Contacts of the helix formed by residues 394 - 404 (chain O) in PDB entry 3H1J
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 ALA 394 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368O TYR* 5.3 0.2 - - - -
392O HIS* 3.4 9.0 + - + +
393O THR* 1.3 75.1 - - - +
395O PRO* 1.3 63.1 - - + +
396O SER* 2.5 26.2 + - - +
397O VAL* 2.7 27.4 + - + +
398O VAL* 3.2 7.8 + - - -
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Residues in contact with PRO 395 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368O TYR* 4.1 23.1 - - + +
369O LEU* 4.6 14.4 - - + +
392O HIS* 4.7 8.7 - - + +
393O THR 3.9 3.8 - - - +
394O ALA* 1.3 83.8 - - + +
396O SER* 1.3 58.4 + - - +
398O VAL* 2.9 27.1 - - + +
399O ALA* 3.4 12.0 + - - +
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Residues in contact with SER 396 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394O ALA* 2.5 16.6 + - - -
395O PRO* 1.3 75.0 - - - +
397O VAL* 1.3 66.5 + - - +
399O ALA* 3.1 20.7 - - - +
400O GLN* 3.3 18.3 + - - +
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Residues in contact with VAL 397 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393O THR* 3.4 18.4 - - + +
394O ALA* 2.7 28.9 + - + +
396O SER* 1.3 71.0 + - - +
398O VAL* 1.3 65.6 + - - +
400O GLN* 2.8 33.8 + - - +
401O LYS* 3.2 36.5 + - - +
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Residues in contact with VAL 398 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368O TYR* 3.8 37.2 - - + +
393O THR* 3.3 15.5 - - + +
394O ALA 3.2 2.2 + - - -
395O PRO* 2.9 42.4 - - + +
397O VAL* 1.3 78.0 - - - +
399O ALA* 1.3 65.4 + - - +
400O GLN 3.3 0.3 + - - -
401O LYS* 3.3 17.3 + - + +
402O ILE* 3.1 30.2 + - + +
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Residues in contact with ALA 399 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365O LYS* 4.4 13.4 - - + +
395O PRO 3.4 11.2 - - - +
396O SER* 3.1 16.6 - - - +
397O VAL 3.0 0.2 - - - -
398O VAL* 1.3 83.5 - - - +
400O GLN* 1.3 58.0 + - - +
402O ILE* 3.3 22.4 + - + +
403O ASP* 2.9 23.3 - - - +
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Residues in contact with GLN 400 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396O SER* 3.5 19.1 + - - +
397O VAL* 2.8 35.1 + - - +
399O ALA* 1.3 67.0 - - - +
401O LYS* 1.3 66.2 + - + +
402O ILE 2.8 13.7 + - - -
403O ASP* 2.5 23.8 - - - +
404O SER* 3.0 15.4 + - - -
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Residues in contact with LYS 401 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270O ASN* 3.8 31.9 + - - +
393O THR* 6.1 0.4 - - + -
397O VAL* 3.5 36.3 - - + +
398O VAL* 3.6 11.4 - - + +
400O GLN* 1.3 86.5 - - + +
402O ILE* 1.3 61.0 + - - +
404O SER* 3.0 20.9 + - - +
405O VAL* 3.8 3.6 - - - +
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Residues in contact with ILE 402 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270O ASN* 4.9 7.2 - - - +
274O VAL* 4.5 2.5 - - + -
361O LYS* 3.9 29.0 - - + +
364O LEU* 4.0 37.0 - - + +
365O LYS* 3.8 28.0 - - + -
368O TYR* 5.7 5.2 - - + -
398O VAL* 3.1 28.0 - - + +
399O ALA* 3.3 13.2 - - - +
400O GLN 2.8 1.8 + - - -
401O LYS* 1.3 74.5 - - + +
403O ASP* 1.3 58.4 + - - +
404O SER 3.0 3.1 - - - -
405O VAL* 2.8 35.1 + - - +
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Residues in contact with ASP 403 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361O LYS* 2.6 39.2 + - + +
365O LYS* 3.3 25.4 + - - +
399O ALA* 2.9 15.5 - - - +
400O GLN* 2.5 33.4 - - - +
402O ILE* 1.3 69.8 - - - +
404O SER* 1.3 57.6 + - - +
405O VAL 3.0 6.4 - - - +
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Residues in contact with SER 404 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400O GLN 3.0 14.6 + - - -
401O LYS* 3.0 23.5 + - - +
402O ILE 2.9 1.0 + - - -
403O ASP* 1.3 75.8 + - - +
405O VAL* 1.3 64.3 + - - +
406O THR* 3.4 13.6 + - - +
409O ASP* 4.0 1.9 - - - +
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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