Contacts of the strand formed by residues 437 - 441 (chain A) in PDB entry 4N7F
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 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A VAL* 4.1 12.8 - - + -
430A ARG 3.2 9.9 - - - +
431A HIS* 3.7 17.9 - - + +
435A GLY 3.5 2.7 - - - +
436A ARG* 1.3 90.8 + - + +
438A PHE* 1.3 59.0 + - - +
439A PHE* 4.1 19.8 - - + -
449A TRP* 3.4 17.5 - - - +
422B PHE* 3.3 42.2 - - + -
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Residues in contact with PHE 438 (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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429A VAL* 3.5 5.2 - - - +
430A ARG* 2.8 59.6 + - + +
431A HIS 3.9 6.5 - - - -
432A ALA* 3.8 30.1 - - + -
437A PRO* 1.3 75.1 - - - +
439A PHE* 1.3 69.2 + - - +
440A ILE* 4.2 14.4 - - + -
447A THR* 3.5 32.3 - - + -
448A THR 3.4 14.1 - - - +
449A TRP* 3.7 26.2 - + + -
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Residues in contact with PHE 439 (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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423A LEU* 4.3 6.1 - - + -
427A TRP* 3.8 22.4 - + + -
428A GLU 3.4 4.0 - - - +
429A VAL* 3.9 24.0 - - + -
437A PRO* 4.1 22.9 - - + -
438A PHE* 1.3 87.0 - - - +
440A ILE* 1.3 63.8 + - - +
441A ASP 4.2 0.2 + - - -
446A THR 3.8 0.2 - - - +
447A THR* 3.4 3.8 - - - +
448A THR* 2.8 43.2 + - + +
449A TRP 3.6 9.4 - - - -
450A GLU 3.6 15.7 - - - +
451A ASP* 3.5 35.0 - - + -
452A PRO* 3.8 13.0 - - + -
453A ARG* 3.7 21.5 - - - -
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Residues in contact with ILE 440 (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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426A GLY 3.9 0.2 - - - +
427A TRP* 3.2 10.5 - - - +
428A GLU* 2.9 38.3 + - + +
430A ARG* 3.3 48.9 - - + +
438A PHE* 4.2 15.5 - - + -
439A PHE* 1.3 78.5 - - - +
441A ASP* 1.3 66.0 + - - +
442A HIS* 3.8 31.2 + - + +
445A LYS* 5.9 1.6 - - - -
446A THR 3.4 8.1 - - - +
447A THR* 4.2 14.6 - - + +
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Residues in contact with ASP 441 (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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425A LYS 4.8 1.6 - - - +
426A GLY 4.0 4.0 - - - +
427A TRP* 3.6 47.7 + - + -
440A ILE* 1.3 71.4 - - - +
442A HIS* 1.3 54.8 + - - +
443A ASN* 3.5 12.0 + - - +
444A THR* 2.4 38.2 + - - +
445A LYS* 2.8 37.6 + - - -
446A THR* 2.8 16.9 + - - +
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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