Contacts of the helix formed by residues 427 - 450 (chain B) in PDB entry 4U7C
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 LYS 427 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ARG* 4.1 18.3 - - - +
119A ASP* 5.2 2.2 + - - -
180A GLU* 4.2 8.1 - - - +
303A GLN 5.3 1.3 - - - -
304A LYS* 3.4 32.5 - - - +
305A THR 4.1 5.4 - - - -
306A THR* 3.3 24.4 + - - -
426B ASN* 1.3 84.3 - - + +
428B ALA* 1.3 67.0 + - - +
429B GLU 3.3 2.0 - - - +
430B GLU* 3.1 46.7 + - + +
431B GLN* 3.1 13.8 + - - +
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ASN 3.4 4.8 + - - -
427B LYS* 1.3 71.5 - - - +
429B GLU* 1.3 57.7 + - - +
431B GLN* 3.1 15.8 + - - +
432B TYR* 2.9 41.8 + - + -
496B ILE* 3.7 26.5 - - + -
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Residues in contact with GLU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS* 4.4 6.1 - - - +
180A GLU* 3.4 31.9 - - + +
183A GLU* 2.8 38.8 - - - +
304A LYS* 3.1 29.5 + - - +
427B LYS* 3.3 1.2 - - - +
428B ALA* 1.3 78.8 - - - +
430B GLU* 1.3 56.9 + - - +
432B TYR* 3.4 11.9 + - + +
433B SER* 2.9 36.4 + - - +
605B PEG 6.0 4.7 - - - -
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Residues in contact with GLU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ARG* 2.8 45.5 + - - -
173A LYS* 5.6 2.3 - - - -
176A ALA* 4.0 24.0 - - + +
177A VAL* 3.3 6.5 - - + +
180A GLU* 3.0 30.3 - - - +
425B ILE* 3.8 23.9 - - + +
426B ASN 4.8 1.4 + - - -
427B LYS* 3.1 27.2 + - + +
429B GLU* 1.3 75.1 - - - +
431B GLN* 1.3 60.0 + - - +
433B SER* 3.2 2.6 + - - -
434B LEU* 2.9 30.7 + - - +
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Residues in contact with GLN 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ILE* 2.9 27.2 + - + -
426B ASN 3.6 7.0 + - - +
427B LYS 3.1 10.8 + - - +
428B ALA* 3.1 10.7 + - - +
430B GLU* 1.3 73.2 - - - +
432B TYR* 1.3 64.8 + - - +
434B LEU* 3.4 7.1 + - - +
435B CYS* 2.9 23.0 + - - +
492B LEU* 3.7 17.0 - - + +
496B ILE* 3.2 26.4 - - + +
504B LEU* 2.8 44.1 + - - +
506B LEU* 3.9 20.1 - - + +
509B MET* 3.9 4.7 - - - +
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Residues in contact with TYR 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B ALA* 2.9 36.9 + - + -
429B GLU* 3.6 9.9 - - + +
430B GLU 3.3 0.2 - - - -
431B GLN* 1.3 74.3 - - - +
433B SER* 1.3 59.1 + - - +
435B CYS* 3.1 5.9 + - - +
436B GLN* 2.9 23.9 + - - +
485B PHE* 3.4 11.2 - + + -
489B LYS* 3.6 35.2 - - + -
492B LEU* 4.0 12.1 - - + +
493B LYS* 3.1 41.8 - - + +
496B ILE* 4.1 22.8 - - + +
605B PEG 3.6 49.2 + - - -
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Residues in contact with SER 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA* 3.6 23.4 + - - +
179A LYS* 3.2 31.0 - - - +
180A GLU* 5.9 0.3 - - - +
429B GLU* 2.9 19.9 + - - +
430B GLU 3.2 5.4 + - - -
432B TYR* 1.3 74.9 - - - +
434B LEU* 1.3 65.0 + - - +
436B GLN* 3.0 13.7 + - - +
437B GLU* 2.9 35.4 + - - +
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 4.1 21.8 - - + +
173A LYS* 4.1 24.2 - - + +
176A ALA* 4.8 2.2 - - + +
420B ARG* 5.2 3.6 - - + -
422B PHE* 3.4 29.6 - - + -
425B ILE* 3.5 30.7 - - + -
430B GLU 2.9 16.3 + - - +
431B GLN* 3.6 7.2 - - - +
433B SER* 1.3 75.5 - - - +
435B CYS* 1.3 63.6 + - - +
437B GLU* 3.1 9.6 + - - +
438B LEU* 2.9 46.0 + - + +
509B MET* 4.3 7.6 - - + -
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Residues in contact with CYS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B GLN 2.9 8.9 + - - +
432B TYR* 3.2 13.2 - - + +
434B LEU* 1.3 76.2 - - - +
436B GLN* 1.3 56.6 + - - +
438B LEU* 3.4 5.3 + - - +
439B CYS* 2.9 35.7 + - - -
458B ILE* 5.0 1.3 - - - -
485B PHE* 3.9 12.6 - - + -
488B ALA* 3.5 40.2 - - - -
489B LYS* 4.4 0.4 - - - -
492B LEU* 4.2 5.2 - - + -
509B MET* 3.4 30.1 - - + +
511B VAL* 4.3 5.6 - - - -
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Residues in contact with GLN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS* 4.1 16.3 + - - +
432B TYR 2.9 10.9 + - - +
433B SER* 3.0 15.3 + - - +
435B CYS* 1.3 77.5 - - - +
437B GLU* 1.3 57.9 + - + +
439B CYS* 3.4 2.5 + - - +
440B SER* 2.9 35.2 + - - +
481B ALA* 5.3 0.9 - - + +
485B PHE* 3.5 41.3 - - + -
605B PEG 3.9 9.7 + - - -
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 3.1 49.1 - - - +
175A ARG* 3.6 42.8 - - - +
176A ALA* 4.4 2.3 + - - -
179A LYS* 6.1 0.3 - - - +
433B SER* 2.9 36.8 + - - +
434B LEU* 3.1 9.1 + - + +
436B GLN* 1.3 76.9 - - + +
438B LEU* 1.3 64.8 + - + +
440B SER* 2.9 18.6 + - - -
441B GLU* 2.9 19.5 + - - +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 5.8 1.1 - - - +
418B VAL* 3.6 36.1 - - + +
420B ARG* 4.6 18.2 - - + +
434B LEU* 2.9 29.7 + - + +
435B CYS* 3.8 4.0 - - - +
437B GLU* 1.3 75.6 - - + +
439B CYS* 1.3 64.5 + - - +
441B GLU* 3.2 15.0 + - - +
442B LEU* 2.9 24.5 + - - +
509B MET* 3.5 46.4 - - + +
510B GLY* 4.0 9.2 - - - -
511B VAL* 4.0 15.5 - - + +
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Residues in contact with CYS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B CYS 2.9 27.2 + - - +
436B GLN 3.6 4.9 - - - +
438B LEU* 1.3 75.9 - - - +
440B SER* 1.3 56.7 + - - +
442B LEU* 3.3 7.1 + - - +
443B ALA* 2.9 31.2 + - - +
481B ALA* 4.1 7.2 - - + +
484B ILE* 3.7 21.2 - - + +
485B PHE* 3.6 42.0 - - + +
488B ALA* 3.9 15.9 - - - -
511B VAL* 4.1 9.6 - - - +
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Residues in contact with SER 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B GLN* 2.9 22.1 + - - +
437B GLU* 2.9 13.2 + - - -
439B CYS* 1.3 75.7 - - - +
441B GLU* 1.3 65.4 + - - +
443B ALA* 3.1 5.2 + - - +
444B GLN* 2.9 24.6 + - - +
481B ALA* 3.8 18.9 - - - +
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASP* 3.9 8.0 - - - +
175A ARG* 5.3 3.8 + - - +
418B VAL* 3.4 20.0 - - + +
420B ARG* 2.7 46.4 + - - -
437B GLU* 2.9 17.4 + - + +
438B LEU* 3.7 10.0 - - - +
440B SER* 1.3 73.3 - - - +
442B LEU* 1.3 59.2 + - - +
444B GLN* 3.1 11.5 + - - +
445B ASP* 2.9 34.1 + - - +
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Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B MET* 3.7 32.1 - - + +
417B SER* 3.8 15.9 - - - +
418B VAL* 4.0 14.1 - - + +
438B LEU 2.9 16.6 + - - +
439B CYS* 3.6 6.1 - - - +
441B GLU* 1.3 75.0 - - - +
443B ALA* 1.3 65.3 + - - +
445B ASP* 3.1 4.9 + - - +
446B LEU* 2.9 28.9 + - + +
484B ILE* 4.3 11.7 - - + -
511B VAL* 3.9 29.4 - - + +
513B ILE* 3.7 35.0 - - + +
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Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B CYS 2.9 16.0 + - - +
440B SER 3.5 5.2 - - - +
442B LEU* 1.3 75.1 - - - +
444B GLN* 1.3 56.6 + - - +
446B LEU* 3.6 3.5 - - - +
447B GLN* 2.9 28.5 + - - +
479B SER* 3.5 19.6 + - - +
480B THR* 3.8 1.6 - - - -
481B ALA* 3.4 33.4 - - + +
484B ILE* 4.1 5.5 - - + +
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Residues in contact with GLN 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLN* 2.8 32.4 - - - +
447A GLN* 4.2 5.5 + - - +
448A LYS* 3.1 59.7 + - + +
440B SER 2.9 14.3 + - - +
441B GLU* 3.1 14.1 - - - +
442B LEU 3.1 0.2 - - - -
443B ALA* 1.3 74.5 - - - +
445B ASP* 1.3 64.5 + - - +
447B GLN* 3.1 23.8 - - - +
448B LYS* 2.9 26.7 + - - +
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Residues in contact with ASP 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B MET* 3.4 25.3 - - - +
418B VAL* 3.9 19.1 - - - +
441B GLU* 2.9 16.1 + - - +
442B LEU* 3.1 4.9 + - - +
444B GLN* 1.3 74.0 - - - +
446B LEU* 1.3 66.8 + - - +
448B LYS* 2.9 41.5 + - - +
449B GLU* 3.0 14.9 + - - +
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B MET* 3.9 20.4 - - + -
442B LEU* 2.9 18.4 + - + +
443B ALA 3.6 4.5 - - - +
445B ASP* 1.3 74.8 - - - +
447B GLN* 1.3 51.6 + - - +
449B GLU 3.1 2.3 + - - -
450B ARG 2.6 32.1 + - - -
451B LEU* 2.9 43.9 + - + +
479B SER* 3.8 24.7 - - - +
484B ILE* 3.9 14.4 - - + -
513B ILE* 3.8 42.6 - - + -
516B PHE* 4.3 7.0 - - + -
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Residues in contact with GLN 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLN* 4.4 5.5 - - - +
447A GLN* 3.1 47.0 + - + +
450A ARG* 4.7 2.8 + - - -
443B ALA 2.9 15.8 + - - +
444B GLN* 3.1 25.4 - - - +
446B LEU* 1.3 74.4 - - - +
448B LYS* 1.3 66.7 + - - +
450B ARG* 3.0 20.3 + - - +
479B SER* 5.4 3.1 + - - -
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Residues in contact with LYS 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLN* 2.8 55.5 + - + +
444B GLN* 2.9 8.5 + - - +
445B ASP* 2.9 41.8 + - - +
447B GLN* 1.3 80.6 - - - +
449B GLU* 1.3 62.1 + - + +
450B ARG* 3.7 4.0 + - - +
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Residues in contact with GLU 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ARG* 2.9 35.8 + - - -
416B MET* 3.8 3.0 - - + +
445B ASP 3.0 13.9 + - - +
446B LEU 4.2 0.2 - - - +
448B LYS* 1.3 81.5 - - + +
450B ARG* 1.3 71.0 + - - +
451B LEU* 3.1 37.6 + - + +
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Residues in contact with ARG 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LEU 2.6 13.1 + - - -
447B GLN* 3.0 16.4 + - - +
448B LYS 4.6 3.4 - - - +
449B GLU* 1.3 75.0 - - - +
451B LEU* 1.3 59.9 + - - +
452B LYS* 4.1 6.3 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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