Contacts of the helix formed by residues 397 - 406 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319B ALA 4.6 2.8 + - - -
383B PHE* 4.5 15.0 - - - -
392B TYR* 4.6 9.2 + - + -
395B TYR* 3.5 32.9 + - + +
396B PHE* 1.3 73.8 - - - +
398B TYR* 1.3 64.5 + - - +
399B GLU* 3.1 32.5 + - - +
400B MET* 3.2 48.3 + - + +
401B GLN* 3.6 13.3 + - - +
465B ILE* 3.9 25.1 - - - +
581B SER* 5.3 1.8 + - - -
582B ILE* 5.7 6.4 - - + +
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Residues in contact with TYR 398 (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 TRP* 3.9 26.6 - + - -
7B ASP 2.7 27.6 + - - -
8B GLU 3.9 1.2 + - - -
10B THR* 3.1 7.5 + - - -
11B PHE* 3.0 43.1 + + + -
14B PHE* 4.1 12.6 - + - -
16B TYR* 5.5 0.7 - - - -
396B PHE* 3.9 17.8 + + + -
397B LYS* 1.3 73.4 - - - +
399B GLU* 1.3 68.6 + - - +
400B MET 3.2 0.3 + - - -
401B GLN* 3.2 4.9 + - - +
402B LEU* 3.0 32.1 + - + +
589B ARG* 5.6 1.6 - - - +
593B TYR* 3.4 56.8 - + - +
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Residues in contact with GLU 399 (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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383B PHE* 4.0 20.4 - - + -
397B LYS* 3.1 31.5 + - - +
398B TYR* 1.3 78.7 + - - +
400B MET* 1.3 58.3 + - - +
402B LEU* 3.7 6.9 - - + +
403B MET* 3.0 35.4 + - - +
581B SER* 4.6 3.6 + - - -
582B ILE* 5.9 3.3 - - - +
592B ARG* 2.9 34.5 + - - +
593B TYR* 3.4 25.7 + - + -
596B PHE* 4.1 27.4 - - + -
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Residues in contact with MET 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ILE* 4.4 11.2 - - + -
383B PHE* 3.7 33.0 - - + -
392B TYR* 3.9 23.8 - - + -
397B LYS* 3.2 33.4 + - + +
399B GLU* 1.3 74.8 - - - +
401B GLN* 1.3 64.3 + - - +
404B ALA* 2.9 33.4 + - - +
410B ILE* 3.5 27.4 - - + +
412B TYR* 3.7 41.5 - - + -
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Residues in contact with GLN 401 (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 TRP* 3.7 25.8 - - + -
319B ALA* 3.2 29.1 + - - +
320B THR* 4.4 5.3 - - - +
348B THR* 3.9 6.8 - - + +
349B PHE* 3.0 52.4 + - - -
351B PRO* 5.3 0.2 - - - +
368B ILE* 4.0 11.1 - - - +
396B PHE* 4.3 15.7 - - + -
397B LYS 3.6 11.9 + - - +
398B TYR* 3.2 5.9 + - - +
400B MET* 1.3 77.5 - - - +
402B LEU* 1.3 63.0 + - - +
404B ALA* 3.7 4.1 - - - +
405B SER* 3.1 24.4 + - - -
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Residues in contact with LEU 402 (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 TRP* 3.6 45.3 - - + +
7B ASP 3.8 12.3 - - - +
398B TYR* 3.0 33.9 + - + +
399B GLU* 3.7 7.0 - - - +
401B GLN* 1.3 76.5 - - - +
403B MET* 1.3 72.1 + - + +
405B SER* 2.7 23.3 + - - -
406B LYS* 3.2 14.3 - - + +
593B TYR* 4.8 14.8 - - + +
596B PHE* 5.4 3.1 - - + -
597B MET* 3.6 36.1 - - + -
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Residues in contact with MET 403 (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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381B ILE* 3.8 27.6 - - + -
383B PHE* 5.0 2.0 - - + -
399B GLU* 3.0 19.2 + - - +
402B LEU* 1.3 78.2 - - + +
404B ALA* 1.3 65.0 + - - +
406B LYS* 3.0 14.5 + - + -
408B TYR* 3.2 55.6 + - + -
410B ILE* 4.0 8.5 - - + -
596B PHE* 3.9 22.4 - - + -
597B MET* 4.0 37.7 - - + +
600B PHE* 3.9 16.4 - - + -
601B GLU* 5.2 0.2 - - - +
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Residues in contact with ALA 404 (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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349B PHE* 3.5 27.7 - - + -
368B ILE* 3.6 23.8 - - + -
370B PRO* 3.6 18.4 - - + +
371B GLU 4.9 0.7 + - - -
400B MET 2.9 20.0 + - - +
401B GLN 3.7 0.2 - - - +
403B MET* 1.3 77.8 - - - +
405B SER* 1.3 62.0 + - - +
406B LYS 3.0 1.1 + - - -
407B GLY 3.1 10.2 + - - -
408B TYR 3.7 11.4 - - - +
410B ILE* 4.0 5.9 - - + +
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Residues in contact with SER 405 (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 TRP* 3.2 37.4 + - - +
347B LYS* 6.3 0.7 - - - -
349B PHE* 3.3 25.0 - - - -
401B GLN 3.1 8.3 + - - -
402B LEU 2.7 18.2 + - - -
404B ALA* 1.3 75.5 - - - +
406B LYS* 1.3 61.0 + - - +
407B GLY 3.3 1.7 + - - -
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Residues in contact with LYS 406 (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 TRP 5.1 8.4 + - - +
402B LEU* 3.2 18.6 - - + +
403B MET* 3.0 17.0 + - - +
405B SER* 1.3 84.5 - - - +
407B GLY* 1.3 59.8 + - - +
408B TYR* 3.6 10.3 - - + -
597B MET* 3.4 45.4 - - + +
601B GLU* 3.8 26.3 + - - -
605B LYS* 3.1 26.0 + - - +
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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