Contacts of the strand formed by residues 404 - 411 (chain D) in PDB entry 1IRI
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 CYS 404 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337D ALA* 3.4 21.1 - - - -
339D LEU* 4.0 15.0 - - + -
395D ILE* 4.1 21.1 - - - -
402D ILE* 3.2 22.2 + - - -
403D PRO* 1.3 75.9 - - - +
405D ASP* 1.3 64.2 + - - +
406D PHE* 3.6 25.1 - - + -
436D LEU* 5.1 0.2 - - - -
473D PRO 3.5 4.6 + - - -
474D THR* 3.2 13.5 - - + +
475D ASN* 2.9 24.3 + - - -
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Residues in contact with ASP 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D LEU* 5.2 3.3 - - - +
336D HIS* 3.0 30.2 + - - -
337D ALA 2.9 10.8 + - - +
338D MET* 4.5 3.3 - - - +
339D LEU* 2.9 27.7 + - - +
404D CYS* 1.3 72.7 - - - +
406D PHE* 1.3 59.9 + - - +
407D LEU* 3.6 10.5 - - + +
475D ASN* 2.9 36.8 - - + +
477D ILE* 4.8 4.9 - - + +
494D TYR* 2.7 36.0 + - - +
497D LYS* 4.7 0.7 + - - +
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Residues in contact with PHE 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D LEU* 3.5 14.4 - - + -
341D TYR* 3.3 41.7 - + - -
392D TYR* 3.4 21.8 - + - -
395D ILE* 6.1 0.4 - - + -
404D CYS* 3.6 28.7 - - + -
405D ASP* 1.3 71.9 - - - +
407D LEU* 1.3 55.3 + - - +
429D PHE* 3.5 23.7 - + + -
432D GLN* 3.8 13.9 - - + -
433D THR* 3.7 22.7 - - + -
436D LEU* 4.1 15.9 - - + -
474D THR* 4.0 16.2 - - + -
475D ASN 2.9 10.8 + - - +
476D SER* 3.5 1.8 - - - +
477D ILE* 2.6 33.8 + - - +
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Residues in contact with LEU 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D MET* 5.0 3.8 - - + -
339D LEU 3.2 17.0 + - - +
340D PRO* 3.6 11.8 - - + +
341D TYR* 2.8 31.5 + - - +
342D ASP* 5.4 0.3 - - - +
345D LEU* 5.3 2.9 - - + -
348D PHE* 4.1 26.9 - - + -
405D ASP* 3.6 27.4 - - + +
406D PHE* 1.3 76.6 - - - +
408D ILE* 1.3 64.1 + - - +
429D PHE* 3.6 1.7 - - - -
477D ILE* 3.1 27.6 - - + +
479D PHE* 4.0 16.6 - - + -
490D LEU* 4.8 6.1 - - + -
494D TYR* 3.9 21.5 - - + +
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Residues in contact with ILE 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D TYR* 3.6 23.3 - - + +
342D ASP* 5.7 0.2 - - - -
407D LEU* 1.3 77.7 - - - +
409D PRO* 1.3 87.0 - - + +
422D HIS* 4.3 1.3 - - + -
425D LEU* 3.8 20.9 - - + -
426D LEU* 3.9 25.4 - - + -
429D PHE* 3.2 44.2 - - + -
477D ILE 2.9 10.7 + - - -
478D VAL* 3.2 12.8 - - + +
479D PHE* 3.0 30.2 + - - -
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Residues in contact with PRO 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D TYR 4.1 5.4 - - - +
342D ASP* 3.7 26.7 - - + +
408D ILE* 1.3 101.7 - - + +
410D VAL* 1.3 60.3 + - - +
411D GLN 3.7 17.3 - - - +
412D THR* 5.5 1.6 - - - -
422D HIS* 3.0 29.0 + - + -
426D LEU* 4.4 0.3 - - - +
479D PHE* 3.0 32.8 - - + +
481D LYS* 4.1 0.9 - - - -
482D LEU* 3.9 15.5 - - + +
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Residues in contact with VAL 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C PHE* 4.4 2.2 - - + -
549C ILE* 3.5 49.1 - - + +
552C GLN* 4.1 14.4 - - + +
553C ARG* 4.0 22.0 - - + +
409D PRO* 1.3 72.3 - - - +
411D GLN* 1.3 56.2 + - + +
422D HIS* 2.7 25.2 + - - -
426D LEU* 4.3 8.6 - - + +
478D VAL* 3.5 27.1 - - + -
479D PHE 2.7 16.1 + - - +
480D THR* 3.6 8.1 - - - +
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Residues in contact with GLN 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552C GLN 3.0 23.9 + - - +
553C ARG* 3.5 13.9 + - + +
555C ALA 2.7 31.3 + - - +
556C ARG* 5.4 0.5 - - - -
557C VAL* 4.6 4.6 + - - +
409D PRO* 3.7 17.3 - - - +
410D VAL* 1.3 79.5 - - + +
412D THR* 1.3 62.9 + - - +
413D GLN* 4.1 0.5 + - - +
422D HIS* 4.0 2.7 - - - -
480D THR* 2.7 29.3 + - - +
481D LYS* 3.8 39.7 + - + +
482D LEU 4.5 0.9 + - - -
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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