Contacts of the helix formed by residues 338 - 343 (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 ASP 338 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428H ARG* 4.3 6.1 + - - +
429H TYR* 2.3 32.3 + - - -
306I GLN* 3.5 25.0 + - - -
309I MET* 4.7 13.5 - - + +
310I LEU* 5.9 1.4 - - - +
313I LEU* 5.0 1.8 - - + +
336I THR 4.1 1.2 + - - -
337I LEU* 1.3 77.5 - - - +
339I PRO* 1.3 80.2 - - - +
340I ALA* 4.0 10.1 - - + +
341I LEU* 2.8 31.5 + - + +
342I ILE* 3.4 6.9 + - - +
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Residues in contact with PRO 339 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H PRO* 5.7 0.2 - - - -
423H PHE 5.3 1.3 - - - +
425H ALA* 2.5 40.0 - - + +
428H ARG* 4.0 24.0 - - + +
429H TYR* 3.8 21.8 - - + -
337I LEU 3.6 6.3 - - - +
338I ASP* 1.3 92.9 - - - +
340I ALA* 1.3 57.1 + - - +
342I ILE* 3.1 7.1 + - + +
343I ARG* 2.7 34.3 + - - +
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Residues in contact with ALA 340 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H PRO* 5.3 6.7 - - + -
322H ASN* 5.6 1.6 - - - +
429H TYR* 3.6 24.4 + - + +
313I LEU* 2.4 43.5 - - + -
338I ASP* 4.2 8.1 - - + +
339I PRO* 1.3 81.3 - - - +
341I LEU* 1.3 58.8 + - - +
343I ARG* 3.5 11.7 - - - +
346I ARG* 2.9 27.9 + - - +
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Residues in contact with LEU 341 (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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309I MET* 3.1 41.7 - - + -
312I LEU* 4.0 27.8 - - + +
313I LEU* 4.4 23.6 - - + +
316I LEU* 5.2 5.6 - - + +
329I MET* 4.3 14.8 - - + -
337I LEU* 3.6 17.7 - - + -
338I ASP* 2.8 19.0 + - + +
340I ALA* 1.3 77.1 - - - +
342I ILE* 1.3 73.3 + - + +
346I ARG* 3.9 4.7 - - - +
347I ILE* 3.3 30.5 + - - +
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Residues in contact with ILE 342 (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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423H PHE* 3.1 31.9 - - + -
425H ALA* 6.2 0.2 - - + -
223I ILE* 3.8 22.4 - - + -
329I MET* 5.3 2.0 - - + -
331I THR* 6.3 0.2 - - + -
334I ILE* 3.9 20.2 - - + +
337I LEU* 3.4 39.3 - - + +
338I ASP 3.4 2.7 + - - +
339I PRO* 3.1 8.6 + - + +
341I LEU* 1.3 83.2 - - + +
343I ARG* 1.3 76.6 + - - +
347I ILE 2.6 15.9 - - - +
350I LYS* 2.9 28.5 + - - +
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Residues in contact with ARG 343 (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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218H PRO* 3.7 25.8 - - + +
383H ALA* 3.8 9.7 - - - +
424H SER 4.9 14.4 - - - +
425H ALA* 5.4 0.9 - - + -
501H ADP 3.1 55.2 + - - -
317I ASP* 3.2 15.1 + - - -
339I PRO 2.7 19.3 + - - +
340I ALA* 3.5 17.9 - - - +
341I LEU 3.8 0.5 - - - +
342I ILE* 1.3 89.3 - - - +
344I PRO* 1.3 88.9 + - + +
345I GLY* 4.2 8.1 - - - -
346I ARG* 2.2 44.1 - - - +
347I ILE 3.0 15.8 + - - -
350I LYS* 4.4 0.7 - - - +
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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