Contacts of the helix formed by residues 349 - 358 (chain N) 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 ASP 349 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348N THR* 1.3 83.5 - - - +
350N LEU* 1.3 59.4 + - - +
351N MET* 3.3 12.9 - - - +
352N ILE* 2.7 43.1 + - - +
353N LEU 3.6 7.6 + - - -
376N MET* 3.3 5.7 - - - +
734N GLN* 5.6 0.3 + - - -
738N ASP* 6.1 0.2 - - - -
815N ALA 4.0 4.7 - - - +
816N PRO* 3.0 59.5 - - + +
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Residues in contact with LEU 350 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348N THR* 3.5 6.9 - - - -
349N ASP* 1.3 74.4 - - - +
351N MET* 1.3 55.9 + - + +
353N LEU* 2.7 6.3 + - + -
354N LYS* 2.1 51.3 + - + +
357N LYS* 4.0 15.7 - - - +
373N ASN* 5.4 2.9 - - - +
376N MET* 3.6 15.4 - - + +
377N HIS* 5.9 2.7 - - + +
384N GLN* 5.0 17.9 - - + -
385N PHE* 6.0 0.4 - - - +
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Residues in contact with MET 351 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349N ASP* 3.1 10.4 - - - +
350N LEU* 1.3 80.9 - - - +
352N ILE* 1.3 53.2 + - - +
354N LYS* 3.2 10.9 - - - +
355N ASN* 2.4 36.1 + - - +
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Residues in contact with ILE 352 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349N ASP* 2.7 34.9 + - - +
351N MET* 1.3 71.6 - - - +
353N LEU* 1.3 51.1 + - - +
355N ASN* 3.1 14.8 - - + +
356N THR* 2.5 39.5 + - - +
714N SER* 4.9 10.1 - - - +
734N GLN* 3.4 20.0 - - - +
816N PRO 5.3 0.7 - - - +
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Residues in contact with LEU 353 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349N ASP 3.6 1.6 + - - +
350N LEU* 2.7 19.8 + - + +
352N ILE* 1.3 72.7 - - - +
354N LYS* 1.3 53.5 + - - +
356N THR* 2.8 15.0 + - - +
357N LYS* 2.3 65.6 + - + +
369N THR* 4.9 0.7 - - - +
372N ALA* 3.9 21.3 - - + -
373N ASN* 3.6 29.6 - - - +
376N MET* 3.4 32.5 - - + -
731N ILE* 4.2 11.0 - - + +
734N GLN* 4.0 11.5 - - + +
735N GLY* 5.4 0.7 - - - -
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Residues in contact with LYS 354 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350N LEU* 2.1 52.6 + - + +
351N MET* 3.2 11.0 - - - +
353N LEU* 1.3 66.1 - - - +
355N ASN* 1.3 50.3 + - - +
357N LYS* 2.7 27.7 + - - +
358N ASP* 2.2 49.3 + - + +
385N PHE* 4.6 8.1 - - + -
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Residues in contact with ASN 355 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351N MET 2.4 29.8 + - - +
352N ILE* 3.1 21.1 - - - +
354N LYS* 1.3 66.1 - - - +
356N THR* 1.3 55.7 + - - +
358N ASP* 3.1 11.2 - - - -
359N ALA* 2.9 25.5 + - - +
714N SER* 6.6 0.2 - - - -
717N ILE* 4.4 3.0 - - - +
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Residues in contact with THR 356 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352N ILE* 2.5 24.4 + - - +
353N LEU* 2.8 23.3 + - - -
355N ASN* 1.3 74.1 - - - +
357N LYS* 1.3 60.0 + - - +
359N ALA* 2.9 21.2 - - - +
360N VAL 4.1 2.1 + - - -
369N THR* 4.6 0.9 - - - -
714N SER* 5.5 0.7 + - - -
717N ILE* 3.8 14.8 - - - +
731N ILE* 3.8 26.4 - - - +
734N GLN* 3.1 23.5 + - - -
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Residues in contact with LYS 357 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350N LEU* 4.0 8.9 - - - +
353N LEU* 2.3 52.6 + - + +
354N LYS* 2.7 38.9 + - - +
356N THR* 1.3 65.2 - - - +
358N ASP* 1.3 56.8 + - - +
359N ALA 3.0 4.4 + - - -
360N VAL 2.9 23.9 - - - +
369N THR* 3.7 32.8 - - - +
373N ASN* 4.2 1.5 + - + -
385N PHE* 2.9 73.0 - - + +
389N ASN* 6.2 0.4 - - - -
392N TRP* 5.1 4.7 - - + -
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Residues in contact with ASP 358 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354N LYS* 2.2 49.0 + - + +
355N ASN* 3.1 20.6 - - - -
357N LYS* 1.3 67.9 - - - +
359N ALA* 1.3 67.5 + - - +
360N VAL* 3.5 1.8 + - - +
385N PHE* 5.4 1.0 - - - -
389N ASN* 6.3 0.4 - - - +
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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