Contacts of the helix formed by residues 428 - 446 (chain B) in PDB entry 2H3W
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 428 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 1.3 70.6 - - - +
429B PRO* 1.3 56.6 - - - +
430B ASP* 4.2 0.5 - - - +
431B ALA* 3.3 25.5 + - - +
432B PHE* 2.7 36.8 + - - +
500B VAL* 4.1 7.0 - - - +
501B GLN* 5.4 2.5 - - - +
504B ARG* 3.9 19.4 + - - -
1701B COA 2.5 44.9 + - - -
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Residues in contact with PRO 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLY 5.6 0.2 - - - -
419B LYS* 3.9 32.8 - - + -
422B PRO* 3.6 20.4 - - + -
423B LYS* 3.8 16.2 - - + -
427B LEU 3.3 5.8 - - - +
428B SER* 1.3 82.4 - - - +
430B ASP* 1.3 56.0 + - - +
432B PHE* 3.3 1.6 + - - +
433B ILE* 2.9 40.9 + - + +
580B PRO* 5.3 2.7 - - + -
1701B COA 3.0 43.1 - - + +
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Residues in contact with ASP 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B SER* 4.2 1.8 - - - +
429B PRO* 1.3 72.9 - - - +
431B ALA* 1.3 57.4 + - - +
433B ILE* 3.2 8.2 + - - +
434B GLN* 2.8 28.6 + - - +
453B GLU* 2.6 29.5 - - - +
503B HIS* 3.8 5.7 - - - -
504B ARG* 5.7 0.2 - - - +
507B THR* 4.8 0.9 + - - -
555B GLN* 2.9 35.2 + - - +
578B TYR* 2.6 26.2 + - - -
1701B COA 2.6 39.2 + - - +
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B SER* 3.3 23.8 + - - +
430B ASP* 1.3 78.5 + - - +
432B PHE* 1.3 57.9 + - - +
434B GLN* 3.2 0.9 + - - +
435B VAL* 2.8 37.5 + - - +
500B VAL* 3.6 27.8 - - + +
503B HIS* 3.5 29.1 + - + +
504B ARG* 4.4 4.5 - - - +
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Residues in contact with PHE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B PHE* 4.0 15.3 - + - -
421B PHE* 3.9 22.2 - + - -
422B PRO* 3.9 22.9 - - + -
427B LEU* 4.1 18.8 - - + -
428B SER 2.7 18.6 + - - +
429B PRO 3.4 6.3 - - - +
431B ALA* 1.3 77.1 - - - +
433B ILE* 1.3 58.7 + - + +
436B ALA* 3.0 25.3 + - - +
496B LEU* 4.9 1.1 - - + -
500B VAL* 4.3 10.3 - - + +
611B LEU* 3.8 30.7 - - + -
614B MET* 3.6 38.3 - - + +
615B ARG 4.2 0.2 - - - -
618B LEU* 3.6 26.9 - - + -
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Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PRO* 6.0 1.8 - - + -
429B PRO* 2.9 25.8 + - + +
430B ASP* 3.2 4.9 + - - +
432B PHE* 1.3 78.3 - - + +
434B GLN* 1.3 59.5 + - - +
436B ALA* 3.3 2.9 + - - +
437B LEU* 2.9 28.0 + - + +
578B TYR* 3.8 34.5 - - + -
580B PRO* 3.9 21.8 - - + -
585B ILE* 3.7 32.5 - - + -
587B PHE* 3.9 24.2 - - + -
607B LEU* 4.6 2.5 - - + +
611B LEU* 4.2 13.2 - - + -
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Residues in contact with GLN 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ASP 2.8 19.8 + - - +
431B ALA 3.7 3.4 - - - +
433B ILE* 1.3 74.7 - - - +
435B VAL* 1.3 64.2 + - - +
437B LEU* 3.2 12.0 + - - +
438B GLN* 3.1 27.1 + - - +
451B THR* 4.2 4.7 - - - +
453B GLU* 3.3 28.5 + - - +
470B SER* 2.5 28.9 + - - +
503B HIS* 3.3 20.4 - - + +
553B THR* 3.1 27.2 + - - +
578B TYR* 2.7 30.5 + - - +
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Residues in contact with VAL 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ALA 2.8 23.0 + - - +
432B PHE 3.9 3.8 - - - +
434B GLN* 1.3 72.1 - - + +
436B ALA* 1.3 64.2 + - - +
438B GLN* 3.1 11.4 + - + +
439B LEU* 3.0 20.1 + - - +
475B SER* 5.3 6.5 - - - -
478B PHE* 3.4 35.8 - - + -
496B LEU 5.0 1.3 - - - +
499B ALA* 3.9 38.6 - - + +
500B VAL* 4.0 9.2 - - + +
503B HIS* 4.8 6.7 - - + -
614B MET* 3.7 11.9 - - + -
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Residues in contact with ALA 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B PHE 3.0 18.8 + - - +
433B ILE 3.5 3.1 - - - +
434B GLN 3.3 0.2 - - - -
435B VAL* 1.3 77.5 - - - +
437B LEU* 1.3 56.2 + - - +
439B LEU* 3.2 3.1 + - - +
440B ALA* 2.9 24.6 + - - +
607B LEU* 4.2 2.5 - - + -
610B ALA* 3.3 11.0 - - + +
611B LEU* 3.4 40.6 - - + +
614B MET* 3.4 20.8 - - - -
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ILE* 2.9 14.2 + - + +
434B GLN* 3.6 19.5 - - - +
435B VAL 3.2 0.2 - - - -
436B ALA* 1.3 72.2 - - - +
438B GLN* 1.3 68.2 + - - +
440B ALA* 3.2 2.9 + - + -
441B TYR* 2.9 21.8 + - - +
451B THR* 5.1 2.2 - - + -
551B LEU* 4.0 21.5 - - + -
553B THR* 3.5 31.4 - - + -
576B ILE* 3.7 31.9 - - + -
578B TYR* 6.2 1.3 - - + -
603B MET* 4.2 17.5 - - - -
607B LEU* 3.8 23.1 - - + +
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Residues in contact with GLN 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B GLN* 3.1 19.7 + - - +
435B VAL* 3.4 9.2 - - + +
437B LEU* 1.3 78.6 - - - +
439B LEU* 1.3 63.5 + - - +
441B TYR* 3.4 5.5 + - - +
442B TYR* 3.0 24.9 + - - +
448B ALA* 4.7 8.0 - - - +
449B CYS* 4.4 2.8 + - - +
451B THR* 2.8 38.7 + - - +
470B SER* 3.7 24.7 - - - +
471B ALA* 3.3 23.9 - - - +
475B SER* 4.1 12.7 + - - +
479B VAL* 3.8 12.8 - - + +
551B LEU* 3.9 9.2 - - - +
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Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B VAL 3.0 12.5 + - - +
436B ALA* 3.2 8.9 + - - +
438B GLN* 1.3 73.4 - - - +
440B ALA* 1.3 65.1 + - - +
442B TYR* 3.4 1.7 + - + +
443B ARG* 3.0 70.1 + - + +
478B PHE* 4.4 7.2 - - + -
479B VAL* 3.5 26.9 - - + +
482B MET* 3.9 31.6 - - + -
610B ALA* 3.9 23.3 - - + +
614B MET* 4.2 16.2 - - + -
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Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ALA 2.9 12.9 + - - +
437B LEU* 3.6 13.2 - - + +
439B LEU* 1.3 77.3 - - - +
441B TYR* 1.3 62.5 + - - +
443B ARG* 3.4 6.2 + - - +
444B ILE* 3.2 28.8 + - - +
603B MET* 4.7 4.0 - - - -
606B TYR* 3.4 39.4 - - + +
607B LEU* 3.6 10.8 - - + +
610B ALA* 4.0 2.2 - - + -
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Residues in contact with TYR 441 (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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437B LEU 2.9 17.1 + - - +
438B GLN* 3.8 6.1 - - - +
440B ALA* 1.3 76.2 - - - +
442B TYR* 1.3 58.2 + - - +
444B ILE* 3.1 2.3 + - - -
445B TYR* 2.8 70.3 + + + +
447B GLN* 3.3 25.7 - - + +
448B ALA* 4.1 2.2 - - - -
449B CYS* 3.2 47.1 - - + +
550B ASN* 4.0 16.2 + - + +
551B LEU* 3.8 17.9 - - + -
574B TYR* 4.7 5.8 - + - -
603B MET* 3.6 27.7 - - + -
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Residues in contact with TYR 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B GLN 3.0 17.9 + - - +
439B LEU* 3.8 4.0 - - + +
440B ALA 3.3 0.2 - - - -
441B TYR* 1.3 76.9 - - - +
443B ARG* 1.3 65.0 + - + +
446B GLY* 2.7 55.9 + - - -
447B GLN* 3.5 30.7 - - - +
448B ALA* 4.0 3.6 - - - -
476B LEU* 4.3 7.2 - - + -
479B VAL* 3.7 42.0 - - + -
480B LYS* 3.4 37.2 - - + +
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Residues in contact with ARG 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B LEU* 3.0 53.0 + - + +
440B ALA* 3.7 7.2 - - - +
442B TYR* 1.3 82.6 - - + +
444B ILE* 1.3 61.3 + - - +
446B GLY 4.8 0.2 + - - -
479B VAL 6.1 0.2 - - - +
482B MET* 3.9 16.6 - - - +
606B TYR* 3.8 27.6 + - + -
609B LYS* 4.3 7.5 - - - +
610B ALA* 3.9 19.0 - - - +
613B ASP* 2.7 37.9 + - - +
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Residues in contact with ILE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ALA 3.2 12.3 - - - +
441B TYR 3.1 6.2 + - - +
442B TYR 3.1 0.8 - - - -
443B ARG* 1.3 81.0 - - - +
445B TYR* 1.3 86.5 + - + +
446B GLY 3.6 0.4 - - - -
574B TYR* 5.4 1.8 - - - +
602B ARG* 3.1 35.4 + - + +
603B MET* 4.1 30.7 - - + -
606B TYR* 3.3 48.7 - - + -
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Residues in contact with TYR 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B TYR* 2.8 71.6 + + + +
444B ILE* 1.3 98.7 - - + +
446B GLY* 1.3 63.9 + - - +
447B GLN* 3.2 16.8 + - + +
574B TYR* 2.7 29.8 + + - -
597B GLU* 2.7 37.0 + - + -
598B THR* 4.3 1.5 - - + +
603B MET* 4.1 8.3 - - + -
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Residues in contact with GLY 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B TYR* 2.7 46.0 + - - -
443B ARG 4.6 0.2 - - - -
444B ILE 3.6 1.4 + - - -
445B TYR* 1.3 70.7 - - - +
447B GLN* 1.3 61.8 + - - +
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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