Contacts of the helix formed by residues 379 - 387 (chain B) in PDB entry 4U7C
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 GLN 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368B LEU 3.2 25.7 + - - -
369B GLY 5.0 2.8 + - - -
370B ILE* 3.9 22.9 - - + +
375B GLU* 3.2 21.5 + - + +
377B TYR 3.3 0.2 - - - -
378B GLN* 1.3 80.0 - - + +
380B ARG* 1.3 63.6 + - - +
381B ALA 3.2 3.4 + - - -
382B LEU* 3.3 33.5 + - + +
383B LEU* 3.0 25.5 + - + +
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Residues in contact with ARG 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLN* 3.8 22.5 + - - +
86B VAL* 3.5 24.6 - - + +
87B ASP* 2.8 36.5 + - - -
90B ALA* 5.3 1.8 - - - -
376B LEU 3.9 7.2 + - - +
377B TYR* 2.9 72.9 + - - +
378B GLN* 3.2 11.3 + - - +
379B GLN* 1.3 75.9 - - - +
381B ALA* 1.3 59.5 + - - +
383B LEU* 3.4 9.0 + - - +
384B SER* 2.9 25.8 + - - -
392B TRP* 5.0 4.7 - - + -
396B LEU* 4.4 14.6 - - + -
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 3.9 11.7 - - + +
82B ALA* 3.8 6.5 - - + +
83B GLN* 3.3 49.1 + - + +
86B VAL* 4.0 10.5 - - - -
379B GLN 3.3 0.8 - - - -
380B ARG* 1.3 77.4 - - - +
382B LEU* 1.3 58.2 + - - +
384B SER* 2.8 22.6 + - - -
385B LEU* 2.9 15.9 + - - +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LYS* 4.1 31.6 - - + +
74B ILE* 4.1 13.9 - - + -
79B LEU* 4.1 17.5 - - + +
368B LEU* 4.6 15.0 - - + +
379B GLN* 3.3 41.8 + - + +
381B ALA* 1.3 77.8 - - - +
383B LEU* 1.3 58.1 + - + +
385B LEU* 3.1 7.1 + - - +
386B LEU* 2.9 57.2 + - + +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B LEU* 3.9 11.4 - - + -
368B LEU* 3.9 20.0 - - + -
370B ILE* 4.0 9.0 - - + -
376B LEU* 3.6 40.8 - - + +
379B GLN* 3.0 22.2 + - + +
380B ARG* 3.5 9.4 - - - +
382B LEU* 1.3 72.8 - - + +
384B SER* 1.3 64.8 + - - +
385B LEU 3.1 0.7 - - - -
386B LEU* 4.5 0.2 - - - -
387B PHE* 3.0 56.8 + - + +
392B TRP* 3.7 14.5 - - + +
395B PHE* 4.3 12.1 - - + -
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Residues in contact with SER 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ALA* 4.5 9.6 - - - +
86B VAL* 3.4 30.7 - - - +
380B ARG 2.9 6.5 + - - -
381B ALA 2.8 12.0 + - - -
383B LEU* 1.3 77.6 - - - +
385B LEU* 1.3 60.3 + - - +
387B PHE 3.6 10.7 - - - +
392B TRP* 3.6 31.9 + - - +
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Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLN* 4.5 10.2 + - - +
74B ILE* 4.0 36.6 - - + +
78B GLN* 4.1 14.8 - - + +
79B LEU* 4.0 33.4 - - + +
82B ALA* 4.0 15.7 - - + -
381B ALA 2.9 13.1 + - - +
382B LEU* 3.5 7.4 - - - +
383B LEU 3.1 0.2 - - - -
384B SER* 1.3 82.8 - - - +
386B LEU* 1.3 61.9 + - - +
387B PHE 3.6 1.2 - - - +
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B MET* 3.9 29.2 - - + +
70B GLN* 3.8 35.6 + - + +
71B LYS* 4.1 14.1 - - + +
74B ILE* 4.4 5.4 - - + -
368B LEU* 3.9 30.5 - - + -
382B LEU* 2.9 44.6 + - + +
383B LEU 3.4 0.4 + - - -
385B LEU* 1.3 81.6 - - - +
387B PHE* 1.3 76.2 + - + +
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Residues in contact with PHE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B MET* 4.2 17.7 - - - -
361B THR* 5.9 3.4 - - + -
364B MET* 4.7 23.3 - - + -
365B LEU* 4.0 18.2 - - + -
368B LEU* 4.4 5.6 - - + -
383B LEU* 3.0 41.8 + - + +
384B SER 3.6 16.3 - - - +
385B LEU 4.6 1.0 - - - +
386B LEU* 1.3 96.4 - - + +
388B SER* 1.3 68.2 + - - +
391B SER* 3.8 20.4 - - - -
392B TRP* 3.8 5.5 - - + +
395B PHE* 4.2 18.6 - + - -
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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