Contacts of the helix formed by residues 432 - 448 (chain B) in PDB entry 4GWF
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 PRO 432 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B SER 4.5 2.9 - - - +
431B ASP* 1.4 89.4 - - - +
433B GLY* 1.3 64.2 + - - +
434B GLY 3.5 1.3 - - - -
435B VAL* 3.3 7.0 + - + +
436B LEU* 3.1 25.1 + - + +
513B PHE* 3.7 28.9 - - + -
516B MET* 3.6 31.0 - - + +
517B ALA* 3.8 18.6 - - + +
520B HIS* 3.8 19.5 - - + -
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Residues in contact with GLY 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ASP* 2.9 17.3 + - - -
432B PRO* 1.3 78.8 - - - +
434B GLY* 1.3 50.1 + - - +
436B LEU* 3.1 5.2 + - - +
437B ASP* 2.8 45.9 + - - +
520B HIS* 3.9 23.0 + - - -
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Residues in contact with GLY 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ASP* 3.8 26.1 - - - +
396B TYR* 5.9 0.3 - - - -
420B PHE* 3.9 9.7 - - - -
431B ASP* 4.3 5.1 + - - -
432B PRO 3.5 0.6 - - - -
433B GLY* 1.3 72.4 - - - +
435B VAL* 1.4 56.4 + - - +
437B ASP* 3.5 10.6 + - - +
438B PHE* 3.0 29.3 + - - +
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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
----------------------------------------------------------
420B PHE* 3.7 27.3 - - + -
423B TRP* 3.9 16.8 - - + -
429B PRO* 4.3 6.1 - - + -
431B ASP 5.4 0.8 + - - -
432B PRO* 3.3 11.4 + - + +
434B GLY* 1.4 74.1 - - - +
436B LEU* 1.4 57.9 + - + +
438B PHE* 3.2 4.3 - - - +
439B LEU* 2.9 42.1 + - + +
469B PHE* 4.0 19.7 - - + -
472B ILE* 4.4 11.4 - - + -
513B PHE* 3.8 31.6 - - + -
517B ALA* 5.7 0.9 - - + -
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B PRO 3.1 20.0 + - - +
433B GLY* 3.1 6.3 + - - +
435B VAL* 1.4 73.1 - - + +
437B ASP* 1.4 58.9 + - - +
439B LEU* 3.4 5.0 + - + +
440B GLU* 2.9 33.1 + - - +
472B ILE* 4.1 15.0 - - + -
476B ILE* 4.0 26.2 - - + -
517B ALA* 3.3 32.8 - - + +
520B HIS* 3.4 32.3 - - + +
521B TYR* 3.9 13.7 - - + +
603B EDO 3.7 18.5 + - - +
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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
----------------------------------------------------------
395B ASP* 5.5 1.1 - - - +
396B TYR* 5.6 4.9 - - + -
433B GLY* 2.8 30.4 + - - +
434B GLY* 3.8 9.0 + - - +
436B LEU* 1.4 70.0 - - - +
438B PHE* 1.4 56.6 + - - +
440B GLU* 3.6 2.7 + - - +
441B GLU* 3.1 28.6 + - - +
603B EDO 3.2 27.2 + - - -
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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
----------------------------------------------------------
354B VAL* 3.7 20.4 - - + -
355B MET 4.5 0.2 - - - -
356B THR* 4.9 0.2 - - + -
396B TYR* 3.6 47.1 - + + -
418B TYR* 3.5 44.9 - + + -
420B PHE* 3.6 25.4 - + + -
434B GLY 3.0 14.1 + - - +
435B VAL 3.2 8.1 - - - +
436B LEU 3.2 0.2 - - - -
437B ASP* 1.4 74.9 - - - +
439B LEU* 1.4 61.5 + - + +
441B GLU* 3.2 8.2 + - - +
442B VAL* 3.0 33.7 + - + +
469B PHE* 3.5 34.3 - + - -
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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
----------------------------------------------------------
354B VAL* 5.2 4.9 - - + -
435B VAL* 2.9 33.2 + - + +
436B LEU* 4.1 6.5 - - + +
438B PHE* 1.4 76.9 - - + +
440B GLU* 1.3 56.3 + - - +
442B VAL* 3.7 14.6 - - + +
443B HIS* 2.8 34.8 + - - +
469B PHE* 3.8 42.6 - - + +
472B ILE* 3.9 25.1 - - + -
473B ASP* 4.0 31.3 - - + +
476B ILE* 5.9 4.0 - - + -
480B ARG* 4.9 2.7 - - - +
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Residues in contact with GLU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LEU 2.9 17.9 + - - +
437B ASP* 3.7 5.2 - - - +
439B LEU* 1.3 75.3 - - - +
441B GLU* 1.4 61.2 + - - +
443B HIS* 3.4 1.7 + - - +
444B HIS* 3.0 58.9 + - + +
476B ILE* 4.4 0.7 - - - +
480B ARG* 2.8 34.6 + - - +
521B TYR* 3.3 24.5 + - - -
603B EDO 4.1 7.7 + - - +
604B EDO 3.8 27.5 - - - +
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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
----------------------------------------------------------
396B TYR* 3.6 24.9 - - + +
398B LEU* 5.4 3.5 - - + +
418B TYR* 3.6 28.6 + - + -
437B ASP 3.1 14.7 + - - +
438B PHE* 3.2 9.6 + - - +
440B GLU* 1.4 75.7 - - - +
442B VAL* 1.4 60.5 + - - +
444B HIS* 3.5 10.7 + - - +
445B LYS* 3.1 29.3 + - - +
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LYS* 5.9 2.7 - - - -
352B VAL* 3.9 12.7 - - + +
354B VAL* 3.8 26.2 - - + -
418B TYR* 3.6 40.8 - - + -
438B PHE* 3.0 29.8 + - + +
439B LEU* 3.7 15.3 - - + +
440B GLU 3.4 0.2 - - - -
441B GLU* 1.4 71.7 - - - +
443B HIS* 1.3 64.6 + - - +
445B LYS* 3.6 1.7 + - - +
446B GLN* 3.1 23.6 + - + +
455B VAL* 4.5 10.8 - - + -
473B ASP* 5.6 3.1 - - - +
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Residues in contact with HIS 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LYS* 2.8 35.2 + - + +
439B LEU 2.8 20.0 + - - +
440B GLU 3.7 4.3 - - - +
442B VAL* 1.3 71.2 - - - +
444B HIS* 1.3 73.8 + + - +
446B GLN* 3.3 5.3 + - - +
447B GLU* 2.9 57.0 + - + +
473B ASP* 5.2 0.2 - - - -
477B ASP* 3.6 13.5 + - - -
480B ARG* 3.4 47.9 + - - +
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Residues in contact with HIS 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B GLU* 3.0 53.3 + - + +
441B GLU* 4.0 12.8 - - - +
443B HIS* 1.3 85.2 - + - +
445B LYS* 1.4 50.9 + - - +
447B GLU* 3.2 12.5 + - - +
448B SER* 2.8 37.7 + - - -
480B ARG* 5.7 0.9 - - - -
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Residues in contact with LYS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B VAL* 4.0 6.5 - - + -
398B LEU* 4.8 2.4 - - - +
416B TRP* 3.3 71.1 - - + +
418B TYR* 3.2 36.1 - - + +
441B GLU* 3.1 18.2 + - - +
442B VAL 3.8 4.5 - - - +
443B HIS 3.4 0.2 - - - -
444B HIS* 1.4 74.4 - - - +
446B GLN* 1.3 61.6 + - - +
448B SER* 2.8 27.7 + - - +
449B ILE* 3.4 15.6 - - + +
605B EDO 5.0 0.4 - - - +
608B EDO 4.6 4.9 + - - -
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Residues in contact with GLN 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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325B LYS* 4.4 20.7 - - + +
326B SER 5.7 0.6 + - - +
351B ARG* 4.8 1.4 + - - +
352B VAL* 3.5 25.6 + - + +
442B VAL* 3.1 19.0 + - + +
443B HIS* 3.6 6.3 - - - +
445B LYS* 1.3 74.6 - - - +
447B GLU* 1.3 62.8 + - - +
449B ILE* 3.4 21.3 + - - +
452B ALA* 3.5 25.4 + - - +
453B GLY 3.1 24.3 + - - +
454B PRO 5.4 0.2 - - - +
455B VAL* 3.7 26.9 - - + +
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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
----------------------------------------------------------
443B HIS* 2.9 45.7 + - + +
444B HIS* 3.6 13.3 + - - +
446B GLN* 1.3 75.6 - - - +
448B SER* 1.3 60.6 + - - +
449B ILE 3.4 4.0 + - - +
450B MET* 4.5 11.3 - - - +
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Residues in contact with SER 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B HIS 2.8 17.7 + - - -
445B LYS* 2.8 28.8 + - - +
447B GLU* 1.3 72.1 - - - +
449B ILE* 1.3 60.8 + - - +
450B MET* 4.1 7.6 + - - +
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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