - - + +
387A TRP* 3.4 44.4 - - + +
573A ILE* 3.5 27.1 - - + -
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Residues in contact with PHE 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 MET* 3.0 53.1 + - + +
373A ASP 3.9 2.7 - - - -
375A MET* 1.3 90.6 - - + +
377A GLY* 1.3 61.8 + - - +
382A ALA* 3.3 22.0 - - + -
384A ILE* 3.4 31.2 - - + -
387A TRP* 4.0 31.4 - + + -
573A ILE* 4.6 2.5 - - + -
577A LEU* 4.4 12.3 - - + -
599A TRP* 3.5 18.8 - + + -
602A ARG* 3.4 35.0 + - - +
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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
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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