Contacts of the strand formed by residues 402 - 407 (chain D) in PDB entry 1T9D
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 GLY 402 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368D ASP 2.8 13.5 + - - -
369D LEU* 3.2 6.7 - - - +
370D ILE 2.7 31.4 + - - -
392D ALA* 3.2 25.2 + - - +
396D ALA* 3.9 1.1 - - - -
401D GLY* 1.3 75.7 - - - -
403D ILE* 1.3 61.8 + - - +
420D GLN* 3.5 8.3 - - - -
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Residues in contact with ILE 403 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369D LEU* 4.3 0.2 - - - +
370D ILE* 3.3 23.8 - - + +
377D PHE* 3.9 28.7 - - + -
388D PHE* 4.5 13.2 - - + -
389D ALA* 5.1 2.0 - - + -
392D ALA* 4.4 9.2 - - + -
402D GLY* 1.3 80.2 - - - +
404D ILE* 1.3 72.2 + - - +
405D HIS* 5.0 0.2 - - + -
417D VAL* 4.1 23.1 - - + -
418D GLN 4.5 7.9 - - - +
419D THR* 3.6 18.1 - - + -
420D GLN* 2.9 43.2 + - - +
421D ILE 3.3 5.5 + - - -
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Residues in contact with ILE 404 (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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292D ALA* 3.5 41.5 - - + +
295D LEU* 4.0 14.4 - - + -
296D ILE* 3.7 20.0 - - + -
369D LEU* 4.0 22.7 - - + -
370D ILE 2.8 9.3 + - - +
371D ILE* 4.4 7.4 - - + -
372D ALA* 2.8 30.1 + - - +
403D ILE* 1.3 76.6 - - - +
405D HIS* 1.3 63.6 + - - +
406D PHE* 3.7 27.6 - - + -
421D ILE* 3.3 15.7 - - + +
423D VAL* 4.4 4.5 - - + -
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Residues in contact with HIS 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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372D ALA* 3.5 22.0 - - + -
375D ALA 3.0 24.8 + - - -
376D ARG* 5.1 0.7 - - - -
377D PHE* 3.8 18.2 - + - -
403D ILE* 4.2 0.9 - - + -
404D ILE* 1.3 74.9 - - - +
406D PHE* 1.3 66.3 + - - +
407D GLU* 3.3 32.8 + - + +
412D ASN* 3.3 26.1 + - + -
413D ILE* 4.5 8.1 - - - +
414D ASN 4.9 0.6 + - - -
419D THR* 4.2 25.2 + - + +
421D ILE 2.8 12.2 + - - +
422D ALA* 3.5 6.3 - - + +
423D VAL 2.8 25.1 + - - -
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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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289D ILE* 5.3 1.3 - - + -
292D ALA* 4.6 0.2 - - + -
296D ILE* 5.4 0.4 - - + -
371D ILE* 3.9 15.7 - - + -
372D ALA 2.8 19.0 + - - +
373D VAL* 4.3 12.8 - - + -
374D GLY* 3.2 22.0 + - - -
404D ILE* 3.7 22.4 - - + -
405D HIS* 1.3 73.4 - - - +
407D GLU* 1.3 58.4 + - - +
423D VAL* 3.4 42.6 - - + +
425D GLY 4.9 0.4 - - - -
427D ALA* 4.0 24.7 - - + -
430D ASN* 3.8 24.0 - - + -
431D LEU* 4.0 16.6 - - + -
434D MET* 3.7 32.3 - - + -
3701D FAD 3.6 9.0 + - - -
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Residues in contact with GLU 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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375D ALA 4.1 0.5 + - - +
405D HIS* 3.3 34.4 + - + +
406D PHE* 1.3 75.1 - - - +
408D VAL* 1.3 62.1 + - - +
409D SER* 2.8 42.4 + - - +
412D ASN* 3.8 6.4 - - + +
413D ILE* 3.5 22.2 - - + +
423D VAL 3.2 6.1 + - - -
424D GLU* 3.3 10.0 - - - +
425D GLY 3.1 21.1 + - - -
3701D FAD 2.7 53.3 + - - +
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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