Contacts of the helix formed by residues 365 - 378 (chain A) in PDB entry 3F7D
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 ASP 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A TYR* 4.1 5.8 - - - -
363A GLN 3.1 1.5 + - - +
364A LEU* 1.3 76.1 - - - +
366A ARG* 1.3 58.8 + - - +
367A GLN* 3.0 11.6 + - - +
368A GLU* 2.9 37.7 + - - +
369A PHE* 2.9 28.2 + - - +
405A TYR* 2.7 25.2 + - - -
410A TYR* 2.6 29.5 + - - +
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Residues in contact with ARG 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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232A LEU* 4.0 21.0 - - + +
235A GLU* 3.6 39.9 + - - +
236A PRO 4.5 7.5 + - - -
313A TYR* 3.4 35.3 + - + +
317A GLN* 4.4 7.5 + - - -
365A ASP* 1.3 77.7 - - - +
367A GLN* 1.3 72.7 + - - +
369A PHE* 3.3 6.0 + - + +
370A VAL* 3.1 26.9 + - + +
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Residues in contact with GLN 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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224A VAL* 4.8 5.8 - - + -
228A ILE* 3.7 32.3 - - + +
232A LEU* 3.6 22.9 - - + +
365A ASP* 3.0 14.2 + - - +
366A ARG* 1.3 88.9 - - - +
368A GLU* 1.3 65.9 + - - +
370A VAL* 3.4 6.7 - - - +
371A CYS* 3.3 23.7 + - - +
405A TYR* 3.1 39.3 + - + -
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Residues in contact with GLU 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 LEU* 3.2 19.1 - - + +
365A ASP* 2.9 34.8 + - - +
367A GLN* 1.3 75.7 - - - +
369A PHE* 1.3 57.6 + - - +
371A CYS* 3.4 2.3 + - - +
372A LEU* 2.9 34.9 + - - +
402A LEU* 4.0 12.5 - - + +
405A TYR* 3.6 16.9 - - + -
406A THR* 3.8 5.2 - - - +
410A TYR* 3.2 13.4 - - - -
416A LYS* 2.9 41.0 + - - +
420A LEU* 4.0 17.0 - - + -
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Residues in contact with PHE 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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235A GLU* 4.4 9.9 - - - -
309A LEU* 3.7 30.7 - - + -
310A ASP* 4.6 16.2 - - + -
313A TYR* 3.3 63.7 - + + -
364A LEU* 4.1 8.5 - - + +
365A ASP 2.9 17.9 + - - +
366A ARG* 3.4 9.4 - - - +
367A GLN 3.2 0.2 - - - -
368A GLU* 1.3 76.7 - - - +
370A VAL* 1.3 73.0 + - + +
372A LEU* 3.0 8.3 + - - +
373A LYS* 3.0 52.2 + - + +
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Residues in contact with VAL 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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228A ILE* 4.4 6.1 - - + -
231A LEU* 3.7 33.8 - - + +
232A LEU* 4.0 19.7 - - + -
235A GLU* 3.5 37.2 - - + +
280A TRP* 4.9 1.8 - - + +
366A ARG* 3.1 18.3 + - + +
367A GLN* 3.4 13.2 - - - +
369A PHE* 1.3 85.2 - - + +
371A CYS* 1.3 60.3 + - - +
373A LYS* 3.5 9.2 - - - +
374A PHE* 3.0 27.2 + - - +
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Residues in contact with CYS 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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227A LEU* 5.3 0.7 - - - -
228A ILE* 4.4 13.2 - - + -
231A LEU* 4.0 11.9 - - - -
367A GLN 3.3 15.7 + - - +
368A GLU 3.6 4.9 - - - +
369A PHE 3.1 0.4 - - - -
370A VAL* 1.3 80.8 - - - +
372A LEU* 1.3 59.8 + - - +
374A PHE* 3.3 2.4 + - - +
375A LEU* 2.9 33.6 + - - +
398A ALA* 3.6 29.8 - - - -
401A ALA* 4.4 8.5 - - - -
402A LEU* 3.8 29.2 - - + -
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Residues in contact with LEU 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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309A LEU* 4.0 23.8 - - + -
359A LEU* 5.7 3.6 - - + -
364A LEU* 3.9 25.1 - - + -
368A GLU* 2.9 26.0 + - + +
369A PHE* 3.0 6.3 + - - +
371A CYS* 1.3 74.5 - - - +
373A LYS* 1.3 59.1 + - - +
375A LEU* 3.3 5.5 + - + +
376A ILE* 2.8 34.8 + - - +
402A LEU* 3.7 26.9 - - + -
420A LEU* 4.3 20.9 - - + +
421A LEU* 5.0 0.2 - - + -
423A SER* 5.8 2.2 - - - -
424A LEU* 4.1 32.9 - - + +
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Residues in contact with LYS 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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235A GLU* 2.7 33.8 + - - +
236A PRO* 5.2 3.2 - - - +
277A ILE* 5.9 6.4 - - - +
280A TRP* 3.8 41.0 - - + +
306A LEU* 3.7 16.9 - - + +
309A LEU* 3.7 23.1 - - + +
310A ASP* 5.9 0.7 - - + +
369A PHE* 3.0 41.4 + - + +
370A VAL* 3.5 11.2 - - - +
372A LEU* 1.3 76.5 - - - +
374A PHE* 1.3 57.0 + - - +
376A ILE* 3.2 2.8 + - - +
377A LEU* 2.9 29.5 + - - +
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Residues in contact with PHE 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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227A LEU* 4.1 17.7 - - + -
231A LEU* 3.8 27.1 - - + -
280A TRP* 4.2 3.1 - - - -
284A CYS* 4.1 14.6 - - + -
285A MET* 4.3 27.6 - - + -
286A VAL* 4.7 3.4 - - + -
370A VAL 3.0 14.2 + - - +
371A CYS 3.6 4.3 - - - +
373A LYS* 1.3 80.5 - - - +
375A LEU* 1.3 60.9 + - - +
377A LEU* 3.3 8.4 + - + +
378A PHE* 3.1 66.4 + + + -
394A ALA* 4.1 19.5 - - + -
397A LYS* 6.0 0.2 - - + -
398A ALA* 3.5 31.4 - - + -
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Residues in contact with LEU 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 CYS 2.9 22.1 + - - +
372A LEU* 3.6 16.4 - - + +
374A PHE* 1.3 72.3 - - - +
376A ILE* 1.3 64.3 + - - +
378A PHE* 3.2 7.7 + - - +
379A SER* 3.1 21.9 + - - -
395A GLN* 4.2 4.5 - - + +
398A ALA* 3.5 28.0 - - + +
399A ASN* 3.5 32.3 - - - +
402A LEU* 3.9 33.4 - - + -
421A LEU* 4.2 14.6 - - + -
424A LEU* 4.6 9.0 - - + -
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Residues in contact with ILE 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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301A ASN* 5.0 0.2 + - - -
302A SER* 3.6 10.1 - - - -
305A GLU* 3.7 29.6 - - + +
306A LEU* 3.8 18.2 - - + -
309A LEU* 3.4 41.5 - - + -
372A LEU 2.8 17.9 + - - +
373A LYS* 3.5 4.0 - - - +
375A LEU* 1.3 73.1 - - - +
377A LEU* 1.3 65.2 + - - +
379A SER* 2.8 29.8 + - - +
424A LEU* 3.9 26.9 - - + -
427A VAL* 4.5 8.1 - - + -
428A ARG* 5.1 7.2 - - - +
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Residues in contact with LEU 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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280A TRP* 3.9 26.0 - - + -
281A ALA* 4.1 9.0 - - + -
284A CYS* 4.6 7.0 - - - -
287A PHE* 4.0 30.3 - - + -
298A LEU* 3.8 22.0 - - + +
299A LEU* 4.1 21.8 - - + -
301A ASN* 5.6 0.5 + - - -
302A SER* 4.0 21.3 + - - +
306A LEU* 4.4 8.2 - - + +
373A LYS 2.9 13.7 + - - +
374A PHE* 3.4 10.5 - - + +
376A ILE* 1.3 77.2 - - - +
378A PHE* 1.3 80.2 + - + +
379A SER 3.4 2.3 + - - -
380A LEU 4.9 0.3 + - - -
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Residues in contact with PHE 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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286A VAL* 4.0 15.9 - - + -
287A PHE* 3.9 29.8 - - + -
290A LEU* 4.2 6.3 - - + -
298A LEU* 3.9 22.2 - - + -
374A PHE* 3.1 56.8 + + + +
375A LEU* 3.3 6.5 - - - +
377A LEU* 1.3 90.9 - - + +
379A SER* 1.3 55.2 + - - +
380A LEU 3.3 6.1 - - - -
391A VAL* 3.8 21.8 - - + -
394A ALA* 4.0 17.3 - - + -
395A GLN* 3.1 43.0 + - + +
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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