Contacts of the helix formed by residues 428 - 442 (chain B) in PDB entry 5HVM
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 428 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B ASN* 2.9 21.8 + - + +
426B PRO 4.3 1.6 - - - -
427B TRP* 1.3 76.5 - - - +
429B THR* 1.3 65.0 + - - +
430B GLU* 3.5 17.0 + - - +
431B GLU* 3.0 43.7 + - + +
432B LEU* 3.1 19.4 + - - +
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Residues in contact with THR 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLN* 5.1 1.3 - - - +
299B HIS* 4.0 13.2 - - + +
300B ALA* 3.9 21.5 - - + +
303B VAL* 3.9 24.2 - - + -
426B PRO 4.9 3.8 + - - -
427B TRP 3.4 8.8 + - - -
428B ASN* 1.3 73.8 + - - +
430B GLU* 1.3 58.2 + - - +
432B LEU* 3.4 8.0 + - - +
433B ALA* 3.1 26.2 + - - +
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Residues in contact with GLU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B VAL* 4.7 13.0 - - + -
307B ASP* 5.7 3.4 - - - +
428B ASN* 3.2 14.8 + - - +
429B THR* 1.3 77.7 - - - +
431B GLU* 1.3 69.6 + - - +
433B ALA* 3.3 8.7 + - - +
434B GLY* 3.0 19.9 + - - -
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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
----------------------------------------------------------
423B ILE 3.9 6.2 - - - +
424B ILE* 3.6 14.8 - - + +
425B ASN* 3.6 28.9 + - - +
428B ASN* 3.0 42.9 + - - +
430B GLU* 1.3 84.5 + - - +
432B LEU* 1.3 55.3 + - - +
434B GLY* 3.2 3.7 + - - +
435B ALA* 3.0 25.3 + - - +
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Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLN* 4.0 12.3 - - + +
297B LYS* 4.2 1.6 - - - -
300B ALA* 3.5 20.9 - - + -
380B ILE* 4.5 4.3 - - + -
382B SER* 4.2 21.3 - - - -
407B VAL* 4.1 12.1 - - + -
424B ILE* 3.7 35.6 - - + +
425B ASN 5.2 2.0 + - - +
426B PRO* 4.7 10.1 - - + +
428B ASN 3.1 12.1 + - - +
429B THR* 3.7 8.7 - - - +
430B GLU 3.3 0.2 - - - -
431B GLU* 1.3 75.3 - - - +
433B ALA* 1.3 64.7 + - - +
435B ALA* 3.3 3.4 + - - +
436B TYR* 3.2 40.1 + - + +
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ALA* 3.4 26.2 - - - +
303B VAL* 3.7 24.7 - - + -
304B PHE* 3.5 16.8 - - + +
308B HIS* 6.0 0.2 - - - -
429B THR 3.1 9.6 + - - +
430B GLU 3.3 7.4 + - - +
432B LEU* 1.3 76.1 - - - +
434B GLY* 1.3 62.1 + - - +
436B TYR* 3.2 12.6 + - - +
437B GLN* 3.2 16.6 + - - +
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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
----------------------------------------------------------
430B GLU* 3.0 14.5 + - - -
431B GLU* 3.2 4.9 + - - -
432B LEU 3.2 0.4 - - - -
433B ALA* 1.3 75.6 - - - +
435B ALA* 1.3 58.5 + - - +
437B GLN* 3.2 11.1 + - - +
438B GLU* 2.8 30.1 + - - +
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B VAL* 4.0 15.1 - - + +
422B ILE* 3.9 16.2 - - + +
424B ILE* 3.7 28.9 - - + -
431B GLU 3.0 8.2 + - - +
432B LEU 3.6 9.2 - - - +
433B ALA 3.3 0.2 - - - -
434B GLY* 1.3 74.1 - - - +
436B TYR* 1.3 61.1 + - + +
438B GLU* 3.8 9.7 - - - +
439B ALA* 2.9 30.5 + - - +
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Residues in contact with TYR 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B MET* 3.6 26.6 - - + +
297B LYS* 2.9 37.8 + - - +
300B ALA* 3.8 11.3 - - + +
301B LEU* 3.5 41.5 - - + -
304B PHE* 4.0 31.6 - - + -
317B LEU* 5.4 2.9 - - + +
380B ILE* 3.8 25.2 - - + +
407B VAL* 5.3 3.1 - - + -
432B LEU* 3.2 26.1 + - + +
433B ALA* 3.2 8.0 + - - +
434B GLY 3.2 0.6 - - - -
435B ALA* 1.3 75.0 - - + +
437B GLN* 1.3 68.4 + - - +
439B ALA 3.3 0.3 + - - -
440B VAL* 3.0 29.7 + - - +
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Residues in contact with GLN 437 (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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304B PHE* 3.7 14.1 - - + -
308B HIS* 2.4 44.2 + - + +
310B GLU* 5.1 0.2 + - - -
311B TRP* 3.9 17.8 - - - +
433B ALA 3.2 6.0 + - - +
434B GLY* 3.2 14.3 + - - +
436B TYR* 1.3 81.3 - - - +
438B GLU* 1.3 62.1 + - - +
440B VAL* 4.0 0.6 - - - -
441B THR* 2.8 44.6 + - - +
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Residues in contact with GLU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ILE* 3.9 29.8 - - + +
434B GLY 2.8 17.4 + - - +
435B ALA* 3.8 7.7 - - - +
436B TYR 3.2 0.2 - - - -
437B GLN* 1.3 80.4 - - + +
439B ALA* 1.3 56.7 + - - +
441B THR* 3.9 4.7 + - - -
442B MET* 3.1 41.9 + - + +
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Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B MET* 4.4 4.7 - - + -
377B ASP* 5.1 4.0 - - - +
378B ALA* 4.1 18.2 - - + -
405B VAL* 3.7 47.8 - - + +
407B VAL* 4.2 8.3 - - + -
422B ILE* 4.3 1.3 - - + +
435B ALA 2.9 18.0 + - - +
436B TYR 3.3 2.9 + - - +
438B GLU* 1.3 77.3 - - - +
440B VAL* 1.3 62.0 + - - +
441B THR 3.6 0.3 + - - -
442B MET* 3.7 6.4 + - - +
447B ARG* 5.3 2.1 + - - -
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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
----------------------------------------------------------
280B LYS* 3.5 35.2 + - + +
282B MET* 3.6 28.0 - - + -
304B PHE* 5.0 6.5 - - + -
311B TRP* 3.0 48.9 - - + +
315B VAL* 4.4 19.1 - - + -
377B ASP* 6.0 4.7 - - + -
378B ALA* 5.7 1.8 - - + -
436B TYR 3.0 13.0 + - - +
437B GLN 4.1 1.3 - - - +
439B ALA* 1.3 79.5 - - - +
441B THR* 1.3 60.9 + - + +
442B MET 3.5 0.9 - - - +
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Residues in contact with THR 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B TRP* 4.0 19.3 - - + +
437B GLN* 2.8 43.8 + - - +
438B GLU* 3.9 4.3 + - - -
440B VAL* 1.3 79.4 - - + +
442B MET* 1.3 66.0 + - - +
443B SER* 3.5 2.6 + - - -
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Residues in contact with MET 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B VAL* 4.0 14.8 - - + -
422B ILE* 3.8 31.9 - - + -
438B GLU* 3.1 26.8 + - + +
439B ALA 3.7 8.8 + - - +
440B VAL 3.5 3.3 - - - +
441B THR* 1.3 78.3 - - - +
443B SER* 1.3 72.9 + - - +
444B ASP* 3.8 1.9 + - - +
446B GLN* 4.0 16.8 - - + +
447B ARG* 3.5 36.6 + - + -
450B ASN* 4.0 23.6 - - - +
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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