Contacts of the helix formed by residues 395 - 414 (chain A) in PDB entry 4R0C
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 SER 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PRO* 5.5 4.5 - - - -
340A LEU* 5.0 1.0 - - - +
393A ILE* 3.5 4.0 - - - +
394A GLY* 1.3 74.3 - - - +
396A ALA* 1.3 62.2 - - - +
397A SER* 3.2 11.1 + - - -
398A ALA* 2.9 37.2 + - - +
399A LYS* 3.2 25.5 + - - +
440A PRO* 6.3 0.4 - - - +
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Residues in contact with ALA 396 (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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170A PHE* 3.8 22.7 - - + -
179A VAL* 5.3 1.3 - - + -
183A LEU* 3.9 17.4 - - + +
394A GLY 3.2 4.8 + - - +
395A SER* 1.3 71.8 - - - +
397A SER* 1.3 64.4 + - - +
400A TRP* 3.2 16.3 + - - +
425A TYR* 2.7 25.4 + - + +
429A ASP* 3.4 25.4 - - - +
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Residues in contact with SER 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A THR* 3.8 28.7 - - - +
186A LEU* 3.9 3.5 - - - +
337A TYR* 4.2 17.3 - - - -
340A LEU* 4.2 11.7 - - - -
341A MET* 4.9 1.6 - - - -
395A SER* 3.1 7.2 + - - -
396A ALA* 1.3 80.6 - - - +
398A ALA* 1.3 61.4 - - - +
401A SER* 2.9 30.4 + - - -
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PRO* 3.6 32.1 - - + -
25A PHE* 3.6 18.9 - - + -
340A LEU* 3.7 21.0 - - + +
393A ILE* 4.4 6.5 - - + -
395A SER* 2.9 21.9 + - - +
397A SER* 1.3 75.6 - - - +
399A LYS* 1.3 65.4 + - - +
401A SER* 3.5 8.1 + - - -
402A ILE* 3.7 5.5 - - - +
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Residues in contact with LYS 399 (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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386A THR* 4.1 8.5 - - - -
389A ILE* 4.0 19.5 - - + -
390A ASN* 2.8 48.5 + - - +
393A ILE* 3.1 38.9 + - + +
394A GLY 3.6 1.0 + - - -
395A SER 3.2 12.7 + - - +
398A ALA* 1.3 77.5 - - - +
400A TRP* 1.3 60.1 + - - +
402A ILE* 3.1 11.4 + - - +
403A LEU* 2.9 36.1 + - + +
425A TYR* 3.1 27.9 + - + +
429A ASP* 3.0 16.7 + - - -
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Residues in contact with TRP 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 3.1 37.6 + - + +
186A LEU* 3.6 20.7 - - + +
187A SER* 3.1 30.9 + - - +
382A PHE* 4.1 17.3 - + - -
396A ALA 3.2 18.9 + - - +
399A LYS* 1.3 76.7 - - - +
401A SER* 1.3 61.2 + - - +
403A LEU* 4.0 2.2 - - + -
404A ALA* 3.0 56.7 + - + +
408A ILE* 3.6 31.2 - - + -
421A SER 4.1 15.7 - - - -
422A GLN* 4.0 13.2 - - + +
425A TYR* 3.4 42.4 - + + -
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Residues in contact with SER 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.3 32.2 - - - -
186A LEU* 3.4 27.7 - - - +
340A LEU* 4.6 0.6 - - - +
341A MET* 3.6 14.7 - - - +
344A ALA* 3.8 10.4 - - - +
347A PHE* 4.9 0.2 - - - -
348A VAL* 4.4 7.3 - - - +
397A SER 2.9 20.8 + - - -
398A ALA* 3.6 3.1 - - - -
399A LYS 3.1 1.0 - - - -
400A TRP* 1.3 77.4 - - - +
402A ILE* 1.3 56.4 + - - +
405A PRO* 3.1 19.1 - - - +
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Residues in contact with ILE 402 (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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24A LEU* 6.0 4.7 - - + -
25A PHE* 3.8 12.8 - - + -
28A PHE* 3.8 31.2 - - + -
347A PHE* 3.9 26.2 - - + -
393A ILE* 6.4 1.8 - - + -
398A ALA 3.7 9.9 - - - +
399A LYS* 3.2 19.3 - - - +
401A SER* 1.3 78.4 - - - +
403A LEU* 1.3 76.4 + - + +
404A ALA 3.2 1.3 - - - -
405A PRO* 3.1 10.6 - - - +
406A VAL* 3.2 31.9 + - + +
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Residues in contact with LEU 403 (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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382A PHE* 4.6 9.6 - - + -
385A LEU* 5.5 3.4 - - + -
386A THR* 3.5 27.6 - - - +
389A ILE* 4.3 28.3 - - + -
399A LYS* 2.9 30.5 + - + +
400A TRP* 4.0 15.5 - - + -
402A ILE* 1.3 81.0 - - + +
404A ALA* 1.3 55.4 + - - +
406A VAL* 4.5 1.8 - - + -
407A PHE* 2.8 56.6 + - + +
425A TYR* 4.0 13.2 - - + -
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Residues in contact with ALA 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 4.1 16.8 - - + +
187A SER* 4.6 0.7 - - - -
190A ALA* 3.4 6.1 - - + +
400A TRP* 3.0 60.7 + - + +
403A LEU* 1.3 73.8 - - - +
405A PRO* 1.3 64.4 - - + +
408A ILE* 2.8 35.1 + - + +
409A PRO* 3.5 0.2 - - - +
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Residues in contact with PRO 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 5.4 1.8 - - + +
190A ALA* 3.7 14.3 - - + -
193A ILE* 3.9 3.4 - - + +
347A PHE* 4.2 10.3 - - + -
348A VAL* 4.1 29.6 - - + -
351A PHE* 3.6 30.7 - - + -
357A GLY 5.6 0.2 - - - +
360A LEU* 5.5 0.2 - - - +
400A TRP 3.9 0.2 - - - +
401A SER* 3.1 26.2 - - - +
402A ILE* 3.1 17.3 - - - +
404A ALA* 1.3 89.6 - - + +
406A VAL* 1.3 55.6 + - - +
409A PRO* 3.2 20.3 - - - +
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Residues in contact with VAL 406 (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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347A PHE* 5.4 0.9 - - + -
351A PHE* 4.8 8.7 - - + -
360A LEU* 4.6 30.0 - - + +
361A ALA* 6.0 1.0 - - - -
402A ILE* 3.2 37.1 + - + +
403A LEU* 3.9 2.7 - - + +
404A ALA 3.1 0.6 - - - -
405A PRO* 1.3 81.2 - - + +
407A PHE* 1.3 91.5 + - + +
408A ILE 3.6 0.2 - - - -
409A PRO* 4.1 4.3 - - - +
410A MET* 4.4 14.1 + - - +
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Residues in contact with PHE 407 (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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382A PHE* 3.3 36.1 - + + -
385A LEU* 3.8 28.5 - - + -
403A LEU* 2.8 38.7 + - + +
406A VAL* 1.3 92.2 - - + +
408A ILE* 1.3 64.9 + - + +
409A PRO 3.5 0.4 - - - -
410A MET* 3.4 34.5 + - + +
411A LEU* 3.1 32.0 + - + +
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Residues in contact with ILE 408 (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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187A SER* 3.7 24.5 - - - +
190A ALA* 3.8 13.9 - - + -
191A ALA* 3.8 16.2 - - - +
382A PHE* 6.3 0.2 - - + -
400A TRP* 3.6 34.1 - - + -
403A LEU 4.0 0.2 + - - -
404A ALA* 2.8 23.2 + - + +
407A PHE* 1.3 75.9 - - - +
409A PRO* 1.3 68.4 - - + +
411A LEU* 3.5 4.1 + - - +
412A MET* 3.3 27.2 + - - +
418A PRO* 3.9 24.2 - - + +
421A SER* 3.7 18.7 + - - -
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Residues in contact with PRO 409 (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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190A ALA 3.9 16.6 - - - +
193A ILE* 4.0 14.8 - - + -
194A ILE* 3.9 19.2 - - + +
357A GLY 4.7 1.8 - - - +
361A ALA* 3.5 23.8 - - + -
404A ALA 3.5 4.5 - - - +
405A PRO* 3.2 27.4 - - + +
406A VAL 4.1 3.6 - - - +
407A PHE 3.8 1.8 - - - -
408A ILE* 1.3 94.0 - - + +
410A MET* 1.3 62.4 + - - +
412A MET* 3.0 15.8 + - + +
413A LEU* 3.1 14.9 + - - +
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Residues in contact with MET 410 (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 LEU* 4.8 7.9 - - - +
361A ALA* 3.5 30.2 - - - +
364A GLY* 3.7 31.0 - - - +
365A ALA* 4.0 4.9 - - - +
367A TRP* 6.4 0.2 - - + -
368A LEU* 3.6 32.8 - - + -
406A VAL* 4.4 10.2 + - - +
407A PHE* 3.4 46.0 - - + +
409A PRO* 1.3 79.3 - - - +
411A LEU* 1.3 69.2 + - + +
413A LEU* 3.2 7.4 + - - +
414A LEU* 3.2 20.4 + - - +
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Residues in contact with LEU 411 (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* 3.9 28.3 - - + -
378A LEU* 4.6 10.1 - - + +
379A LEU* 4.6 12.8 - - + -
382A PHE* 4.8 15.7 - - + -
407A PHE* 3.1 30.4 + - + +
408A ILE 3.9 2.7 - - - +
409A PRO 3.2 0.4 - - - -
410A MET* 1.3 81.8 - - + +
412A MET* 1.3 59.0 + - - +
414A LEU* 3.3 8.0 + - + +
415A GLY 3.2 3.8 + - - -
416A ILE* 2.8 49.2 + - + +
421A SER* 3.2 33.2 - - - +
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Residues in contact with MET 412 (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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50A LEU* 5.6 2.5 - - - +
191A ALA* 3.8 36.3 - - + +
194A ILE* 3.6 37.5 - - + -
195A ASP* 4.5 10.5 - - + -
198A ARG* 4.5 16.4 - - + +
408A ILE* 3.3 22.1 + - + +
409A PRO* 3.0 9.9 + - - +
411A LEU* 1.3 73.3 - - - +
413A LEU* 1.3 56.5 + - - +
414A LEU 3.0 4.3 - - - -
415A GLY* 2.5 26.5 + - - -
416A ILE 3.5 15.5 - - - +
418A PRO* 4.2 14.6 - - + -
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Residues in contact with LEU 413 (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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48A HIS* 4.6 6.7 - - + +
49A PRO* 4.6 14.1 - - + -
50A LEU* 3.8 30.4 - - + +
194A ILE* 3.7 24.2 - - + -
358A LEU* 5.6 0.4 - - + -
361A ALA* 3.3 37.7 - - + +
362A VAL* 3.8 17.9 - - + +
365A ALA* 3.7 12.7 - - + +
409A PRO 3.1 11.2 + - - +
410A MET 3.2 8.7 + - - +
412A MET* 1.3 75.6 - - - +
414A LEU* 1.3 61.7 + - - +
415A GLY 3.3 1.3 - - - -
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Residues in contact with LEU 414 (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 ALA* 4.0 18.6 - - + +
368A LEU* 4.0 23.1 - - + -
369A GLY* 4.2 14.8 - - - +
375A LYS* 2.6 48.1 + - - +
378A LEU* 3.7 29.2 - - + -
410A MET 3.2 12.2 + - - +
411A LEU* 3.3 10.9 + - + +
412A MET 3.0 1.4 - - - -
413A LEU* 1.3 80.6 - - - +
415A GLY* 1.3 57.2 + - - +
416A ILE* 3.3 7.7 + - + -
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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
------------------------------------------------------------
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