Contacts of the helix formed by residues 420 - 437 (chain B) in PDB entry 1BHG
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 ASN 420 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B PHE 3.9 0.8 + - - -
419B ASN* 1.3 71.7 - - - +
421B VAL* 1.3 56.3 + - + +
423B LEU* 3.0 22.9 + - + +
424B HIS* 2.7 37.9 + - - +
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Residues in contact with VAL 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B THR* 4.2 19.5 - - + +
419B ASN* 3.1 18.1 + - + +
420B ASN* 1.3 78.0 - - + +
422B SER* 1.3 58.9 + - - +
424B HIS* 3.3 13.1 - - + +
425B HIS* 2.9 22.0 + - - +
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Residues in contact with SER 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PRO 2.7 15.6 + - - -
179B THR* 2.7 36.8 + - - +
180B THR 5.4 1.6 - - - -
181B LEU* 5.8 2.2 - - - +
417B PHE 4.6 9.4 - - - -
419B ASN* 2.8 23.6 + - - -
421B VAL* 1.3 68.8 - - - +
423B LEU* 1.3 60.7 + - - +
424B HIS 3.0 1.3 - - - -
425B HIS* 3.3 8.6 - - - +
426B HIS* 2.8 31.0 + - - +
462B TYR* 4.0 4.3 + - - -
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Residues in contact with LEU 423 (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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418B PHE 5.2 0.9 - - - +
419B ASN 2.9 16.4 + - - +
420B ASN* 3.0 29.6 + - + +
422B SER* 1.3 75.1 - - - +
424B HIS* 1.3 64.2 + - + +
426B HIS* 3.7 2.9 - - - +
427B MET* 3.1 32.3 + - - +
462B TYR* 3.4 45.6 - - + +
465B MET* 4.0 40.6 - - + -
466B VAL* 4.3 8.2 - - + +
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Residues in contact with HIS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ASN 2.7 15.3 + - - +
421B VAL* 3.3 11.2 - - + +
423B LEU* 1.3 83.7 - - + +
425B HIS* 1.3 58.7 + - - +
427B MET* 2.7 35.9 - - + +
428B GLN* 2.9 16.0 + - + +
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Residues in contact with HIS 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLU* 4.3 30.0 + - + +
144B GLY* 5.8 2.0 - - - -
179B THR* 2.6 38.1 + - + +
180B THR* 4.4 7.8 - - - +
181B LEU* 5.1 8.6 + - + +
421B VAL 2.9 9.5 + - - +
422B SER* 2.9 19.8 + - - +
424B HIS* 1.3 74.7 - - - +
426B HIS* 1.3 67.4 + - - +
428B GLN* 3.0 37.5 + - - +
429B VAL* 3.2 18.7 + - + +
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Residues in contact with HIS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 3.2 37.4 - - + +
407B CYS* 4.3 5.4 - - - -
409B GLY* 4.4 6.3 - - - -
412B LEU* 4.7 2.0 - - + +
422B SER 2.8 12.3 + - - +
423B LEU 3.7 5.2 - - - +
425B HIS* 1.3 71.9 - - - +
427B MET* 1.3 62.6 + - - +
429B VAL* 2.9 24.4 + - + +
430B MET* 3.2 13.3 + - + +
448B VAL* 2.9 38.3 + - + +
449B ALA* 4.3 10.1 - - + -
462B TYR* 2.6 38.1 + + + +
463B LEU* 5.6 0.2 - - + -
466B VAL* 3.7 21.0 - - + +
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Residues in contact with MET 427 (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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423B LEU* 3.1 21.8 + - + +
424B HIS* 2.7 29.2 - - + +
426B HIS* 1.3 81.3 - - - +
428B GLN* 1.3 59.1 + - - +
430B MET* 3.7 10.0 + - - +
431B GLU* 3.6 16.8 + - - +
465B MET* 3.5 48.0 - - + +
466B VAL* 4.1 13.0 - - + +
469B HIS* 3.4 43.2 + - + +
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Residues in contact with GLN 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLU* 3.0 30.1 + - - +
424B HIS* 2.9 16.3 + - + +
425B HIS* 3.0 39.6 + - - +
427B MET* 1.3 74.4 - - - +
429B VAL* 1.3 68.9 + - - +
431B GLU* 2.9 33.7 + - - +
432B GLU* 3.3 28.7 + - + +
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Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLU 5.9 0.2 - - - +
144B GLY 5.3 6.1 - - - +
145B GLY* 5.9 2.2 - - - -
147B LEU* 4.5 18.2 - - + -
181B LEU* 3.7 19.1 - - + -
407B CYS* 3.3 31.9 - - - -
408B PRO* 5.1 3.8 - - + -
425B HIS* 3.2 26.2 + - + +
426B HIS* 2.9 23.3 + - + +
428B GLN* 1.3 79.8 - - - +
430B MET* 1.3 65.7 + - - +
431B GLU 2.8 1.0 + - - -
432B GLU* 3.0 11.6 + - + +
433B VAL* 3.0 23.2 + - - +
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Residues in contact with MET 430 (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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407B CYS* 3.5 31.0 - - + -
426B HIS* 3.2 24.0 + - + +
427B MET* 3.7 7.8 + - - +
428B GLN 3.2 1.0 + - - -
429B VAL* 1.3 81.4 - - - +
431B GLU* 1.3 58.5 + - - +
433B VAL* 4.0 7.1 - - - -
434B VAL* 3.1 35.5 + - + +
446B TRP* 3.8 31.4 - - + -
447B SER 4.6 3.6 - - - +
448B VAL* 3.9 17.3 - - + -
466B VAL* 5.2 4.3 - - + +
469B HIS* 5.8 2.9 - - + +
470B THR* 3.4 44.6 - - + +
473B LEU* 3.4 9.5 - - + +
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Residues in contact with GLU 431 (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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23B LEU* 4.0 33.9 - - + +
427B MET* 3.6 15.1 - - - +
428B GLN* 2.9 22.7 + - - +
429B VAL 2.8 0.6 + - - -
430B MET* 1.3 75.0 - - - +
432B GLU* 1.3 56.3 + - + +
434B VAL* 3.1 4.2 + - - +
435B ARG* 2.7 39.0 + - - +
469B HIS* 2.7 29.4 + - + -
473B LEU* 3.6 26.5 - - + -
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Residues in contact with GLU 432 (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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142B HIS* 3.2 39.8 + - - -
143B GLU 4.5 2.3 - - - +
144B GLY 4.6 1.1 - - - +
147B LEU* 3.5 30.3 - - + +
148B PRO* 4.1 5.2 - - + +
428B GLN* 3.7 36.8 + - + +
429B VAL* 3.0 12.6 + - - +
431B GLU* 1.3 78.4 - - + +
433B VAL* 1.3 56.0 + - - +
435B ARG* 3.4 27.5 + - - +
436B ARG* 3.0 31.8 + - - +
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Residues in contact with VAL 433 (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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147B LEU* 3.6 31.9 - - + -
387B PRO* 4.0 18.8 - - + -
405B ASP* 3.7 14.8 - - - +
407B CYS* 4.6 18.6 - - + +
408B PRO* 5.1 0.2 - - + -
429B VAL* 3.0 22.0 + - + +
430B MET* 4.3 8.1 - - - +
432B GLU* 1.3 73.2 - - - +
434B VAL* 1.3 60.6 + - - +
436B ARG* 3.4 1.8 + - - +
437B ASP* 3.1 29.1 + - - +
446B TRP* 3.4 23.3 - - + -
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Residues in contact with VAL 434 (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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430B MET* 3.1 27.1 + - + +
431B GLU 3.1 2.5 + - - +
433B VAL* 1.3 72.4 - - + +
435B ARG* 1.3 57.1 + - - +
436B ARG 2.9 5.6 + - - -
438B LYS* 2.8 43.1 + - + +
446B TRP* 3.3 33.4 - - + +
470B THR* 5.0 3.1 - - + -
473B LEU* 3.9 24.7 - - + +
474B ASP* 3.7 35.0 - - + +
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Residues in contact with ARG 435 (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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23B LEU* 4.8 25.7 - - + +
24B GLN 5.6 0.6 + - - -
25B GLY* 3.1 30.7 + - - +
26B GLY* 4.9 0.9 - - - -
27B MET* 3.6 62.3 - - - +
148B PRO* 4.8 4.8 + - - +
230B ASP* 5.3 6.7 - - - +
431B GLU 2.7 22.4 + - - +
432B GLU* 3.4 37.5 + - - +
434B VAL* 1.3 75.8 - - - +
436B ARG* 1.3 57.0 + - - +
438B LYS* 5.0 1.8 - - - -
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Residues in contact with ARG 436 (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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27B MET* 4.9 11.6 - - + +
146B TYR 3.3 18.6 + - - -
147B LEU* 4.0 3.7 - - + +
148B PRO* 3.7 37.6 - - + +
216B ARG* 4.1 2.2 - - - +
387B PRO* 3.5 13.3 - - - +
388B TYR 3.1 26.3 + - - +
389B ALA* 4.9 3.7 + - - +
392B VAL* 4.3 14.6 - - - +
432B GLU 3.0 15.7 + - - +
433B VAL* 3.6 7.9 - - - +
434B VAL 2.9 0.4 - - - -
435B ARG* 1.3 82.3 - - - +
437B ASP* 1.3 93.4 + - - +
438B LYS 3.9 0.4 - - - -
440B HIS* 3.8 9.8 + - - -
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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
----------------------------------------------------------
387B PRO* 4.9 1.7 - - - +
392B VAL* 4.1 6.4 - - - +
405B ASP* 3.0 33.5 - - - +
433B VAL* 3.1 22.9 + - - +
434B VAL 3.8 0.4 - - - -
436B ARG* 1.3 110.6 + - - +
438B LYS* 1.3 64.7 + - - +
439B ASN 3.1 4.8 + - - -
440B HIS* 3.0 42.2 + - + -
443B VAL* 3.4 15.3 - - + +
446B TRP* 3.8 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
------------------------------------------------------------
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