Contacts of the strand formed by residues 425 - 432 (chain A) in PDB entry 4IDT
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 425 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A HIS* 2.7 30.7 + - - -
416A ARG* 5.5 0.3 - - - +
417A MET 3.4 5.9 - - - +
418A GLU* 3.0 37.9 + - - +
423A GLY 3.8 7.4 + - - +
424A PHE* 1.3 91.5 - - - +
426A CYS* 1.3 62.7 + - - +
471A LEU* 4.5 20.1 + - + +
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Residues in contact with CYS 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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386A LEU* 4.2 22.0 - - - -
416A ARG* 3.7 4.7 - - - -
417A MET* 3.0 63.1 + - - +
424A PHE* 3.7 15.9 - - + -
425A GLN* 1.3 76.3 - - - +
427A ALA* 1.3 67.2 + - - +
456A TYR* 3.7 7.0 - - + -
468A PHE* 4.5 1.8 - - - -
469A MET 3.3 11.7 - - - +
471A LEU* 3.7 18.9 - - - +
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Residues in contact with ALA 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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406A LEU* 4.0 12.6 - - + -
414A VAL* 4.3 4.5 - - + -
415A HIS 3.3 10.8 - - - +
417A MET* 4.0 2.5 - - - -
426A CYS* 1.3 78.9 - - - +
428A VAL* 1.3 61.8 + - - +
468A PHE* 3.3 4.3 - - - -
469A MET* 2.7 44.5 + - + +
470A GLU 4.1 1.6 - - - +
471A LEU* 4.0 3.5 - - + +
701A T28 3.3 29.8 - - - +
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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
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399A TRP* 4.1 12.1 - - + -
401A THR* 4.3 4.5 - - + -
413A GLU 3.8 0.9 - - - +
414A VAL* 3.2 5.7 - - - -
415A HIS* 2.8 59.5 + - + +
417A MET* 3.9 19.3 - - + -
427A ALA* 1.3 76.3 - - - +
429A LYS* 1.3 67.0 + - - +
430A LYS* 4.1 4.7 + - + +
466A ASN* 3.8 22.7 - - + +
467A ILE 3.2 8.1 - - - +
468A PHE* 3.5 29.8 - - + -
469A MET* 4.7 0.2 - - - -
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Residues in contact with LYS 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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409A GLY* 4.6 0.7 - - - -
410A SER* 5.0 1.0 + - - -
411A PHE 5.5 1.1 - - - +
412A GLY* 3.8 25.4 - - - +
413A GLU 3.3 11.4 - - - +
414A VAL* 3.9 8.3 - - + -
428A VAL* 1.3 74.2 - - - +
430A LYS* 1.3 61.2 + - - +
431A VAL* 3.7 13.1 + - + +
440A GLU* 2.4 38.9 + - - -
465A VAL 3.4 3.6 - - - +
467A ILE* 2.8 48.2 + - + +
469A MET* 3.8 18.4 - - + +
534A ASP* 2.7 29.8 + - - +
535A PHE 4.6 0.2 - - - +
701A T28 3.8 19.8 - - + +
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Residues in contact with LYS 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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395A GLU* 2.4 33.8 + - - -
399A TRP* 5.1 2.2 - - - -
401A THR* 5.6 3.6 - - - -
411A PHE 4.1 0.2 - - - +
412A GLY* 3.2 19.4 - - - -
413A GLU* 3.1 14.8 + - + +
415A HIS* 5.8 6.7 - - + +
428A VAL* 4.0 5.3 - - + +
429A LYS* 1.3 72.2 - - - +
431A VAL* 1.3 60.4 + - - +
432A ARG 4.3 0.5 + - - -
464A TRP* 3.4 39.0 - - + +
465A VAL 3.5 3.8 - - - +
466A ASN* 2.8 30.7 + - - +
408B ARG* 4.0 10.1 - - - +
413B GLU* 3.1 36.8 + - - +
464B TRP* 5.3 2.3 - - - -
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Residues in contact with VAL 431 (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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411A PHE* 3.7 26.5 - - + +
429A LYS* 4.1 20.4 - - + +
430A LYS* 1.3 79.2 - - - +
432A ARG* 1.3 75.5 + - - +
433A LEU 3.4 0.2 + - - -
435A VAL* 3.8 10.1 - - + -
436A PHE* 3.9 25.4 - - + -
440A GLU* 4.5 5.8 - - - +
464A TRP* 3.6 5.3 - - - -
465A VAL* 2.8 44.0 + - + +
467A ILE* 4.0 24.2 - - + -
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Residues in contact with ARG 432 (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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411A PHE 4.5 1.8 + - - -
430A LYS 4.3 0.2 + - - -
431A VAL* 1.3 76.3 - - - +
433A LEU* 1.3 64.8 + - - +
434A GLU* 2.9 46.0 + - + +
435A VAL* 3.0 26.6 + - + +
436A PHE* 3.1 9.1 + - - -
463A PRO* 3.5 35.8 + - - +
464A TRP* 3.4 42.7 - - + +
410B SER 3.0 23.4 + - - -
411B PHE* 3.6 33.3 - - - +
432B ARG* 4.5 23.0 - - + +
435B VAL* 4.6 9.0 - - + +
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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