Contacts of the helix formed by residues 343 - 351 (chain J) in PDB entry 5GJQ
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 ASN 343 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341J GLY 3.9 0.6 - - - -
342J ILE* 1.3 73.5 - - - +
344J LEU* 1.3 63.6 + - - +
345J ARG* 2.8 53.4 + - - +
346J LYS* 3.4 40.4 - - + +
347J ILE* 3.7 6.6 + - - +
380J GLN* 3.2 24.4 + - - +
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Residues in contact with LEU 344 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326J LEU* 4.0 11.0 - - + -
329J LEU* 3.3 33.5 - - + +
330J LYS* 3.7 30.1 - - + -
333J SER* 3.8 17.5 - - - +
338J LEU* 4.8 2.5 - - + -
342J ILE* 3.4 40.7 + - + +
343J ASN* 1.3 72.8 + - - +
345J ARG* 1.3 68.2 + - - +
347J ILE* 2.8 27.0 + - + +
348J ALA 3.0 10.7 + - - -
383J PHE* 5.1 1.1 - - + -
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Residues in contact with ARG 345 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322J GLU* 4.5 7.9 - - + +
326J LEU* 3.0 37.8 - - + +
343J ASN* 2.8 30.9 + - - +
344J LEU* 1.3 75.8 - - - +
346J LYS* 1.3 64.0 + - - +
348J ALA* 2.8 17.5 + - - +
349J GLU* 2.9 28.7 + - - +
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Residues in contact with LYS 346 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343J ASN* 3.3 39.4 + - + +
344J LEU 3.2 0.2 - - - -
345J ARG* 1.3 78.2 - - + +
347J ILE* 1.3 66.1 + - - +
349J GLU* 3.3 17.5 + - - +
350J LEU* 3.2 25.5 + - + +
380J GLN* 2.9 31.2 + - - +
384J GLU* 4.1 7.0 + - - +
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Residues in contact with ILE 347 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329J LEU* 4.2 6.1 - - + -
342J ILE* 5.0 0.9 - - + -
343J ASN 3.9 13.9 - - - +
344J LEU* 2.8 31.0 + - + +
346J LYS* 1.3 72.3 - - + +
348J ALA* 1.3 54.4 + - - +
350J LEU* 3.0 14.9 + - - +
351J MET* 3.0 45.2 + - + +
380J GLN* 4.3 14.8 - - + +
383J PHE* 3.1 48.0 - - + -
384J GLU* 4.3 16.4 - - + -
387J VAL* 4.0 15.5 - - + -
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Residues in contact with ALA 348 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322J GLU* 3.9 32.1 - - + +
325J ARG* 3.8 23.7 + - + -
326J LEU* 4.2 6.5 - - - +
329J LEU* 4.2 6.2 - - + +
344J LEU 3.0 8.8 + - - +
345J ARG* 2.8 11.1 + - - +
347J ILE* 1.3 68.5 - - - +
349J GLU* 1.3 56.4 + - - +
351J MET* 2.7 43.6 - - - +
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Residues in contact with GLU 349 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322J GLU* 4.2 18.5 - - + +
345J ARG* 2.9 21.7 + - - +
346J LYS* 3.3 24.4 + - - +
348J ALA* 1.3 75.5 - - - +
350J LEU* 1.3 67.1 + - + +
351J MET 3.0 9.4 - - - +
352J PRO* 4.7 2.9 - - - +
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Residues in contact with LEU 350 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346J LYS* 3.6 14.6 - - + +
347J ILE* 3.0 14.5 + - + +
349J GLU* 1.3 76.7 - - + +
351J MET* 1.3 57.7 + - - +
352J PRO* 3.1 19.8 - - - +
384J GLU* 4.6 24.0 - - + +
387J VAL* 4.0 25.2 - - + +
391J MET* 3.7 10.2 - - - +
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Residues in contact with MET 351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325J ARG* 3.5 25.0 + - - +
329J LEU* 4.9 7.9 - - + -
347J ILE* 3.0 36.3 + - + +
348J ALA* 2.7 37.3 - - - +
349J GLU 3.0 9.6 - - - +
350J LEU* 1.3 71.5 - - - +
352J PRO* 1.3 67.6 - - + +
354J ALA* 5.0 8.7 - - + -
359J VAL* 4.0 34.8 - - + -
362J VAL* 3.8 34.8 - - + -
387J VAL* 5.1 5.2 - - + -
391J MET* 4.3 6.7 - - - -
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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