Contacts of the helix formed by residues 444 - 458 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A HIS* 4.0 23.8 - - + -
391A LEU* 4.2 18.2 - - + -
404A PHE* 4.3 12.6 - - + -
440A VAL* 4.3 3.1 - - + -
441A PRO* 3.4 32.8 - - + +
443A ALA* 1.3 84.1 - - - +
445A GLN* 1.3 62.6 + - - +
446A ALA* 3.2 3.6 - - - +
447A VAL* 3.1 26.5 + - + +
448A ALA* 3.1 11.4 + - - +
619A COH 4.3 24.0 - - + -
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Residues in contact with GLN 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 3.7 14.4 - - + +
179A GLU* 5.0 5.2 - - - +
183A LEU* 3.8 40.8 - - + +
441A PRO 3.6 2.9 + - - -
442A ILE* 3.0 32.6 + - - +
443A ALA 3.6 0.8 - - - -
444A VAL* 1.3 76.5 - - - +
446A ALA* 1.3 62.5 + - + +
448A ALA* 3.3 6.6 + - - +
449A LYS* 2.8 29.9 + - - +
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ALA 5.4 0.9 + - - +
444A VAL* 3.2 1.5 - - - -
445A GLN* 1.3 82.1 - - + +
447A VAL* 1.3 61.7 + - + +
449A LYS* 3.5 8.4 + - - +
450A ALA* 3.0 28.4 + - - +
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Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A HIS* 5.0 3.1 - - + -
388A HIS* 3.6 32.3 - - + +
444A VAL* 3.1 20.3 + - + +
446A ALA* 1.3 76.4 - - + +
448A ALA* 1.3 63.5 + - - +
450A ALA* 3.2 9.3 + - + +
451A SER* 3.1 24.1 + - - -
619A COH 3.8 51.4 - - + +
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 3.6 18.6 - - + -
182A LEU* 5.1 0.9 - - + -
388A HIS* 5.4 5.7 + - + -
440A VAL* 3.8 24.2 - - + -
444A VAL 3.1 6.4 + - - +
445A GLN 3.6 7.6 - - - +
447A VAL* 1.3 74.9 - - - +
449A LYS* 1.3 64.7 + - - +
451A SER* 3.3 9.1 + - - -
452A ILE* 3.5 5.0 + - - +
504A TYR* 3.5 39.4 - - + +
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Residues in contact with LYS 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP* 5.2 0.7 - - - -
174A SER* 3.2 26.5 + - - +
175A LYS* 4.0 28.0 - - + +
178A LEU* 4.0 15.1 - - + +
445A GLN 2.8 20.3 + - - +
446A ALA* 3.7 9.2 - - - +
447A VAL 3.3 0.2 - - - -
448A ALA* 1.3 72.7 - - - +
450A ALA* 1.3 57.8 + - - +
452A ILE* 3.2 10.0 + - - +
453A ASP* 2.7 52.9 + - - +
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Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A ALA 3.0 14.7 + - - +
447A VAL* 3.2 14.1 + - + +
449A LYS* 1.3 76.8 - - - +
451A SER* 1.3 55.1 + - - +
453A ASP* 4.5 7.0 - - - -
454A GLN* 2.8 53.8 + - - +
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Residues in contact with SER 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A THR* 5.1 3.5 - - - +
386A HIS* 2.9 35.1 - - - +
388A HIS* 5.4 0.2 - - - -
447A VAL 3.1 12.6 + - - -
448A ALA* 3.5 9.5 - - - -
449A LYS 3.2 0.4 - - - -
450A ALA* 1.3 75.8 - - - +
452A ILE* 1.3 60.4 + - - +
454A GLN* 4.4 4.4 - - - +
455A SER* 2.8 30.7 + - - -
504A TYR* 3.6 31.1 + - - +
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Residues in contact with ILE 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A SER* 3.6 34.5 - - - +
177A VAL* 4.1 16.2 - - + -
178A LEU* 4.5 4.7 - - + +
182A LEU* 4.1 23.1 - - + -
448A ALA 3.5 8.0 + - - +
449A LYS* 3.2 9.4 + - - +
451A SER* 1.3 75.1 - - - +
453A ASP* 1.3 65.0 + - - +
455A SER* 3.3 8.7 + - - -
456A ARG* 3.2 48.9 + - - +
495A TYR* 5.6 0.2 - - - +
502A GLU* 4.0 9.6 - - - +
504A TYR* 3.6 19.7 - - + -
505A PRO* 4.3 8.1 - - + -
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Residues in contact with ASP 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A SER* 2.6 28.3 + - - -
449A LYS* 2.7 45.6 + - - +
450A ALA* 4.1 5.9 - - - +
452A ILE* 1.3 73.9 - - - +
454A GLN* 1.3 57.3 + - + +
456A ARG* 3.3 13.7 + - - +
457A GLU* 2.9 40.3 + - - +
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Residues in contact with GLN 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A THR* 5.7 0.9 - - - +
214A HIS* 4.7 20.7 + - - -
218A PRO* 3.9 30.5 - - + +
386A HIS* 5.8 1.9 + - - -
450A ALA* 2.8 38.7 + - - +
451A SER* 4.4 3.8 - - - +
453A ASP* 1.3 68.2 - - + +
455A SER* 1.3 65.8 + - - +
456A ARG 3.1 0.9 - - - -
457A GLU* 3.6 19.6 - - - +
458A MET* 2.9 35.3 + - + +
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Residues in contact with SER 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A EDO 4.2 2.2 - - - -
383A THR* 4.0 12.1 + - - +
451A SER 2.8 23.8 + - - -
452A ILE* 3.3 8.3 + - - -
454A GLN* 1.3 76.4 - - - +
456A ARG* 1.3 63.0 + - - +
458A MET* 3.4 11.9 + - - +
459A LYS 3.2 4.5 + - - -
460A TYR* 3.1 53.6 + - - +
502A GLU* 5.0 7.0 - - - -
504A TYR* 4.3 7.9 + - - +
505A PRO* 6.5 0.7 - - - -
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Residues in contact with ARG 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A EDO 3.4 22.7 - - - -
171A LEU* 3.6 32.3 + - + +
172A PRO* 2.8 32.1 + - - +
173A ASP* 4.8 0.8 - - - +
174A SER* 3.9 16.9 - - - +
177A VAL* 4.6 1.4 - - - +
452A ILE* 3.2 27.4 + - - +
453A ASP* 3.5 11.7 + - - +
454A GLN 3.1 0.4 - - - -
455A SER* 1.3 77.7 - - - +
457A GLU* 1.3 65.5 + - - +
459A LYS* 3.0 16.5 + - - +
495A TYR* 4.3 4.2 + - - -
502A GLU* 2.8 44.0 + - - +
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Residues in contact with GLU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 5.0 2.6 - - - +
218A PRO* 3.9 24.5 - - + +
453A ASP* 2.9 30.7 + - - +
454A GLN* 3.2 18.1 + - - +
456A ARG* 1.3 76.7 - - + +
458A MET* 1.3 58.3 + - - +
459A LYS* 3.1 12.6 + - - +
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Residues in contact with MET 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 3.9 20.3 - - + +
150A ARG* 2.8 37.2 + - - +
154A PRO* 3.8 3.5 - - - +
218A PRO* 3.6 47.3 - - + +
219A GLY* 3.7 7.6 - - - +
379A SER* 3.5 26.2 - - - +
383A THR* 4.6 4.3 - - - +
454A GLN* 2.9 30.5 + - + +
455A SER* 3.9 4.9 - - - +
457A GLU* 1.3 74.0 - - - +
459A LYS* 1.3 66.9 + - - +
460A TYR* 3.4 19.7 - - + +
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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