Contacts of the helix formed by residues 370 - 379 (chain K) in PDB entry 3HX0
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 THR 370 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569A GLU* 4.7 0.7 - - - -
343K GLY 4.5 1.4 + - - -
368K SER 5.9 0.2 - - - +
369K LEU* 1.3 76.2 - - - +
371K THR* 1.3 68.4 + - - +
372K GLN* 2.6 10.3 + - - +
373K GLN* 2.7 51.4 + - - +
374K ALA* 2.8 9.7 + - - -
10L C 5.1 0.7 - - - -
11L T 3.8 35.2 - - - +
12L G 5.8 1.1 - - - +
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Residues in contact with THR 371 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A GLU* 3.3 43.0 + - + +
571A ALA* 5.6 2.9 - - - +
370K THR* 1.3 69.7 - - - +
372K GLN* 1.3 66.3 + - + +
374K ALA* 3.5 3.8 - - - +
375K ILE* 3.4 29.9 + - + +
460K ASP 5.2 5.4 - - - +
461K LEU 6.2 0.4 - - - +
10L C 4.9 2.5 - - - -
11L T 2.8 27.0 + - - -
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Residues in contact with GLN 372 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342K TRP* 3.2 39.7 - - + +
343K GLY* 4.5 9.7 - - - +
370K THR* 2.6 11.5 + - - +
371K THR* 1.3 74.1 - - + +
373K GLN* 1.3 60.6 + - - +
375K ILE* 2.8 23.6 + - - +
376K GLY 2.8 10.6 + - - -
461K LEU* 2.9 36.4 + - - +
462K VAL* 3.2 15.8 - - - +
10L C 4.9 22.6 - - - +
11L T 4.8 0.2 + - - -
5M A 5.9 3.1 + - - +
6M T 5.4 3.1 - - - +
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Residues in contact with GLN 373 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341K ILE* 3.6 9.7 - - + +
342K TRP 3.3 11.0 + - - +
343K GLY* 2.7 31.8 + - - +
344K ALA* 3.2 9.3 - - - +
348K THR* 3.0 35.4 + - - +
352K TRP* 3.7 16.4 - - - -
368K SER 4.3 1.0 - - - +
369K LEU* 3.8 13.8 - - + +
370K THR* 2.7 45.7 + - - +
372K GLN* 1.3 72.1 - - - +
374K ALA* 1.3 62.2 + - - +
376K GLY 3.1 0.3 + - - -
377K LEU* 2.9 26.5 + - - +
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Residues in contact with ALA 374 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A LYS* 6.3 0.7 - - - +
569A GLU* 4.2 17.0 - - - +
369K LEU* 3.9 22.5 - - + +
370K THR 2.8 11.7 + - - +
371K THR* 3.5 11.7 - - - +
373K GLN* 1.3 77.7 - - - +
375K ILE* 1.3 59.4 + - + +
377K LEU* 3.5 2.9 + - - +
378K LYS* 3.0 27.1 + - - +
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Residues in contact with ILE 375 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371K THR* 3.4 21.1 - - + +
372K GLN* 2.8 8.0 + - - +
374K ALA* 1.3 75.1 - - + +
376K GLY* 1.3 65.7 + - - +
377K LEU 3.0 1.8 - - - -
378K LYS* 3.0 20.6 + - - +
379K HIS* 3.2 14.2 + - + +
383K PHE* 3.9 7.8 - - + -
459K ASP* 3.7 43.5 - - + +
460K ASP 3.7 21.8 - - - +
461K LEU* 3.7 23.1 - - + -
476K VAL* 4.1 10.8 - - + -
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Residues in contact with GLY 376 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340K ASN 5.3 0.7 - - - +
341K ILE* 3.8 8.1 - - - +
342K TRP* 3.8 34.5 + - - -
372K GLN 2.8 10.9 + - - -
373K GLN 3.1 4.0 + - - -
375K ILE* 1.3 77.4 - - - +
377K LEU* 1.3 57.0 + - - +
379K HIS 3.8 1.9 - - - -
380K TYR* 3.3 24.6 + - - +
383K PHE* 3.8 12.2 - - - -
461K LEU* 4.8 0.4 - - - +
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Residues in contact with LEU 377 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341K ILE* 3.8 22.6 - - + +
360K LEU* 4.3 28.0 - - + +
363K ILE* 3.7 17.3 - - + -
364K ARG* 4.0 24.2 - - + +
369K LEU* 3.7 24.7 - - + -
373K GLN 2.9 16.6 + - - +
374K ALA 3.7 4.0 - - - +
376K GLY* 1.3 74.1 - - - +
378K LYS* 1.3 65.3 + - - +
379K HIS 3.0 3.4 + - - -
380K TYR* 3.0 26.1 + - + +
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Residues in contact with LYS 378 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374K ALA 3.0 14.1 + - - +
375K ILE* 3.0 16.1 + - - +
377K LEU* 1.3 76.8 - - - +
379K HIS* 1.3 97.4 + - + +
380K TYR 4.1 0.2 + - - -
382K ASP* 5.0 0.7 - - - +
459K ASP* 3.4 24.9 + - - -
486K HIS* 4.9 1.6 - - - -
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Residues in contact with HIS 379 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375K ILE* 3.2 7.0 + - + -
376K GLY 3.8 3.8 - - - -
377K LEU 3.0 0.6 - - - -
378K LYS* 1.3 124.3 + - + +
380K TYR* 1.3 64.8 + - - +
381K SER 3.3 2.7 - - - -
382K ASP* 3.0 16.2 + - + +
383K PHE* 2.9 57.2 + + + -
458K THR* 4.0 0.2 - - - -
459K ASP* 3.5 17.9 - - - -
476K VAL* 3.6 10.8 - - + +
486K HIS* 2.8 42.8 + + - -
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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