Contacts of the helix formed by residues 316 - 325 (chain A) in PDB entry 5JQE
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 LEU 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A PHE* 5.7 0.4 - - + -
100A LYS* 3.5 35.7 - - + +
101A LEU* 4.2 10.6 - - + +
120A ILE 4.8 1.0 + - - -
297A LEU* 3.5 23.9 - - + +
298A THR* 3.5 26.5 - - - +
299A ASP* 3.5 24.2 - - - +
302A LEU* 3.7 20.6 - - + +
314A VAL* 3.3 3.4 - - + +
315A ALA* 1.3 75.5 - - - +
317A LYS* 1.3 66.6 + - - +
318A SER* 3.7 16.2 - - - +
319A TYR* 3.9 5.4 - - + +
320A GLU* 3.1 24.4 + - - +
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Residues in contact with LYS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP* 2.8 27.6 + - - +
100A LYS 2.8 20.8 + - - +
101A LEU 3.2 21.4 + - - -
102A TYR* 3.5 48.5 - - + +
103A PRO* 4.5 6.7 - - - +
315A ALA 3.2 0.8 + - - -
316A LEU* 1.3 72.1 - - - +
318A SER* 1.3 61.6 + - - +
320A GLU* 3.4 4.5 + - - +
321A GLU* 3.1 35.3 + - - +
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS* 4.6 6.9 + - - +
299A ASP* 3.0 28.6 - - - +
316A LEU* 3.2 18.0 - - - +
317A LYS* 1.3 82.1 - - - +
319A TYR* 1.3 59.6 + - - +
321A GLU* 3.6 18.1 + - - +
322A GLU* 3.8 6.8 + - - +
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Residues in contact with TYR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ASP* 3.2 23.1 + - + +
302A LEU* 3.5 25.4 - - + -
303A GLU* 3.3 41.1 + - + +
306A ASN* 3.4 24.4 + - + -
314A VAL* 4.0 11.0 - - + -
316A LEU* 3.6 13.3 + - + +
317A LYS 3.5 0.2 - - - -
318A SER* 1.3 77.7 - - - +
320A GLU* 1.3 64.5 + - - +
322A GLU* 3.1 29.5 - - + +
323A LEU* 3.0 43.3 + - + +
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR* 3.1 36.8 - - + +
313A ALA* 3.3 10.9 - - - +
314A VAL* 2.6 43.4 + - - +
316A LEU 3.1 19.1 + - - +
317A LYS 3.8 1.3 - - - +
318A SER 3.2 0.2 - - - -
319A TYR* 1.3 76.1 - - - +
321A GLU* 1.3 51.7 + - - +
323A LEU* 2.8 5.9 + - - +
324A ALA* 2.7 39.6 + - + +
329A ILE* 3.5 24.0 - - - +
330A ALA* 5.1 0.3 - - - -
333A MET* 3.9 17.3 - - + +
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR* 4.3 8.9 + - - +
317A LYS* 3.1 29.1 - - - +
318A SER* 3.6 11.0 - - - +
319A TYR 3.4 0.2 - - - -
320A GLU* 1.3 73.9 - - - +
322A GLU* 1.3 63.3 + - - +
324A ALA* 3.2 20.8 + - - +
325A LYS* 3.8 5.0 + - - +
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Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A SER 3.8 4.4 + - - +
319A TYR* 3.1 42.9 + - + +
321A GLU* 1.3 80.0 - - - +
323A LEU* 1.3 60.7 + - + +
324A ALA 3.4 0.2 + - - -
325A LYS* 3.7 13.2 + - - +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ASN* 3.9 17.3 - - - +
312A GLY 3.7 19.5 - - - +
314A VAL* 3.7 37.2 - - + +
319A TYR* 3.0 43.0 + - + +
320A GLU* 2.8 9.7 + - - +
322A GLU* 1.3 69.1 - - + +
324A ALA* 1.3 59.5 + - - +
325A LYS 3.1 3.6 - - - -
326A ASP* 2.9 30.5 + - - +
329A ILE* 3.7 24.7 - - + +
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A GLU* 2.7 27.5 + - + +
321A GLU* 3.2 16.0 + - - +
323A LEU* 1.3 67.5 - - - +
325A LYS* 1.3 56.5 + - - +
326A ASP 2.9 23.5 - - - +
327A PRO* 4.6 0.5 - - - +
330A ALA* 3.4 27.0 - - + +
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A GLU 3.8 4.2 + - - +
322A GLU 3.7 12.0 + - - +
323A LEU 3.1 1.6 + - - -
324A ALA* 1.3 76.1 - - - +
326A ASP* 1.3 55.9 + - - +
327A PRO* 3.4 11.7 - - - +
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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