Contacts of the helix formed by residues 362 - 374 (chain A) in PDB entry 1RL3
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 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A GLY 3.7 7.5 - - - +
359A PRO 3.8 5.5 - - - +
360A CYS 2.7 22.6 + - - +
361A SER* 1.3 76.3 + - - +
363A ILE* 1.3 67.8 + - + +
364A LEU 3.4 0.2 - - - -
365A LYS* 3.4 4.4 + - - +
366A ARG* 3.0 39.0 + - - +
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Residues in contact with ILE 363 (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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256A SER* 4.1 31.2 - - - +
359A PRO 5.5 2.5 - - - +
360A CYS* 4.7 12.8 - - - -
362A ASP* 1.3 81.6 - - + +
364A LEU* 1.3 64.8 + - + +
365A LYS 3.0 4.3 - - - -
366A ARG* 3.0 10.7 + - + +
367A ASN* 2.9 43.5 + - - +
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Residues in contact with LEU 364 (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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253A ILE* 3.7 51.8 - - + +
256A SER* 5.0 0.2 - - - +
324A GLU* 5.4 0.7 - - + -
328A LEU* 3.3 32.9 - - + +
353A PHE* 5.4 0.2 - - + -
357A LEU* 4.7 13.0 - - + -
360A CYS* 3.7 24.9 - - + -
361A SER* 3.3 19.3 - - - +
362A ASP 3.4 0.8 - - - +
363A ILE* 1.3 80.6 - - + +
365A LYS* 1.3 57.7 + - - +
367A ASN* 3.5 17.6 - - - +
368A ILE* 3.0 29.7 + - - +
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Residues in contact with LYS 365 (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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328A LEU* 4.7 13.0 - - + +
329A MET* 6.1 2.7 - - + -
361A SER 3.6 14.7 + - - +
362A ASP* 3.4 12.8 + - - +
363A ILE 3.0 0.2 - - - -
364A LEU* 1.3 77.4 - - - +
366A ARG* 1.3 74.1 + - - +
367A ASN 3.1 0.9 - - - -
368A ILE* 2.9 26.4 + - + +
369A GLN* 3.2 6.9 + - - +
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Residues in contact with ARG 366 (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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362A ASP* 3.0 29.3 + - - +
363A ILE* 3.2 15.5 - - + +
365A LYS* 1.3 83.7 - - - +
367A ASN* 1.3 66.4 + - - +
369A GLN* 3.1 9.9 + - - +
370A GLN* 2.9 39.8 + - - +
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Residues in contact with ASN 367 (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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253A ILE* 5.6 3.8 - - - +
363A ILE* 2.9 29.0 + - - +
364A LEU* 3.5 23.4 - - - +
366A ARG* 1.3 76.9 - - - +
368A ILE* 1.3 65.8 + - + +
370A GLN* 2.8 22.9 + - - +
371A TYR* 3.0 15.2 + - - +
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Residues in contact with ILE 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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324A GLU* 5.0 9.0 - - + -
325A ILE* 4.5 26.7 - - + +
328A LEU* 5.1 8.3 - - + -
329A MET* 4.5 22.4 - - + -
364A LEU 3.0 16.6 - - - +
365A LYS* 2.9 14.5 + - - +
367A ASN* 1.3 82.9 - - + +
369A GLN* 1.3 58.8 + - + +
371A TYR* 3.6 2.0 + - - +
372A ASN* 2.7 43.0 + - - +
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Residues in contact with GLN 369 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A LYS 3.2 5.3 + - - +
366A ARG* 3.1 12.2 + - - +
368A ILE* 1.3 79.4 - - + +
370A GLN* 1.3 85.8 + - - +
372A ASN* 3.4 5.9 + - - +
373A SER* 2.7 54.1 + - - -
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Residues in contact with GLN 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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366A ARG* 2.9 35.5 + - - +
367A ASN* 2.8 16.9 + - - +
369A GLN* 1.3 108.2 + - - +
371A TYR* 1.3 56.7 + - - +
373A SER* 3.1 5.9 + - - -
374A PHE* 2.8 29.7 + - - +
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Residues in contact with TYR 371 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367A ASN 3.0 9.1 + - - +
368A ILE* 4.1 1.6 - - - +
370A GLN* 1.3 78.7 - - - +
372A ASN* 1.3 76.9 + - - +
374A PHE* 3.1 34.3 + + - +
375A VAL* 3.3 18.7 - - + +
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Residues in contact with ASN 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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368A ILE* 2.7 32.4 + - - +
369A GLN* 3.8 5.8 - - - +
370A GLN 3.3 0.2 - - - -
371A TYR* 1.3 88.0 - - - +
373A SER* 1.3 65.8 + - - +
375A VAL* 2.9 27.5 + - - +
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Residues in contact with SER 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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369A GLN* 2.7 43.1 + - - -
370A GLN* 3.2 6.5 - - - -
372A ASN* 1.3 73.3 - - - +
374A PHE* 1.3 53.0 + - - +
375A VAL 2.7 11.8 + - - -
376A SER* 2.9 24.9 + - - -
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Residues in contact with PHE 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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370A GLN 2.8 13.0 + - - +
371A TYR* 3.1 31.4 + + + +
373A SER* 1.3 73.8 + - - +
375A VAL* 1.3 62.8 + - + +
376A SER 3.8 2.2 + - - +
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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