Contacts of the helix formed by residues 444 - 458 (chain B) in PDB entry 3HS5
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 VAL 444 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B HIS* 4.0 21.3 - - + -
391B LEU* 4.2 17.7 - - + -
404B PHE* 4.2 13.7 - - + -
440B VAL* 4.0 3.8 - - + -
441B PRO* 3.4 34.3 - - + +
442B ILE 3.1 0.6 - - - -
443B ALA* 1.3 82.5 - - - +
445B GLN* 1.3 63.1 + - - +
446B ALA 3.2 2.9 - - - -
447B VAL* 3.1 28.5 + - + +
448B ALA* 3.2 10.2 + - - +
619B COH 4.3 21.8 - - + -
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Residues in contact with GLN 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 3.8 18.2 - - + +
179B GLU* 5.0 1.9 - - - +
183B LEU* 3.5 33.7 - - + +
440B VAL* 5.0 0.2 - - - -
441B PRO 3.8 1.0 + - - -
442B ILE* 3.0 18.1 + - - +
443B ALA 3.5 1.6 + - - -
444B VAL* 1.3 77.2 - - - +
446B ALA* 1.3 62.1 + - + +
448B ALA* 3.5 1.7 + - - -
449B LYS* 3.1 28.6 + - - +
703B BOG 2.9 52.2 + - - +
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Residues in contact with ALA 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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443B ALA 5.4 0.2 + - - -
444B VAL* 3.2 1.0 - - - +
445B GLN* 1.3 84.2 - - + +
447B VAL* 1.3 62.6 + - + +
449B LYS* 3.9 6.4 - - - +
450B ALA* 3.0 27.2 + - - +
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B HIS* 5.3 0.9 - - + +
388B HIS* 3.9 17.3 - - + +
444B VAL* 3.1 23.1 + - + +
446B ALA* 1.3 80.0 - - + +
448B ALA* 1.3 64.5 + - - +
450B ALA* 3.3 6.7 + - - +
451B SER* 3.0 26.8 + - - +
619B COH 3.8 71.3 - - + +
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Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B LEU* 3.6 24.0 - - + -
182B LEU* 5.0 2.0 - - + -
388B HIS* 5.5 4.6 + - + -
440B VAL* 3.8 27.6 - - + -
444B VAL 3.2 4.7 + - - +
445B GLN 3.8 2.7 - - - +
447B VAL* 1.3 78.9 - - - +
449B LYS* 1.3 60.9 + - - +
451B SER* 3.2 14.0 + - - -
452B ILE* 3.4 12.8 + - - +
504B TYR* 3.7 26.9 - - + +
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Residues in contact with LYS 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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173B ASP* 4.9 3.2 + - - -
174B SER* 3.0 26.4 + - - +
175B LYS* 4.2 28.9 - - + +
178B LEU* 4.1 14.5 - - + +
445B GLN 3.1 17.9 + - - +
446B ALA* 3.9 7.9 - - - +
448B ALA* 1.3 75.6 - - - +
450B ALA* 1.3 57.5 + - - +
452B ILE* 3.2 11.4 + - - +
453B ASP* 2.9 47.1 + - - +
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Residues in contact with ALA 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ALA 3.0 19.8 + - - +
447B VAL* 3.3 9.4 + - - +
449B LYS* 1.3 74.1 - - - +
451B SER* 1.3 59.6 + - - +
453B ASP* 4.3 8.3 - - - -
454B GLN* 2.8 43.0 + - + +
619B COH 3.9 21.1 - - + +
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Residues in contact with SER 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B THR* 5.1 2.7 + - - +
386B HIS* 2.7 37.9 + - - +
388B HIS* 5.3 0.7 - - - -
447B VAL 3.0 13.9 + - - -
448B ALA 3.2 11.2 + - - -
450B ALA* 1.3 76.8 - - - +
452B ILE* 1.3 55.8 + - - +
454B GLN* 4.1 3.6 - - - +
455B SER* 2.7 34.3 + - - -
504B TYR* 3.5 29.1 + - - -
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Residues in contact with ILE 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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174B SER* 3.8 28.7 - - - +
177B VAL* 4.1 14.8 - - + -
178B LEU* 4.5 2.2 - - + +
182B LEU* 3.9 24.7 - - + -
448B ALA 3.4 8.3 + - - +
449B LYS* 3.2 9.7 + - - +
451B SER* 1.3 74.7 - - - +
453B ASP* 1.3 66.0 + - - +
455B SER* 3.3 8.1 + - - -
456B ARG* 3.2 49.0 + - - +
502B GLU* 3.7 16.3 - - - +
504B TYR* 3.7 21.5 - - + -
505B PRO* 4.3 7.9 - - + -
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Residues in contact with ASP 453 (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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174B SER* 2.7 25.0 + - - -
449B LYS* 2.9 46.8 + - - +
450B ALA* 3.9 7.0 + - - +
452B ILE* 1.3 76.0 - - - +
454B GLN* 1.3 60.3 + - + +
456B ARG* 3.3 14.2 + - - +
457B GLU* 2.9 27.2 + - - +
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Residues in contact with GLN 454 (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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212B THR* 6.0 0.8 - - - +
214B HIS* 5.5 8.3 - - - -
218B PRO* 4.0 30.4 - - + +
386B HIS* 5.6 3.5 - - - -
450B ALA* 2.8 30.9 + - + +
451B SER* 4.4 4.0 + - - +
453B ASP* 1.3 71.4 - - + +
455B SER* 1.3 59.5 + - - +
457B GLU* 3.5 19.2 + - - +
458B MET* 2.9 41.8 + - + +
619B COH 3.5 26.1 + - - +
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Residues in contact with SER 455 (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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6B EDO 4.3 0.7 - - - -
383B THR* 3.9 22.7 + - - +
451B SER 2.7 24.8 + - - -
452B ILE* 3.3 8.0 + - - -
454B GLN* 1.3 77.0 - - - +
456B ARG* 1.3 59.1 + - - +
458B MET* 3.4 5.4 + - - +
459B LYS 3.2 3.8 + - - -
460B TYR* 3.0 54.5 + - - +
502B GLU* 5.1 7.4 - - - -
504B TYR* 4.3 8.1 - - - +
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Residues in contact with ARG 456 (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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6B EDO 3.4 34.1 - - - -
171B LEU* 3.6 23.6 + - + +
172B PRO* 2.8 33.1 + - - +
173B ASP* 4.7 1.0 - - - +
174B SER* 3.8 17.3 - - - +
177B VAL* 4.4 1.2 - - - +
452B ILE* 3.2 26.2 + - - +
453B ASP* 3.5 13.1 + - - +
455B SER* 1.3 75.2 - - - +
457B GLU* 1.3 64.6 + - - +
459B LYS* 2.9 16.3 + - - +
495B TYR* 4.1 5.1 + - - -
502B GLU* 2.7 44.5 + - - +
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Residues in contact with GLU 457 (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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132B VAL* 5.1 1.9 - - - +
217B GLY* 5.3 0.2 - - - -
218B PRO* 3.4 33.3 - - + +
453B ASP 2.9 15.6 + - - +
454B GLN* 3.5 17.9 + - - +
456B ARG* 1.3 76.0 - - - +
458B MET* 1.3 57.4 + - - +
459B LYS* 3.1 12.2 + - - +
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Residues in contact with MET 458 (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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132B VAL* 3.9 19.4 - - + +
150B ARG* 2.9 35.1 + - - +
154B PRO* 3.8 4.2 - - - +
218B PRO* 3.5 47.6 - - + +
219B GLY* 3.6 7.6 - - - +
379B SER* 3.5 25.4 - - - +
383B THR* 4.4 5.6 - - - +
454B GLN* 2.9 35.8 + - + +
455B SER* 3.8 2.5 - - - +
456B ARG 3.2 0.2 - - - -
457B GLU* 1.3 74.3 - - - +
459B LYS* 1.3 66.6 - - - +
460B TYR* 3.3 21.1 - - + +
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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