Contacts of the helix formed by residues 397 - 406 (chain A) in PDB entry 4HXG
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 LYS 397 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ALA 4.6 3.0 + - - -
383A PHE* 4.1 23.2 - - - -
392A TYR* 4.7 7.9 + - - +
395A TYR* 3.7 28.3 + - + +
396A PHE* 1.3 75.0 - - - +
398A TYR* 1.3 65.1 + - - +
399A GLU* 3.2 34.3 + - - +
400A MET* 3.1 50.3 + - + +
401A GLN* 3.4 14.6 + - - +
465A ILE* 4.2 19.2 - - - +
581A SER* 5.5 0.4 + - - -
582A ILE* 6.1 2.6 - - - +
592A ARG* 5.4 0.6 - - - +
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Residues in contact with TYR 398 (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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6A TRP* 3.4 31.1 - + - -
7A ASP 2.6 26.1 + - - -
8A GLU 4.0 1.2 - - - -
10A THR* 3.1 18.7 + - - -
11A PHE* 3.2 28.7 + - + -
14A PHE* 4.1 12.1 - + - -
16A TYR* 5.7 0.2 - - - -
396A PHE* 3.8 18.4 + + + -
397A LYS* 1.3 72.5 - - - +
399A GLU* 1.3 64.5 + - - +
400A MET 3.2 0.3 + - - -
401A GLN* 3.2 5.2 + - - +
402A LEU* 2.9 40.5 + - + +
589A ARG* 5.8 0.9 - - - +
593A TYR* 3.4 55.0 - + - +
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Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A PHE* 3.9 19.7 - - + -
397A LYS* 3.2 33.2 + - - +
398A TYR* 1.3 79.9 + - - +
400A MET* 1.3 58.1 + - - +
402A LEU* 3.7 8.2 - - + +
403A MET* 2.9 35.2 + - - +
581A SER* 4.6 4.9 + - - -
582A ILE* 5.8 4.0 - - - +
592A ARG* 3.1 32.7 + - - +
593A TYR* 3.5 25.5 + - + -
596A PHE* 4.1 24.5 - - + -
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Residues in contact with MET 400 (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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368A ILE* 4.4 9.8 - - + +
383A PHE* 3.6 35.4 - - + -
392A TYR* 3.9 18.2 - - + -
397A LYS* 3.1 33.5 + - + +
399A GLU* 1.3 75.7 - - - +
401A GLN* 1.3 69.0 + - - +
404A ALA* 3.0 24.6 + - - +
410A ILE* 3.6 29.2 - - + +
412A TYR* 3.6 50.0 - - + -
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Residues in contact with GLN 401 (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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6A TRP* 3.7 26.8 - - + -
319A ALA* 3.6 20.1 + - - +
348A THR* 3.8 10.8 - - + +
349A PHE* 2.9 52.2 + - - -
368A ILE* 3.9 16.8 - - - +
396A PHE* 4.3 20.4 - - + -
397A LYS 3.4 11.6 + - - +
398A TYR 3.2 4.8 + - - +
400A MET* 1.3 77.9 - - - +
402A LEU* 1.3 64.7 + - - +
404A ALA* 3.2 5.1 + - - +
405A SER* 3.0 24.9 + - - -
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TRP* 3.6 46.8 - - + +
7A ASP* 3.8 13.7 - - - +
398A TYR* 2.9 38.6 + - + +
399A GLU* 3.7 7.4 - - - +
401A GLN* 1.3 77.5 - - - +
403A MET* 1.3 74.1 + - - +
405A SER* 2.8 21.6 + - - -
406A LYS* 3.3 20.6 + - + +
593A TYR* 4.6 15.5 - - + +
596A PHE* 5.9 2.7 - - + -
597A MET* 4.2 18.2 - - + -
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Residues in contact with MET 403 (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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381A ILE* 3.6 29.6 - - + -
383A PHE* 4.9 1.1 - - + -
399A GLU 2.9 25.0 + - - +
402A LEU* 1.3 81.5 - - - +
404A ALA* 1.3 59.9 + - - +
406A LYS* 3.3 12.4 + - + -
408A TYR* 3.0 66.6 + - + +
410A ILE* 3.7 10.5 - - + -
596A PHE* 3.9 23.1 - - + -
597A MET* 4.3 29.6 - - - +
600A PHE* 4.2 12.6 - - + -
601A GLU* 4.8 0.7 - - - +
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Residues in contact with ALA 404 (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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349A PHE* 3.8 31.4 - - + -
368A ILE* 3.9 17.0 - - + -
370A PRO* 3.5 15.4 - - + +
371A GLU 4.8 0.9 + - - -
400A MET 3.0 19.7 + - - +
401A GLN* 3.2 4.7 + - - +
403A MET* 1.3 72.5 - - - +
405A SER* 1.3 57.0 + - - +
406A LYS 2.9 4.7 - - - -
407A GLY* 2.9 17.0 + - - -
408A TYR 3.6 14.6 + - - +
410A ILE* 4.3 2.4 - - + +
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Residues in contact with SER 405 (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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6A TRP* 3.1 44.6 + - - +
347A LYS* 6.1 0.7 - - - -
349A PHE* 3.7 18.5 - - - -
401A GLN 3.0 8.6 + - - -
402A LEU 2.8 16.5 + - - -
404A ALA* 1.3 76.8 - - - +
406A LYS* 1.3 61.8 + - - +
407A GLY 3.7 0.3 + - - -
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TRP 4.8 8.3 + - - +
402A LEU* 3.3 20.6 + - + +
403A MET* 3.3 14.7 + - - +
404A ALA 2.9 1.4 - - - -
405A SER* 1.3 85.3 - - - +
407A GLY* 1.3 55.8 + - - +
408A TYR* 3.6 10.1 - - + -
597A MET* 3.6 44.5 - - + +
598A GLU* 5.6 1.1 + - - -
601A GLU* 4.0 25.1 + - - +
605A LYS* 2.8 29.6 + - - +
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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