Contacts of the strand formed by residues 425 - 432 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402B HIS* 3.8 23.4 + - + -
416B ARG* 5.6 0.7 - - - -
417B MET 3.1 7.2 - - - +
418B GLU* 3.4 30.2 + - + +
423B GLY 3.5 7.0 + - - +
424B PHE* 1.3 92.3 - - - +
426B CYS* 1.3 63.8 + - - +
456B TYR* 5.4 0.2 - - - -
471B LEU* 4.4 22.7 + - + +
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Residues in contact with CYS 426 (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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386B LEU* 4.1 21.3 - - - -
416B ARG* 3.6 4.9 - - - -
417B MET* 3.0 61.7 + - - -
424B PHE* 3.9 5.2 - - + -
425B GLN* 1.3 75.2 - - - +
427B ALA* 1.3 68.8 + - - +
456B TYR* 3.8 15.5 - - + -
468B PHE* 4.4 4.0 - - - -
469B MET 3.3 11.0 - - - +
471B LEU* 3.7 19.6 - - - +
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Residues in contact with ALA 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LEU* 4.0 14.1 - - + -
414B VAL* 4.3 4.5 - - + -
415B HIS 3.2 9.4 - - - +
417B MET* 4.2 2.5 - - - -
426B CYS* 1.3 79.1 - - - +
428B VAL* 1.3 61.1 + - - +
467B ILE 3.7 0.2 - - - +
468B PHE* 3.3 5.0 - - - -
469B MET* 2.8 41.1 + - + +
470B GLU 4.1 1.3 - - - +
471B LEU* 3.9 3.5 - - - +
701B T28 3.5 29.4 - - + +
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Residues in contact with VAL 428 (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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399B TRP* 4.0 23.8 - - + -
401B THR* 4.1 14.8 - - + -
413B GLU 3.7 0.9 - - - +
414B VAL* 3.3 5.4 - - - -
415B HIS* 2.8 50.4 + - + +
417B MET* 4.0 7.9 - - + -
427B ALA* 1.3 75.8 - - - +
429B LYS* 1.3 66.1 + - - +
430B LYS* 4.1 4.2 + - + +
466B ASN* 4.0 20.4 - - + +
467B ILE 3.2 7.2 - - - +
468B PHE* 3.6 30.5 - - + -
469B MET* 4.6 0.2 - - - -
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Residues in contact with LYS 429 (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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409B GLY* 4.5 6.3 - - - -
410B SER* 5.2 0.6 + - - +
411B PHE 5.6 1.1 - - - +
412B GLY 3.8 22.0 - - - +
413B GLU 3.3 12.1 - - - +
414B VAL* 3.9 7.6 - - + -
428B VAL* 1.3 74.6 - - - +
430B LYS* 1.3 61.1 + - - +
431B VAL* 3.7 15.9 + - + +
440B GLU* 2.4 39.6 + - - +
465B VAL 3.5 3.5 - - - +
466B ASN* 3.8 0.2 - - - -
467B ILE* 2.7 49.9 + - + +
469B MET* 3.7 16.2 - - + +
534B ASP* 3.0 22.4 + - - +
701B T28 3.9 20.0 - - + +
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Residues in contact with LYS 430 (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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408A ARG* 3.1 23.2 - - - +
413A GLU* 3.1 34.3 + - - +
464A TRP* 5.3 2.3 - - - -
395B GLU* 2.8 28.3 + - - -
399B TRP* 5.2 1.6 - - - -
401B THR* 6.4 0.7 - - - -
411B PHE 4.1 0.3 - - - +
412B GLY* 3.3 19.6 - - - -
413B GLU* 3.1 13.3 + - + +
428B VAL* 4.0 5.4 - - + -
429B LYS* 1.3 71.1 - - - +
431B VAL* 1.3 60.5 + - - +
432B ARG 4.3 0.5 + - - -
464B TRP* 3.2 39.7 - - + +
465B VAL 3.6 4.5 - - - +
466B ASN* 3.2 27.5 + - - +
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Residues in contact with VAL 431 (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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411B PHE* 3.7 26.5 - - + +
429B LYS* 4.0 30.5 - - + +
430B LYS* 1.3 79.9 - - - +
432B ARG* 1.3 77.0 + - - +
433B LEU 3.4 0.2 + - - -
435B VAL* 3.9 9.0 - - + -
436B PHE* 4.0 24.7 - - + -
440B GLU* 4.5 5.8 - - - +
464B TRP* 3.7 4.4 - - - -
465B VAL* 2.8 42.4 + - - +
467B ILE* 4.1 13.5 - - + -
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Residues in contact with ARG 432 (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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410A SER 3.0 22.4 + - - -
411A PHE* 3.4 35.1 - - - +
432A ARG* 4.5 22.2 - - + +
435A VAL* 4.5 9.8 - - + +
411B PHE 4.5 1.8 + - - -
431B VAL* 1.3 75.0 - - - +
433B LEU* 1.3 66.0 + - - +
434B GLU* 2.7 46.9 + - + +
435B VAL* 3.0 29.1 + - + +
436B PHE* 3.1 8.9 + - - -
463B PRO* 3.5 35.5 + - - +
464B TRP* 3.4 41.5 - - + +
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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