Contacts of the helix formed by residues 435 - 452 (chain B) in PDB entry 4HXG
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 LEU 435 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B GLU 4.5 2.9 - - - +
432B ARG* 2.9 56.6 + - - +
433B THR 4.1 2.7 - - - +
434B GLY* 1.3 85.1 - - - +
436B GLU* 1.3 74.9 + - - +
437B ASP* 3.2 2.2 + - - -
438B PHE* 3.7 3.2 + - - +
439B GLN* 3.0 31.4 + - - +
474B TRP* 5.0 4.7 - - + -
525B LEU* 4.0 22.2 - - + -
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Residues in contact with GLU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ILE* 4.3 16.6 - - + +
416B ARG* 3.4 35.9 - - - +
432B ARG* 2.8 53.8 + - + +
435B LEU* 1.3 82.5 - - - +
437B ASP* 1.3 55.4 + - - +
439B GLN* 2.7 12.6 + - + +
440B ASP* 2.7 39.1 + - - +
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Residues in contact with ASP 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B PRO* 3.7 9.6 - - + +
416B ARG* 3.7 27.4 - - + +
429B VAL* 3.8 12.5 - - + +
432B ARG* 3.7 3.2 - - - +
434B GLY 3.1 19.2 + - - -
435B LEU 3.2 5.2 + - - -
436B GLU* 1.3 74.8 - - - +
438B PHE* 1.3 65.1 + - - -
440B ASP* 3.3 14.3 + - - +
441B ILE* 3.1 27.0 + - - +
467B TYR* 2.7 31.2 + - - -
471B MET* 3.3 15.5 - - + +
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Residues in contact with PHE 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B GLY 3.6 22.2 - - - +
435B LEU 3.7 1.1 + - - +
436B GLU 3.1 0.2 - - - -
437B ASP* 1.3 81.3 + - - +
439B GLN* 1.3 73.4 + - - +
441B ILE* 3.1 12.7 + - + +
442B LEU* 3.0 55.5 + - + +
471B MET* 3.9 25.8 - - + -
474B TRP* 3.6 17.9 - + + -
475B ALA* 3.8 34.5 - - + -
478B GLN* 3.6 26.7 - - + -
479B SER* 4.3 9.6 - - - -
482B PHE* 4.7 2.0 - + - -
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Residues in contact with GLN 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B SER* 3.8 2.0 - - - -
359B ILE* 4.5 16.2 - - + -
435B LEU 3.0 21.2 + - - +
436B GLU* 2.7 18.7 + - - +
438B PHE* 1.3 79.1 - - - +
440B ASP* 1.3 63.5 + - - +
442B LEU* 3.2 26.4 + - - +
443B ASN* 2.9 39.1 + - - +
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Residues in contact with ASP 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B PHE* 3.2 12.3 - - + -
358B SER* 2.7 20.4 + - - -
359B ILE* 5.1 0.5 - - - +
363B LEU* 3.3 24.0 - - + +
413B VAL* 4.9 0.9 - - - -
415B PRO* 3.8 9.9 - - + -
416B ARG* 2.8 58.1 + - - +
436B GLU 2.7 17.7 + - - +
437B ASP* 3.4 8.9 - - - +
439B GLN* 1.3 72.3 - - - +
441B ILE* 1.3 63.6 + - - +
444B GLY 2.9 20.1 + - - -
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Residues in contact with ILE 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B VAL* 4.6 14.8 - - + -
384B VAL* 3.8 21.3 - - + -
413B VAL* 4.0 24.4 - - + +
415B PRO* 4.4 11.7 - - + -
437B ASP 3.1 14.7 + - - +
438B PHE* 3.1 17.7 + - + +
440B ASP* 1.3 81.1 - - - +
442B LEU* 1.3 63.9 + - + +
444B GLY* 3.3 1.7 + - - -
445B ILE* 3.1 36.9 + - + +
462B ILE* 4.9 7.4 - - + -
471B MET* 3.5 38.6 - - + -
482B PHE* 5.3 0.9 - - + -
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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
----------------------------------------------------------
438B PHE* 3.0 54.1 + - + +
439B GLN* 3.6 29.6 - - - +
441B ILE* 1.3 76.0 - - + +
443B ASN* 1.3 61.8 + - - +
445B ILE* 2.9 24.0 + - + +
446B GLU* 3.1 12.9 + - - +
479B SER* 4.6 8.5 - - - +
481B LEU* 4.4 14.9 - - + +
482B PHE* 4.3 20.4 - - + -
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Residues in contact with ASN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B PHE* 3.7 3.6 - - + -
357B LYS 4.0 14.8 + - - +
358B SER* 2.6 38.9 + - - +
359B ILE* 4.1 7.7 - - - +
439B GLN* 2.9 27.4 + - - +
440B ASP 3.8 1.1 - - - +
442B LEU* 1.3 77.9 - - - +
444B GLY* 1.3 62.4 + - - +
446B GLU* 3.3 9.0 + - - +
447B GLU* 3.0 24.8 + - - +
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Residues in contact with GLY 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B PHE* 3.7 9.1 - - - -
356B PHE* 3.2 33.7 - - - -
411B VAL* 4.8 2.0 - - - +
413B VAL* 4.3 8.1 - - - -
440B ASP 2.9 12.3 + - - -
441B ILE 3.3 2.4 + - - -
442B LEU 3.2 0.4 - - - -
443B ASN* 1.3 76.3 - - - +
445B ILE* 1.3 57.9 + - - +
447B GLU 3.7 0.2 + - - -
448B PHE* 3.0 27.7 + - - +
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B VAL* 6.0 0.4 - - + -
382B VAL* 3.8 23.3 - - + -
411B VAL* 5.2 6.5 - - + -
441B ILE* 3.1 23.8 - - + +
442B LEU* 2.9 11.7 + - - +
444B GLY* 1.3 75.1 - - - +
446B GLU* 1.3 56.0 + - - +
448B PHE* 3.0 12.5 + - + +
449B LEU* 2.7 54.6 + - + +
460B ILE* 4.4 9.4 - - + -
481B LEU* 4.3 18.2 - - + -
482B PHE* 3.7 35.9 - - + -
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Residues in contact with GLU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B LEU 3.1 11.3 + - - +
443B ASN* 3.7 11.7 - - - +
445B ILE* 1.3 76.3 - - - +
447B GLU* 1.3 61.7 + - - +
449B LEU* 3.2 11.3 + - - +
450B ARG* 3.0 23.0 + - - +
457B ARG* 5.4 1.5 + - - +
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Residues in contact with GLU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B PHE* 4.0 9.9 - - + -
355B ARG 3.8 13.5 - - - +
356B PHE* 3.5 35.2 - - + -
443B ASN 3.0 11.8 + - - +
444B GLY 4.0 2.5 - - - +
446B GLU* 1.3 75.4 - - - +
448B PHE* 1.3 62.8 + - - +
450B ARG* 2.9 43.8 + - - +
451B LEU* 3.1 29.8 + - + +
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Residues in contact with PHE 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B PHE* 3.9 14.8 - - + -
367B TYR* 3.5 48.2 - + + -
380B VAL* 3.9 19.5 - - + -
409B TYR* 3.5 37.5 - + + -
411B VAL* 4.1 19.3 - - + -
444B GLY 3.0 19.8 + - - +
445B ILE* 3.0 8.9 + - + +
447B GLU* 1.3 77.4 - - - +
449B LEU* 1.3 70.9 + - + +
451B LEU* 3.2 8.5 + - - +
452B GLU* 3.1 23.9 + - + +
455B ALA* 3.9 23.3 - - + -
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B VAL* 4.9 0.9 - - + -
445B ILE* 2.7 38.9 + - + +
446B GLU* 3.2 9.6 + - - +
448B PHE* 1.3 81.5 - - + +
450B ARG* 1.3 62.8 + - - +
452B GLU 3.2 19.3 - - - +
453B PRO* 3.8 2.1 - - - +
455B ALA* 3.8 26.7 - - + +
457B ARG* 3.6 56.8 + - + +
460B ILE* 4.2 23.6 - - + -
481B LEU* 5.5 5.4 - - + -
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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
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446B GLU 3.0 12.9 + - - +
447B GLU* 2.9 43.6 + - - +
449B LEU* 1.3 79.6 - - - +
451B LEU* 1.3 83.7 + - - +
452B GLU 3.1 1.4 + - - -
453B PRO* 3.9 9.9 - - - +
457B ARG* 4.9 6.0 - - - +
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B PHE* 3.8 38.4 - - + -
355B ARG 5.7 0.2 - - - +
367B TYR* 4.3 15.2 + - + +
447B GLU* 3.1 22.2 + - - +
448B PHE* 3.2 7.1 + - - +
450B ARG* 1.3 108.5 - - - +
452B GLU* 1.3 72.4 + - + +
453B PRO* 3.6 6.8 - - - +
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Residues in contact with GLU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B TYR* 2.8 46.6 + - + +
369B LYS* 3.4 19.9 + - - +
409B TYR* 2.7 36.1 + - + +
448B PHE* 3.1 22.8 + - + +
449B LEU 3.2 11.8 - - - +
450B ARG 3.1 0.2 + - - -
451B LEU* 1.3 84.5 - - - +
453B PRO* 1.3 65.4 - - - +
454B GLN* 3.0 7.8 - - - +
455B ALA* 3.1 17.2 + - - +
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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