Contacts of the helix formed by residues 367 - 377 (chain A) in PDB entry 4LEY
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 PHE 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A TRP* 3.5 48.9 - + + -
319A PRO* 5.2 0.4 - - + -
322A THR* 3.8 25.8 - - + -
345A PHE* 3.9 16.6 - - + -
365A LEU* 4.1 27.1 - - + -
366A SER* 1.3 80.6 + - - +
368A SER* 1.3 64.3 + - - +
369A HIS* 3.1 15.5 - + - -
370A THR* 3.2 2.6 + - - +
371A GLU* 3.0 31.3 + - - +
467A HIS* 4.5 7.6 - + - -
469A PHE* 3.7 46.9 - + + -
470A ILE* 4.7 3.6 - - + -
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Residues in contact with SER 368 (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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197A THR* 3.6 30.4 + - - +
198A GLY 5.4 1.3 + - - -
202A GLU* 4.5 3.0 - - - +
215A MET* 3.6 14.8 - - - +
309A ILE* 5.8 1.6 - - - +
346A TYR* 5.8 0.2 - - - -
366A SER* 3.2 15.4 + - - -
367A PHE* 1.3 77.2 - - - +
369A HIS* 1.3 57.9 + - - +
371A GLU* 3.7 15.2 + - - +
372A LYS* 2.9 28.2 + - - +
424A LYS* 6.0 0.7 - - - -
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Residues in contact with HIS 369 (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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195A LEU* 4.2 25.4 - - + -
197A THR* 4.3 6.0 - - + +
215A MET* 5.5 2.5 - - - +
318A TRP* 4.7 0.8 - + - -
343A GLU* 4.2 23.1 - - + +
344A PRO* 2.7 28.7 + - + -
346A TYR* 3.3 33.0 - + + -
367A PHE* 3.5 23.8 - + - -
368A SER* 1.3 75.6 + - - +
370A THR* 1.3 91.9 + - - -
372A LYS* 3.1 9.1 + - - +
373A TYR* 2.9 23.3 + - - +
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Residues in contact with THR 370 (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 TRP* 3.6 21.1 - - + -
326A LEU* 4.5 2.5 - - + -
340A LEU* 4.0 31.1 + - + +
343A GLU* 5.5 0.9 - - - +
367A PHE* 3.2 7.0 + - - +
369A HIS* 1.3 100.3 + - - +
371A GLU* 1.3 58.0 + - - +
373A TYR* 3.3 7.6 + - - +
374A ILE* 2.9 36.4 + - + +
469A PHE* 3.5 29.2 - - + -
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Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 3.9 1.8 - - - -
367A PHE* 3.0 30.1 + - - +
368A SER* 3.7 11.1 + - - +
370A THR* 1.3 74.5 - - - +
372A LYS* 1.3 59.2 + - - +
374A ILE* 3.3 9.2 + - - +
375A LEU* 2.9 35.0 + - - +
421A TYR* 2.8 36.8 + - - -
424A LYS* 2.6 43.3 + - - +
428A PHE* 3.9 13.0 - - + -
469A PHE* 3.9 21.1 - - + -
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Residues in contact with LYS 372 (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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195A LEU* 4.6 13.4 - - + +
196A ASN* 3.1 34.8 + - - +
197A THR* 4.9 5.2 - - + -
201A TYR* 4.1 25.8 - - + +
202A GLU* 3.8 18.6 + - + +
368A SER 2.9 19.0 + - - +
369A HIS* 3.1 6.9 + - - +
371A GLU* 1.3 76.3 - - - +
373A TYR* 1.3 62.7 + - - +
375A LEU* 3.3 2.9 + - - +
376A ASN* 3.0 43.1 + - - +
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Residues in contact with TYR 373 (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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332A LEU* 5.7 1.6 - - + -
336A VAL* 4.2 29.8 - - + +
340A LEU* 3.8 35.2 - - + -
369A HIS 2.9 12.2 + - - +
370A THR* 3.4 9.0 - - - +
372A LYS* 1.3 77.6 - - - +
374A ILE* 1.3 56.0 + - + +
376A ASN* 3.0 4.4 + - - +
377A ASN* 2.7 74.7 + - + +
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Residues in contact with ILE 374 (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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326A LEU* 3.8 28.9 - - + -
328A ILE* 4.9 0.9 - - + -
331A TRP* 4.0 24.0 - - + -
332A LEU* 4.2 18.4 - - + -
340A LEU* 4.5 11.9 - - + -
370A THR* 2.9 28.1 + - + +
371A GLU* 3.3 8.9 + - - +
373A TYR* 1.3 77.7 - - + +
375A LEU* 1.3 62.0 + - - +
377A ASN 3.2 22.0 - - - -
378A HIS* 3.3 7.4 + - - +
428A PHE* 4.0 22.4 - - + -
431A TRP* 4.7 2.2 - - + -
468A TYR* 4.8 9.9 - - + -
469A PHE* 4.4 6.5 - - + -
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Residues in contact with LEU 375 (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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202A GLU* 3.9 31.2 - - + +
204A VAL* 4.1 13.5 - - + -
371A GLU 2.9 24.3 + - - +
372A LYS 3.6 5.2 - - - +
374A ILE* 1.3 76.1 - - - +
376A ASN* 1.3 59.0 + - - +
378A HIS* 3.1 25.3 + - - +
395A LYS* 3.3 20.9 - - + -
398A LEU* 4.0 18.4 - - + -
424A LYS* 4.2 12.8 - - + -
428A PHE* 3.7 31.0 - - + -
431A TRP* 4.0 21.8 - - + -
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Residues in contact with ASN 376 (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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201A TYR 4.2 8.3 + - - +
202A GLU* 4.3 4.0 - - - +
203A HIS* 3.9 23.3 - - - -
372A LYS* 3.0 45.3 + - - +
373A TYR* 3.7 4.8 - - - +
375A LEU* 1.3 80.1 - - - +
377A ASN* 1.3 69.6 + - - +
378A HIS* 3.8 5.8 + - - -
395A LYS* 4.2 5.8 + - - +
335C LYS* 4.0 16.6 + - + +
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Residues in contact with ASN 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 3.7 14.2 - - - +
373A TYR* 2.7 72.2 + - + +
374A ILE* 3.2 7.2 - - - +
376A ASN* 1.3 84.1 - - - +
378A HIS* 1.3 57.9 + - - +
379A GLY 3.7 1.6 - - - -
335C LYS* 3.2 27.6 - - - +
382C LYS* 3.5 23.0 + - - +
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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
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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