Contacts of the strand formed by residues 425 - 430 (chain A) in PDB entry 2N5T
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 GLU 425 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A LYS* 3.9 10.4 + - - +
386A LEU 4.5 3.4 + - - -
387A ARG* 3.4 39.7 + - + +
388A ILE 2.9 25.6 + - - +
423A SER 3.6 12.6 - - - +
424A ILE* 1.3 77.0 - - - +
426A ILE* 1.3 63.1 + - - +
447A ASP* 3.2 35.3 - - + +
448A PHE* 4.0 12.7 - - + -
498A TRP* 4.6 8.6 + - - -
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Residues in contact with ILE 426 (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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388A ILE* 3.3 16.8 - - + +
390A PHE* 4.2 15.3 - - + -
399A VAL* 6.4 0.7 - - + -
403A ARG* 3.2 41.5 - - + +
406A ILE* 3.4 46.4 - - + -
407A GLU* 5.8 0.4 - - - +
410A LYS* 5.0 4.9 - - - +
424A ILE* 4.0 15.9 - - + +
425A GLU* 1.3 79.3 - - - +
427A GLY* 1.3 57.8 + - - +
446A VAL* 3.6 7.6 - - + +
447A ASP* 2.6 40.3 + - - +
448A PHE* 3.6 3.1 - - - -
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Residues in contact with GLY 427 (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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388A ILE 2.8 9.9 + - - -
389A MET* 3.4 7.8 - - - -
390A PHE* 3.3 22.3 + - - -
426A ILE* 1.3 75.2 - - - +
428A VAL* 1.3 70.6 + - - +
446A VAL* 3.9 4.9 - - - -
448A PHE* 3.2 28.6 - - - -
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Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A MET* 3.8 7.3 - - - +
390A PHE* 3.7 11.9 - - + -
393A ILE* 3.8 16.4 - - + -
399A VAL* 3.7 21.5 - - + -
427A GLY* 1.3 81.7 - - - +
429A MET* 1.3 71.3 + - - +
430A VAL* 3.5 1.3 + - + -
442A LEU* 4.8 11.2 - - + -
446A VAL* 3.6 22.9 - - + -
448A PHE* 3.2 3.8 + - - +
449A PHE* 3.3 34.8 - - + -
450A SER 3.2 20.1 + - - -
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Residues in contact with MET 429 (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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332A ARG* 3.4 28.3 - - - +
389A MET* 3.4 30.0 - - + +
390A PHE 2.7 23.1 + - - +
391A PRO* 3.7 11.2 - - + -
392A MET 4.3 0.7 - - - +
393A ILE* 4.0 15.2 + - - +
428A VAL* 1.3 78.7 - - - +
430A VAL* 1.3 60.7 + - - +
431A GLU* 3.3 22.7 + - + +
435A ALA* 4.5 2.4 - - - +
450A SER* 3.2 10.8 - - - +
452A GLY* 3.1 41.5 - - - +
502A CYS* 3.7 19.1 - - - -
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Residues in contact with VAL 430 (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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428A VAL* 4.5 1.1 - - + -
429A MET* 1.3 74.0 - - - +
431A GLU* 1.3 57.2 + - - +
432A THR 4.3 0.4 - - - +
435A ALA* 3.7 11.4 - - + +
436A ALA* 3.6 26.9 - - + +
439A ALA* 5.4 0.4 - - + -
442A LEU* 5.3 0.7 - - + -
449A PHE* 3.0 50.3 - - + -
450A SER 2.8 10.9 + - - +
451A ILE* 3.2 15.5 - - + +
452A GLY 2.9 17.5 + - - -
456A LEU* 4.4 2.4 - - + +
488A VAL* 3.5 35.4 - - + -
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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