Contacts of the helix formed by residues 379 - 385 (chain I) 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 THR 379 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377I ASP 4.0 8.1 - - - +
378I VAL* 1.3 82.4 - - - +
380I LEU* 1.3 54.2 + - - +
381I ASP* 2.4 32.6 + - - +
382I ASP* 2.7 29.5 + - - +
383I LEU* 4.0 2.5 + - - +
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Residues in contact with LEU 380 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362I LYS* 4.7 3.1 - - + +
365I PHE* 3.2 29.4 - - + -
366I GLN* 3.3 34.8 - - + +
369I THR* 3.1 44.6 - - + +
374I LEU* 3.7 15.0 - - + +
378I VAL* 4.1 3.6 + - + +
379I THR* 1.3 68.6 - - - +
381I ASP* 1.3 66.2 + - - +
382I ASP 3.4 0.2 - - - -
383I LEU* 3.2 16.3 + - + -
384I ILE* 3.0 21.8 + - + +
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Residues in contact with ASP 381 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362I LYS* 3.2 37.2 + - - +
379I THR* 2.4 27.5 + - - +
380I LEU* 1.3 69.2 - - - +
382I ASP* 1.3 66.3 + - - +
384I ILE* 2.8 18.9 + - - +
385I MET* 2.8 17.8 + - + +
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Residues in contact with ASP 382 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379I THR* 2.7 25.1 + - - +
381I ASP* 1.3 73.0 - - - +
383I LEU* 1.3 58.2 + - + +
385I MET* 3.7 20.3 - - - +
386I ALA* 3.0 26.0 + - - +
416I ASN* 5.5 0.5 - - - +
420I LYS* 3.4 25.8 + - - -
423I LYS* 3.5 12.2 + - - +
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Residues in contact with LEU 383 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365I PHE* 2.7 44.2 - - + -
378I VAL* 6.4 1.3 - - + -
379I THR 5.0 2.0 - - - +
380I LEU* 3.2 18.4 + - + +
381I ASP 3.0 1.0 - - - -
382I ASP* 1.3 74.1 - - + +
384I ILE* 1.3 58.5 + - - +
386I ALA* 2.8 24.3 + - - +
387I LYS 3.7 3.1 + - - -
390I LEU* 4.0 8.3 - - - +
398I ILE* 3.9 8.4 - - + +
419I PHE* 4.0 33.0 - - + -
423I LYS* 1.4 77.0 - - + +
427I LEU* 5.8 0.2 - - - +
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Residues in contact with ILE 384 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357I ASP 4.4 2.2 - - - +
358I GLU* 3.9 30.9 - - + +
361I LYS* 3.8 40.9 + - + +
362I LYS* 3.1 57.0 - - + +
365I PHE* 3.6 16.6 - - + -
380I LEU* 3.0 20.7 + - + +
381I ASP* 2.8 16.0 + - - +
383I LEU* 1.3 74.3 - - - +
385I MET* 1.3 58.0 + - - +
386I ALA 3.1 4.3 + - - -
387I LYS 4.1 9.0 + - - +
390I LEU* 4.5 3.2 - - - +
395I ILE* 5.8 0.4 - - + -
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Residues in contact with MET 385 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358I GLU* 4.2 19.3 - - - +
381I ASP* 2.8 17.6 + - + +
382I ASP* 3.7 23.1 - - - +
384I ILE* 1.3 71.2 - - - +
386I ALA* 1.3 64.2 + - - +
387I LYS 4.1 4.2 - - - +
176j LYS* 4.9 18.9 + - + +
50k VAL 6.1 0.9 - - - +
52k LYS* 5.9 8.1 - - + -
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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