Contacts of the helix formed by residues 464 - 474 (chain A) in PDB entry 4EWS
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 PRO 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A LEU 4.0 17.0 - - - +
441A PHE* 4.2 22.7 - - + -
442A ASP 5.7 0.2 - - - +
462A GLY 3.7 5.8 - - - +
463A PHE* 1.4 111.0 - - + +
465A GLU* 1.4 63.4 + - - +
466A HIS* 3.7 9.6 - - + -
467A LEU* 3.6 37.8 + - + +
468A LEU 3.8 3.6 + - - -
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Residues in contact with GLU 465 (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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25A HIS* 5.3 4.9 - - - +
26A GLU* 3.4 30.2 - - - +
29A LYS* 3.3 25.3 + - - +
463A PHE* 3.4 6.8 + - - +
464A PRO* 1.4 68.8 - - - +
466A HIS* 1.4 65.5 + - - +
468A LEU* 3.2 16.8 + - - +
469A VAL* 3.4 16.3 + - + +
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Residues in contact with HIS 466 (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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440A LEU* 5.8 2.4 - - - +
464A PRO* 5.0 8.5 - - + -
465A GLU* 1.4 79.2 + - - +
467A LEU* 1.4 87.9 + - + +
469A VAL* 3.3 11.9 + - + +
470A ASP* 2.8 50.0 + - - +
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Residues in contact with LEU 467 (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 ARG* 5.9 3.4 - - - +
440A LEU* 3.9 45.8 - - + +
441A PHE* 6.3 0.9 - - + -
463A PHE* 6.3 0.4 - - + -
464A PRO* 3.6 35.8 + - + +
465A GLU 3.3 1.4 + - - -
466A HIS* 1.4 93.1 - - + +
468A LEU* 1.4 59.9 + - - +
470A ASP* 3.5 12.5 - - + +
471A PHE* 3.1 27.4 + - - +
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Residues in contact with LEU 468 (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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26A GLU* 3.5 36.3 - - + +
29A LYS* 4.8 6.5 - - + -
30A VAL* 4.8 3.6 - - + -
194A MET* 3.5 28.9 - - + -
463A PHE* 3.8 26.1 - - + -
464A PRO 3.8 2.0 + - - -
465A GLU 3.2 10.1 + - - +
467A LEU* 1.4 73.8 - - - +
469A VAL* 1.4 56.4 + - + +
471A PHE* 3.1 17.1 + - + +
472A LEU* 2.7 46.8 + - + +
505A PGE 3.7 22.9 - - - +
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Residues in contact with VAL 469 (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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29A LYS* 4.2 27.6 - - + -
465A GLU* 3.4 15.4 + - + +
466A HIS* 3.3 12.5 + - - +
468A LEU* 1.4 75.5 - - - +
470A ASP* 1.4 56.9 + - - +
472A LEU* 3.5 8.3 + - + +
473A GLN* 3.0 49.3 + - + +
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Residues in contact with ASP 470 (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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466A HIS* 2.8 35.8 + - - +
467A LEU* 3.5 20.1 - - + +
469A VAL* 1.4 77.0 - - - +
471A PHE* 1.4 62.8 + - - +
473A GLN* 3.3 14.6 + - - +
474A SER* 3.1 23.0 + - - -
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Residues in contact with PHE 471 (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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190A ILE* 5.8 1.1 - - + -
193A ILE* 3.7 31.2 - - + -
194A MET* 3.8 31.6 - - + -
197A PHE* 3.9 42.8 - + + -
467A LEU 3.1 10.8 + - - +
468A LEU* 3.5 23.1 - - + +
470A ASP* 1.4 78.1 - - - +
472A LEU* 1.3 78.3 + - + +
474A SER* 2.7 37.5 + - - +
475A LEU* 4.2 8.5 - - + +
505A PGE 4.5 5.6 - - - -
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Residues in contact with LEU 472 (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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29A LYS* 3.4 44.4 - - + +
30A VAL* 4.0 5.6 - - + +
33A THR* 3.4 26.1 - - + +
190A ILE* 4.8 7.4 - - + -
194A MET* 3.8 17.3 - - + -
468A LEU* 2.7 28.7 + - + +
469A VAL* 3.7 8.3 - - - +
471A PHE* 1.3 93.9 - - + +
473A GLN* 1.3 64.1 + - + +
475A LEU* 3.3 25.6 - - + +
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Residues in contact with GLN 473 (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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469A VAL* 3.0 38.4 + - + +
470A ASP* 3.6 11.2 - - - +
472A LEU* 1.3 75.9 - - + +
474A SER* 1.4 56.8 + - - +
475A LEU* 3.2 7.4 + - - +
476A SER* 5.0 1.4 + - - +
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Residues in contact with SER 474 (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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470A ASP 3.1 9.5 + - - -
471A PHE* 2.7 36.0 + - - +
473A GLN* 1.4 72.3 - - - +
475A LEU* 1.3 65.4 + - - +
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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