Contacts of the helix formed by residues 435 - 452 (chain B) in PDB entry 2HIW
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 435 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B ILE* 3.6 19.5 - - - +
433B LYS* 3.0 30.0 + - - -
434B PHE* 1.3 76.0 - - - +
436B ILE* 1.3 60.6 + - - +
437B LYS* 2.9 21.4 + - - +
438B SER* 2.6 31.3 + - - -
439B ASP* 3.3 11.1 + - - +
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Residues in contact with ILE 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B MET* 4.1 4.3 - - + +
373B GLU* 3.4 60.8 - - + +
376B ASN* 5.8 1.3 - - - -
377B PHE 3.8 19.5 - - - +
378B ILE* 3.8 4.5 - - + +
435B SER* 1.3 75.7 - - - +
437B LYS* 1.3 72.2 + - + +
439B ASP* 3.4 13.0 - - + +
440B VAL* 2.9 32.1 + - + +
503B SER* 5.7 0.2 - - - -
504B PHE* 3.4 25.4 - - + -
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Residues in contact with LYS 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LYS* 5.3 0.2 - - - +
435B SER* 2.9 10.6 + - - +
436B ILE* 1.3 86.1 - - + +
438B SER* 1.3 55.5 + - - +
440B VAL* 3.4 6.4 + - + +
441B TRP 3.1 15.9 + - - -
498B PRO* 3.0 41.5 - - + +
499B SER* 4.7 8.5 + - - +
501B ARG* 2.3 61.1 + - + +
502B PRO* 3.0 21.9 + - - +
503B SER* 3.6 11.7 - - - +
506B GLU* 5.1 1.0 + - - -
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Residues in contact with SER 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ILE* 4.6 0.9 - - - +
380B ARG* 5.6 0.3 - - - -
423B TRP 4.7 1.4 - - - +
425B ALA* 4.0 15.5 + - - +
427B GLU* 4.1 4.4 + - - -
428B SER* 3.5 24.9 - - - -
433B LYS 4.2 1.3 - - - -
434B PHE* 3.7 12.7 - - - +
435B SER* 2.6 37.9 + - - -
437B LYS* 1.3 73.6 - - - +
439B ASP* 1.3 62.0 + - - +
441B TRP* 3.4 4.7 + - - +
442B ALA* 3.1 26.0 + - - +
501B ARG* 3.9 1.3 - - - +
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Residues in contact with ASP 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B MET* 4.2 6.1 - - + +
377B PHE 4.3 0.2 - - - +
378B ILE* 3.4 9.2 - - - -
379B HIS* 3.0 30.0 + - - +
380B ARG* 2.9 29.4 + - - -
381B ASP 4.6 0.3 + - - -
382B LEU* 3.9 7.7 + - + +
435B SER 3.3 14.2 + - - +
436B ILE* 3.4 17.6 - - - +
438B SER* 1.3 83.6 + - - +
440B VAL* 1.3 52.5 + - - +
442B ALA* 3.2 7.7 + - - +
443B PHE* 2.7 34.0 + - - +
504B PHE* 3.5 15.9 - - + -
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Residues in contact with VAL 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ILE* 2.9 31.3 + - + +
437B LYS* 3.6 13.5 - - + +
438B SER 3.2 0.6 - - - -
439B ASP* 1.3 73.4 - - - +
441B TRP* 1.3 66.6 + - - +
443B PHE* 3.4 2.3 + - - +
444B GLY 3.1 15.6 + - - -
493B CYS* 3.3 22.8 - - - +
501B ARG* 4.1 7.6 - - + -
502B PRO* 3.5 27.8 - - + +
504B PHE* 3.4 31.2 - - + +
507B ILE* 3.7 19.7 - - + -
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Residues in contact with TRP 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B LYS 4.7 1.6 + - - -
423B TRP 3.4 20.5 + - - -
424B THR 3.8 8.3 + - - -
425B ALA* 3.6 17.3 - - + -
426B PRO* 3.5 33.9 - - + -
437B LYS 3.1 8.3 + - - -
438B SER 3.5 9.0 - - - +
440B VAL* 1.3 73.7 - - - +
442B ALA* 1.3 57.8 + - - +
444B GLY* 2.9 19.6 + - - -
445B VAL* 3.2 24.2 + - + +
458B TYR* 3.8 9.0 + - - -
470B LEU* 3.7 30.5 - - + +
475B ARG* 3.8 20.2 - - - -
493B CYS 3.4 11.5 + - - -
494B TRP* 3.2 49.9 + + + -
495B GLN 3.7 6.5 - - - -
501B ARG* 3.8 17.5 - - - +
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Residues in contact with ALA 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ARG 6.4 0.4 - - - -
382B LEU* 3.6 35.9 - - + +
423B TRP* 3.6 22.0 - - + +
438B SER 3.1 11.8 + - - +
439B ASP* 3.5 11.0 - - - +
440B VAL 3.2 0.2 - - - -
441B TRP* 1.3 79.6 - - - +
443B PHE* 1.3 62.3 + - - +
445B VAL* 3.1 8.0 + - - +
446B LEU* 3.0 21.1 + - - +
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Residues in contact with PHE 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ALA* 3.9 15.5 - - + -
365B ILE* 3.2 36.1 - - + -
366B SER* 3.9 10.5 - - - -
382B LEU* 3.7 11.6 - - + +
439B ASP 2.7 19.5 + - - +
440B VAL 3.6 4.3 - - - +
442B ALA* 1.3 72.2 - - - +
444B GLY* 1.3 59.9 + - - +
446B LEU* 3.1 8.1 + - + +
447B LEU* 2.8 61.5 + - + +
450B ILE* 6.5 0.7 - - + -
489B LEU* 5.9 0.2 - - + -
493B CYS* 4.1 13.7 - - - -
504B PHE* 3.5 23.6 - + + -
507B ILE* 3.6 31.4 - - + -
511B PHE* 4.0 3.8 - + - -
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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
----------------------------------------------------------
440B VAL 3.1 6.9 + - - -
441B TRP 2.9 9.7 + - - -
443B PHE* 1.3 78.2 - - - +
445B VAL* 1.3 58.4 + - - +
447B LEU* 3.4 6.7 - - - +
448B TRP 3.3 13.3 + - - -
490B MET* 3.3 10.7 - - - +
493B CYS* 3.7 20.2 - - - -
494B TRP* 3.2 25.5 - - - -
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Residues in contact with VAL 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B LYS 3.5 27.1 - - - +
423B TRP* 3.7 26.5 - - + +
441B TRP* 3.6 23.3 - - + +
442B ALA* 3.1 6.6 + - - +
444B GLY* 1.3 72.3 - - - +
446B LEU* 1.3 61.7 + - - +
448B TRP* 2.9 19.6 + - - +
449B GLU* 2.9 16.9 + - - +
457B PRO* 3.8 22.7 - - + -
458B TYR* 5.0 1.6 - - - +
476B MET* 4.2 7.6 - - + -
494B TRP* 3.5 23.1 - - + +
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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
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341B LEU* 3.8 13.0 - - + -
365B ILE* 3.9 19.7 - - + -
382B LEU* 3.7 33.0 - - + -
383B ALA* 4.3 4.5 - - - -
384B ALA* 3.2 40.2 - - + +
387B CYS* 3.8 14.4 - - - -
423B TRP* 4.6 0.6 - - - +
442B ALA 3.0 12.4 + - - +
443B PHE* 3.1 11.4 + - + +
445B VAL* 1.3 76.4 - - - +
447B LEU* 1.3 56.0 + - - +
449B GLU* 3.3 9.2 + - - +
450B ILE* 3.0 44.6 + - + +
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Residues in contact with LEU 447 (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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362B ALA* 3.7 19.5 - - + -
443B PHE* 2.8 38.1 + - + +
444B GLY* 3.4 11.2 - - - +
445B VAL 3.2 0.2 - - - -
446B LEU* 1.3 71.8 - - - +
448B TRP* 1.3 57.8 + - - +
450B ILE* 3.9 9.9 - - + +
451B ALA* 3.1 27.5 + - - +
486B VAL* 4.3 11.0 - - + +
489B LEU* 4.5 3.4 - - + -
490B MET* 3.8 40.1 - - + +
493B CYS* 5.1 0.2 - - - -
511B PHE* 3.4 39.5 - - + -
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Residues in contact with TRP 448 (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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444B GLY 3.3 8.1 + - - +
445B VAL 2.9 10.9 + - - +
447B LEU* 1.3 78.4 - - - +
449B GLU* 1.3 64.0 + - - +
451B ALA* 3.1 2.9 + - - +
452B THR* 2.9 48.6 + - + +
455B MET* 3.6 34.5 - - + -
456B SER 3.5 28.5 - - - -
457B PRO* 3.7 8.7 - - + -
459B PRO* 3.7 22.2 - - + -
476B MET* 3.3 35.0 - - + +
477B GLU 3.4 21.4 + - - -
479B PRO* 3.7 16.1 - - + +
490B MET* 3.9 18.6 - - - -
494B TRP* 3.9 11.0 - + + -
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Residues in contact with GLU 449 (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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342B LEU* 3.6 15.6 - - - +
345B LEU* 3.7 2.3 - - - +
384B ALA* 3.1 41.5 + - + +
385B ARG* 4.9 0.7 + - - -
423B TRP* 2.6 45.6 + - + +
445B VAL 2.9 18.5 + - - +
446B LEU* 3.3 10.6 + - - +
448B TRP* 1.3 80.2 - - + +
450B ILE* 1.3 59.4 + - - +
452B THR* 3.2 6.5 + - - -
453B TYR 3.2 1.4 + - - -
454B GLY* 2.5 35.8 + - - +
455B MET 4.5 11.3 - - - +
457B PRO* 4.6 6.3 - - + -
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Residues in contact with ILE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 4.2 7.4 - - + -
345B LEU* 3.7 18.5 - - + +
358B LEU* 3.7 42.3 - - + +
361B MET* 3.8 16.6 - - + -
362B ALA* 4.6 19.7 - - + +
365B ILE* 3.9 28.3 - - + -
443B PHE* 6.5 0.4 - - + -
446B LEU* 3.0 32.0 + - + +
447B LEU* 3.9 10.1 - - + +
449B GLU* 1.3 76.1 - - - +
451B ALA* 1.3 59.4 + - - +
452B THR 3.1 0.7 - - - -
453B TYR* 3.0 19.1 + - - -
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Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B LEU* 4.3 12.6 - - + +
447B LEU 3.1 20.1 + - - +
448B TRP* 3.1 6.0 + - - +
450B ILE* 1.3 75.8 - - - +
452B THR* 1.3 59.1 + - - +
453B TYR* 3.4 11.2 + - - -
479B PRO* 3.8 26.4 - - + +
480B GLU 4.4 7.8 - - - +
481B GLY 6.0 0.2 - - - -
482B CYS* 3.9 24.2 - - + +
486B VAL* 5.5 1.6 - - + -
490B MET* 4.5 0.2 - - + -
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Residues in contact with THR 452 (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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350B ARG* 4.6 3.8 + - - -
448B TRP* 2.9 45.8 + - + +
449B GLU* 3.2 6.6 + - - -
451B ALA* 1.3 76.4 - - - +
453B TYR* 1.3 70.5 + - - +
454B GLY 2.9 1.2 + - - -
455B MET* 3.1 52.6 + - + +
479B PRO* 3.7 28.5 - - + -
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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