Contacts of the helix formed by residues 455 - 473 (chain A) in PDB entry 4R1Z
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 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A LEU* 6.1 0.9 - - - -
453A CYS* 3.3 8.6 - - - -
454A LEU* 1.3 78.6 - - - +
456A GLU* 1.3 65.5 + - - +
457A ALA 3.2 2.7 - - - -
458A LEU* 2.9 9.5 + - - -
459A ALA* 2.8 25.8 + - - +
600A HEM 3.6 33.8 - - - +
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Residues in contact with GLU 456 (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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446A PHE* 3.0 52.4 - - + +
452A VAL* 4.2 16.1 - - - +
453A CYS* 3.2 18.2 - - + +
454A LEU 3.3 2.2 - - - -
455A GLY* 1.3 77.2 - - - +
457A ALA* 1.3 67.4 + - - +
459A ALA* 3.3 2.1 + - - +
460A LYS* 3.1 49.0 + - + +
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Residues in contact with ALA 457 (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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142A HIS* 5.8 7.6 - - + +
145A LEU* 4.6 15.0 - - + -
358A ARG* 5.0 2.4 + - - -
454A LEU 4.6 3.9 + - - +
455A GLY 3.2 1.2 - - - -
456A GLU* 1.3 82.4 - - - +
458A LEU* 1.3 59.6 + - - +
460A LYS* 3.5 7.7 + - - +
461A MET* 3.4 29.7 + - + +
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Residues in contact with LEU 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 4.3 36.6 - - + +
155A ILE* 4.8 4.7 - - + -
159A ILE* 4.3 15.0 - - + -
191A VAL* 4.5 10.1 - - + -
192A VAL* 5.2 11.0 - - + -
195A LEU* 4.5 17.5 - - + -
310A ILE* 6.1 0.4 - - + -
314A GLY* 6.2 0.7 - - - -
455A GLY* 2.9 12.3 + - - +
457A ALA* 1.3 73.8 - - - +
459A ALA* 1.3 65.6 + - - +
460A LYS 3.1 1.6 - - - -
461A MET* 3.2 11.6 + - - +
462A GLU* 3.1 48.0 + - + +
600A HEM 5.3 14.6 - - + -
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Residues in contact with ALA 459 (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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318A THR* 4.6 10.1 - - - -
446A PHE* 3.9 13.9 - - + -
455A GLY 2.8 18.9 + - - +
456A GLU 3.6 4.3 - - - +
458A LEU* 1.3 73.7 - - - +
460A LYS* 1.3 56.3 + - - +
462A GLU* 3.9 3.3 - - - +
463A LEU* 3.0 36.8 + - + +
600A HEM 3.6 39.8 - - + +
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Residues in contact with LYS 460 (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 ARG* 4.6 17.0 + - - +
365A GLU* 4.7 19.4 - - - +
368A ILE* 5.5 4.8 - - + +
369A ARG* 5.6 8.5 - - - +
372A LEU* 5.8 4.0 - - + -
446A PHE* 3.7 28.2 - - + -
456A GLU* 3.1 40.4 + - + +
457A ALA* 3.8 7.0 - - - +
458A LEU 3.1 0.6 - - - -
459A ALA* 1.3 78.6 - - - +
461A MET* 1.3 62.9 + - - +
463A LEU* 4.0 6.2 - - + +
464A PHE* 3.1 26.3 + - - +
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Residues in contact with MET 461 (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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145A LEU* 5.7 6.3 - - + -
155A ILE* 3.9 29.4 - - + -
156A GLU 5.4 0.4 - - - -
159A ILE* 4.0 17.3 - - + -
355A LEU* 3.9 41.3 - - + -
358A ARG* 4.4 12.3 - - - +
457A ALA* 3.4 19.2 + - + +
458A LEU* 3.2 15.8 + - - +
460A LYS* 1.3 76.2 - - - +
462A GLU* 1.3 67.4 + - - +
464A PHE* 3.9 2.2 - - - +
465A LEU* 3.2 27.4 + - - +
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Residues in contact with GLU 462 (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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159A ILE* 4.0 20.6 - - + -
188A VAL* 3.7 24.8 - - - +
191A VAL* 3.9 15.1 - - + +
192A VAL* 5.5 2.3 - - - +
314A GLY* 4.7 4.0 - - - +
318A THR* 3.3 36.4 + - + +
458A LEU* 3.1 40.3 + - + +
459A ALA 3.9 0.4 - - - +
461A MET* 1.3 79.3 - - - +
463A LEU* 1.3 66.9 + - - +
464A PHE 3.0 0.9 + - - -
465A LEU* 3.7 0.2 - - - -
466A PHE* 2.8 46.9 + - + -
600A HEM 5.0 1.4 - - - +
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Residues in contact with LEU 463 (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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318A THR* 4.1 13.9 - - + +
321A VAL* 3.6 35.4 - - + -
322A LEU* 3.4 35.4 - - + -
325A SER* 5.3 1.8 - - - +
368A ILE* 4.1 27.1 - - + -
372A LEU* 4.8 7.6 - - + -
446A PHE* 5.6 1.6 - - + -
459A ALA* 3.0 26.5 + - + +
460A LYS* 4.0 4.9 - - - +
462A GLU* 1.3 77.9 - - - +
464A PHE* 1.3 61.6 + - - +
467A LEU* 3.2 33.3 + - + +
600A HEM 4.6 11.2 - - + -
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Residues in contact with PHE 464 (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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353A PRO* 4.9 3.4 - - + -
354A GLN 3.5 26.0 - - - -
355A LEU* 4.5 2.7 - - + -
357A ASP* 4.3 1.1 - - + -
358A ARG* 3.6 48.0 - - + -
361A LEU* 3.4 38.8 - - + -
364A LEU* 3.5 24.9 - - + +
365A GLU* 4.6 12.1 - - + +
368A ILE* 3.9 10.7 - - + +
460A LYS 3.1 19.1 + - - +
461A MET 3.9 1.8 - - - +
463A LEU* 1.3 77.3 - - - +
465A LEU* 1.3 77.6 + - + +
467A LEU 3.8 0.2 - - - -
468A ALA* 2.8 36.7 + - + +
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Residues in contact with LEU 465 (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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156A GLU* 4.6 6.3 - - - +
159A ILE* 3.5 39.9 - - + +
160A CYS* 3.9 14.6 - - - -
163A ALA* 5.0 0.7 - - + -
353A PRO* 3.7 13.9 - - + +
354A GLN 4.1 3.1 - - - -
355A LEU* 3.5 37.7 - - + +
461A MET 3.2 9.8 + - - +
462A GLU 3.1 1.6 + - - -
464A PHE* 1.3 90.2 - - + +
466A PHE* 1.3 58.5 + - - +
468A ALA* 4.4 1.6 - - - -
469A TRP* 2.8 60.4 + - + +
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Residues in contact with PHE 466 (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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159A ILE* 4.1 13.9 - - + -
162A GLU* 4.1 17.3 - - + -
163A ALA* 4.0 30.9 - - + +
166A MET* 4.6 8.7 - - + -
184A LEU* 5.2 5.8 - - + -
187A ALA* 3.9 32.5 - - + -
188A VAL* 4.3 6.7 - - + -
191A VAL* 4.2 5.6 - - + -
322A LEU* 4.2 29.6 - - + -
462A GLU* 2.8 53.2 + - + +
465A LEU* 1.3 80.0 - - - +
467A LEU* 1.3 63.1 + - - +
469A TRP* 3.9 1.2 - - - +
470A ILE* 3.2 33.8 + - + +
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Residues in contact with LEU 467 (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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322A LEU* 3.8 21.3 - - + -
325A SER* 4.0 29.8 - - - +
326A ILE* 4.7 12.8 - - + -
329A LEU* 4.4 16.2 - - + -
339A ILE* 6.3 0.2 - - + -
364A LEU* 4.3 15.7 - - + -
367A THR* 5.9 4.0 - - + -
368A ILE* 3.8 23.8 - - + -
371A VAL* 6.1 0.2 - - + -
463A LEU* 3.2 21.3 + - + +
464A PHE 4.0 1.3 - - - +
466A PHE* 1.3 77.0 - - - +
468A ALA* 1.3 59.4 + - - +
470A ILE* 3.5 7.9 + - + +
471A LEU* 2.9 41.2 + - + +
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Residues in contact with ALA 468 (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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339A ILE* 6.0 0.2 - - - -
343A LEU* 3.8 17.8 - - + +
353A PRO* 3.7 25.9 - - + +
364A LEU* 3.9 18.7 - - + +
464A PHE* 2.8 26.8 + - + +
465A LEU* 3.8 2.2 - - - +
467A LEU* 1.3 77.0 - - - +
469A TRP* 1.3 63.1 + - - +
471A LEU* 5.0 0.4 - - - -
472A GLN* 3.1 27.7 + - - +
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Residues in contact with TRP 469 (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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160A CYS* 3.8 35.4 - - + -
163A ALA* 3.7 18.8 - - + -
164A SER* 3.9 34.1 - - - -
167A CYS* 3.7 6.4 - - - -
352A HIS* 3.3 46.7 - + + -
353A PRO* 3.1 38.4 + - + -
465A LEU* 2.8 49.0 + - + +
466A PHE 3.9 2.0 - - - +
468A ALA* 1.3 73.2 - - - +
470A ILE* 1.3 62.0 + - - +
472A GLN* 3.9 2.5 + - - +
473A ARG* 3.6 43.0 + - - -
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Residues in contact with ILE 470 (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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163A ALA* 6.3 0.7 - - + -
166A MET* 4.8 21.3 - - + -
167A CYS* 4.3 12.1 - - - -
170A LEU* 4.2 26.5 - - + -
180A LEU* 6.1 3.8 - - + -
184A LEU* 4.9 9.6 - - + -
322A LEU* 6.3 0.4 - - + -
326A ILE* 5.2 9.6 - - + -
466A PHE* 3.2 26.5 + - + +
467A LEU* 3.9 13.0 - - + +
469A TRP* 1.3 78.2 - - + +
471A LEU* 1.3 66.4 + - + +
473A ARG 3.0 3.1 + - - -
474A PHE* 2.7 38.3 + - + -
476A LEU* 4.6 18.8 - - + -
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Residues in contact with LEU 471 (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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329A LEU* 4.0 23.8 - - + -
336A GLN* 3.6 31.6 - - + +
339A ILE* 3.7 36.8 - - + -
340A GLN* 3.1 30.6 - - + +
343A LEU* 3.9 13.9 - - + -
364A LEU* 5.0 0.4 - - + -
467A LEU* 2.9 31.7 + - + +
470A ILE* 1.3 86.7 - - + +
472A GLN* 1.3 60.7 + - - +
473A ARG 3.2 0.2 - - - -
474A PHE 3.3 13.4 - - - +
476A LEU* 4.8 7.9 - - + -
507A ARG* 3.4 2.1 + - - -
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Residues in contact with GLN 472 (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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343A LEU* 3.6 18.5 - - + +
344A ASP* 5.4 1.8 - - - +
347A ILE* 3.5 21.4 - - - +
348A GLY 3.9 9.0 + - - +
351A ARG 2.9 24.0 + - - -
352A HIS* 3.3 24.6 + - - +
353A PRO* 3.7 13.9 - - + +
468A ALA 3.1 17.1 + - - +
469A TRP* 3.9 4.5 - - - +
471A LEU* 1.3 79.3 - - - +
473A ARG* 1.3 64.1 + - - +
507A ARG* 3.1 21.5 + - - +
510A TRP* 3.3 32.6 + - + +
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Residues in contact with ARG 473 (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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164A SER* 4.6 8.5 + - - +
167A CYS* 3.0 34.9 - - - +
352A HIS* 3.7 22.9 + - - -
469A TRP* 3.6 30.9 + - - -
470A ILE 3.0 2.8 + - - +
472A GLN* 1.3 89.1 - - - +
474A PHE* 1.3 85.1 + - + +
506A VAL* 3.6 3.8 - - - +
507A ARG* 3.0 26.7 + - - +
510A TRP* 3.7 46.1 - - + +
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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