Contacts of the helix formed by residues 358 - 368 (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 GLY 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352B ARG* 3.7 10.3 - - - -
356B GLY 3.7 0.8 + - - -
357B ILE* 1.3 73.6 - - - +
359B LYS* 1.3 65.8 + - - -
360B VAL 3.4 2.5 - - - -
362B GLU* 3.0 24.8 + - - +
11P C 3.3 30.2 + - - -
12P A 3.9 13.7 - - - -
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Residues in contact with LYS 359 (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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352B ARG* 3.6 23.6 - - - +
358B GLY* 1.3 72.3 - - - +
360B VAL* 1.3 60.8 + - + +
362B GLU* 3.4 6.8 - - - +
363B LYS* 3.0 30.3 + - + +
11P C 3.8 5.6 + - - +
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Residues in contact with VAL 360 (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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60B VAL* 4.1 28.7 - - + -
63B ARG* 4.4 14.1 - - - +
359B LYS* 1.3 79.2 - - + +
361B THR* 1.3 60.2 + - - +
363B LYS* 2.9 23.5 + - - +
364B MET* 2.9 29.5 + - - +
10P T 3.7 32.8 - - + +
11P C 3.3 18.1 + - - +
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Residues in contact with THR 361 (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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356B GLY 4.7 3.1 + - - -
357B ILE* 3.7 37.2 - - + -
358B GLY 4.2 2.2 + - - -
360B VAL* 1.3 74.5 - - - +
362B GLU* 1.3 62.7 + - - +
364B MET* 3.8 8.8 - - + +
365B LEU* 2.9 29.4 + - + +
387B PHE* 5.9 3.4 - - + -
395B PHE* 3.9 20.6 - - + -
10P T 3.9 4.2 + - - -
11P C 2.5 29.7 + - - -
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Residues in contact with GLU 362 (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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351B ILE* 4.3 16.8 - - + +
352B ARG* 3.1 46.9 + - + +
357B ILE* 3.8 8.6 - - + +
358B GLY 3.0 19.2 + - - +
359B LYS* 3.4 8.3 - - - +
361B THR* 1.3 76.7 - - - +
363B LYS* 1.3 58.1 + - - +
365B LEU* 3.8 1.0 - - - +
366B LYS* 2.9 36.3 + - + +
371B ILE* 6.1 1.0 - - - +
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Residues in contact with LYS 363 (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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57B GLU* 2.2 44.6 + - - +
60B VAL* 4.7 7.0 - - + -
61B ASN* 3.5 14.0 + - - +
64B ILE* 3.9 18.3 - - + +
359B LYS* 3.0 13.5 + - + +
360B VAL* 2.9 11.7 + - - +
362B GLU* 1.3 75.4 - - - +
364B MET* 1.3 60.4 + - - +
366B LYS* 3.2 11.6 + - + +
367B ALA* 2.9 27.2 + - - +
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Residues in contact with MET 364 (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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60B VAL* 5.0 2.2 - - + -
63B ARG* 4.4 39.3 - - + +
64B ILE* 3.9 20.2 - - + -
67B MET* 3.6 36.3 - - + +
360B VAL* 2.9 37.6 + - + +
361B THR* 3.8 7.6 - - + +
363B LYS* 1.3 75.0 - - - +
365B LEU* 1.3 63.9 + - + +
367B ALA* 3.2 16.6 - - - +
368B LEU* 3.6 5.5 + - - +
387B PHE* 4.7 20.4 - - + -
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Residues in contact with LEU 365 (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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351B ILE* 3.6 31.0 - - + -
357B ILE* 4.9 2.7 - - + -
361B THR* 2.9 27.5 + - + +
362B GLU 4.1 0.2 - - - +
364B MET* 1.3 74.3 - - + +
366B LYS* 1.3 64.2 + - - +
368B LEU* 3.1 10.9 + - + +
370B ILE* 2.8 39.9 + - + +
376B LEU* 3.9 13.2 - - + -
383B LEU* 3.9 27.4 - - + -
387B PHE* 4.0 18.6 - - + -
395B PHE* 3.8 30.1 - - + -
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Residues in contact with LYS 366 (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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362B GLU* 2.9 25.3 + - + +
363B LYS* 3.5 13.0 - - + +
365B LEU* 1.3 77.5 - - - +
367B ALA* 1.3 58.7 + - - +
369B GLY* 2.9 19.4 + - - -
370B ILE 3.4 10.9 + - - +
371B ILE* 3.5 25.4 - - + -
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Residues in contact with ALA 367 (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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64B ILE* 3.7 29.8 - - + -
67B MET* 4.1 7.0 - - + -
68B MET* 3.5 24.5 - - + +
363B LYS 2.9 12.7 + - - +
364B MET 3.2 15.3 - - - +
366B LYS* 1.3 78.0 - - - +
368B LEU* 1.3 57.0 + - - +
369B GLY 3.2 2.6 + - - -
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Residues in contact with LEU 368 (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* 3.6 31.4 - - + -
68B MET* 4.0 13.0 - - - -
71B LYS* 5.0 15.4 + - + +
364B MET 3.6 11.0 - - - +
365B LEU* 3.1 9.6 + - + +
367B ALA* 1.3 77.7 - - - +
369B GLY* 1.3 58.9 + - - +
370B ILE* 3.5 12.1 + - + -
379B GLN* 3.2 25.6 + - - +
382B LEU* 4.6 9.4 - - + -
383B LEU* 3.9 28.9 - - + -
386B LEU* 3.9 23.1 - - + -
387B PHE* 4.4 3.6 - - + -
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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