Contacts of the helix formed by residues 327 - 335 (chain L) 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 327 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325L GLU 2.8 9.7 + - - +
326L ILE* 1.3 69.7 - - - +
328L TYR* 1.3 55.9 + - - +
329L GLU 3.9 0.7 + - - -
330L ALA* 2.0 56.4 + - - +
331L ILE* 2.8 35.0 + - + +
364L GLN* 3.8 28.7 + - + +
367L PHE* 6.1 0.6 - - - -
368L MET* 3.2 19.7 - - + +
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Residues in contact with TYR 328 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310L LEU* 4.0 7.4 - - + -
313L LEU* 3.9 24.7 - - + -
314L LYS* 3.1 54.2 - - + +
317L ALA* 4.2 11.2 - - + +
318L GLY* 4.0 11.8 + - - -
322L LYS* 1.6 38.4 + - - -
326L ILE* 2.6 34.9 + - + +
327L ASP* 1.3 75.0 - - - +
329L GLU* 1.3 62.2 + - - +
331L ILE* 5.2 6.1 - - + -
332L VAL* 3.0 32.3 + - - +
367L PHE* 5.6 2.2 - + - -
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Residues in contact with GLU 329 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306L GLU* 4.2 10.6 - - - +
310L LEU* 4.9 14.3 - - + +
327L ASP* 3.4 0.6 + - - -
328L TYR* 1.3 78.8 - - - +
330L ALA* 1.3 57.4 + - - +
332L VAL* 4.6 4.4 - - - +
333L LYS* 3.1 44.2 + - + +
211h LYS* 5.5 7.2 - - - +
214h GLU* 5.2 4.7 - - - +
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Residues in contact with ALA 330 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327L ASP* 2.0 55.1 + - - +
329L GLU* 1.3 72.9 - - - +
331L ILE* 1.3 65.0 + - - +
333L LYS* 3.1 12.7 + - - +
334L LEU* 3.2 16.5 + - + +
368L MET* 4.0 12.7 - - + +
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Residues in contact with ILE 331 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313L LEU* 3.9 21.3 - - + -
326L ILE* 6.0 0.7 - - + -
327L ASP* 2.8 40.5 + - + +
328L TYR* 5.2 4.9 - - + -
330L ALA* 1.3 72.6 - - - +
332L VAL* 1.3 59.9 + - - +
334L LEU* 3.3 1.4 + - - -
335L SER* 2.2 35.0 + - - +
343L LEU* 6.3 0.7 - - + -
346L VAL* 4.2 10.3 - - + -
367L PHE* 2.5 62.8 - - + -
368L MET* 4.2 11.6 - - + -
371L VAL* 3.4 26.2 - - + +
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Residues in contact with VAL 332 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306L GLU* 3.1 42.2 - - + +
309L ARG* 3.7 10.5 + - + -
310L LEU* 3.4 29.4 - - + +
313L LEU* 2.9 33.9 - - + -
328L TYR 3.0 15.4 + - - +
329L GLU* 4.6 4.3 - - - +
331L ILE* 1.3 76.1 - - - +
333L LYS* 1.3 56.7 + - - +
335L SER* 2.7 34.4 - - - +
343L LEU* 5.9 0.2 - - - -
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Residues in contact with LYS 333 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306L GLU* 3.9 37.5 + - - +
329L GLU* 3.1 35.1 + - + +
330L ALA* 3.1 7.8 + - - +
331L ILE 3.1 0.6 - - - -
332L VAL* 1.3 81.3 - - - +
334L LEU* 1.3 66.3 + - + +
335L SER 2.9 4.7 + - - +
336L ASP* 4.3 7.6 + - - +
54h LYS 5.3 1.4 + - - -
55h LYS* 5.1 5.9 - - - +
56h VAL* 3.5 31.7 + - - +
57h PRO* 4.2 21.8 - - + +
214h GLU* 5.2 10.4 + - - +
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Residues in contact with LEU 334 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330L ALA 3.2 9.3 + - - +
331L ILE 4.0 2.2 - - - +
333L LYS* 1.3 78.5 - - + +
335L SER* 1.3 57.5 + - - +
336L ASP* 3.2 9.8 + - - +
338L PHE* 4.8 2.8 - - - -
368L MET* 4.0 21.1 - - + -
371L VAL* 4.4 12.1 - - + +
372L ARG* 3.1 56.1 - - + +
375L ALA* 5.0 5.5 - - - +
57h PRO* 3.8 26.7 - - + +
58h ASP* 5.3 2.7 - - + -
170n GLN* 5.9 1.1 - - - +
173n LYS* 5.5 4.9 - - - +
177n GLU* 4.5 7.9 - - - +
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Residues in contact with SER 335 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309L ARG* 2.5 33.5 + - - -
331L ILE* 2.2 35.5 + - - +
332L VAL* 2.7 18.1 - - - +
333L LYS 2.9 1.8 + - - +
334L LEU* 1.3 75.7 - - - +
336L ASP* 1.3 53.1 + - - +
338L PHE* 3.4 26.2 - - - -
343L LEU* 4.2 15.8 - - - +
346L VAL* 5.3 0.9 - - - +
371L VAL* 3.1 14.0 - - - +
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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
------------------------------------------------------------
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