Contacts of the strand formed by residues 402 - 407 (chain B) in PDB entry 1T9C
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368B ASP 2.8 12.9 + - - -
369B LEU* 3.2 7.4 - - - +
370B ILE 2.8 24.9 + - - -
392B ALA* 3.2 25.5 + - - +
396B ALA* 4.0 1.8 - - - -
401B GLY* 1.3 75.0 - - - -
403B ILE* 1.3 67.2 + - - +
420B GLN* 3.3 9.0 - - - -
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Residues in contact with ILE 403 (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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295B LEU* 5.5 0.2 - - - -
369B LEU* 4.2 0.2 - - - +
370B ILE* 3.4 25.6 - - + +
377B PHE* 4.2 17.5 - - + -
388B PHE* 4.5 15.0 - - + -
389B ALA* 4.7 5.6 - - + -
392B ALA* 4.3 7.4 - - + -
393B ARG 6.2 0.2 - - - +
401B GLY 4.3 0.4 - - - -
402B GLY* 1.3 79.3 - - - +
404B ILE* 1.3 71.3 + - - +
405B HIS* 5.0 0.2 - - + -
417B VAL* 4.2 32.1 - - + -
418B GLN 4.4 4.0 - - - +
419B THR* 3.6 22.7 - - + -
420B GLN* 2.7 40.5 + - - +
421B ILE 3.2 6.8 + - - -
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Residues in contact with ILE 404 (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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292B ALA* 3.6 42.2 - - + +
295B LEU* 3.9 24.9 - - + -
296B ILE* 3.7 19.5 - - + -
369B LEU* 4.0 11.7 - - + -
370B ILE 2.9 9.1 + - - +
371B ILE* 4.5 7.4 - - + -
372B ALA* 2.8 29.7 + - - +
403B ILE* 1.3 77.7 - - - +
405B HIS* 1.3 62.3 + - - +
406B PHE* 3.5 27.8 - - + -
421B ILE* 3.3 17.7 - - + +
423B VAL* 4.4 2.7 - - + -
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Residues in contact with HIS 405 (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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372B ALA* 3.7 19.5 - - + -
375B ALA 2.9 26.9 + - - -
376B ARG* 5.0 0.7 - - - -
377B PHE* 3.7 20.1 - + - -
403B ILE* 5.0 0.4 - - + -
404B ILE* 1.3 75.3 - - - +
406B PHE* 1.3 72.0 + - - +
407B GLU* 3.3 26.4 + - + +
412B ASN 3.4 25.4 + - - -
413B ILE* 4.4 10.0 - - + +
414B ASN 4.9 0.8 + - - -
419B THR* 4.1 23.0 - - + +
421B ILE 2.9 12.4 + - - +
422B ALA* 3.6 6.4 - - + +
423B VAL 3.0 23.6 + - - -
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Residues in contact with PHE 406 (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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289B ILE* 5.7 0.7 - - + -
292B ALA* 4.7 0.2 - - + -
296B ILE* 5.6 0.2 - - + -
371B ILE* 4.0 15.7 - - + -
372B ALA 2.9 20.3 + - - +
373B VAL* 4.3 12.8 - - + -
374B GLY* 3.3 21.8 + - - -
404B ILE* 3.5 25.4 - - + -
405B HIS* 1.3 75.1 + - - +
407B GLU* 1.3 59.0 + - - +
423B VAL* 3.4 41.1 - - + +
425B GLY 4.9 0.4 - - - -
427B ALA* 4.1 20.2 - - + -
430B ASN* 4.0 22.2 - - + +
431B LEU* 3.8 24.5 - - + -
434B MET* 3.9 27.4 - - + -
1701B FAD 3.7 8.9 + - - -
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Residues in contact with GLU 407 (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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375B ALA 3.9 1.4 + - - +
405B HIS* 3.3 27.8 + - + +
406B PHE* 1.3 76.1 - - - +
408B VAL* 1.3 63.6 + - - +
409B SER* 2.8 43.8 + - - +
412B ASN* 3.7 7.4 - - + -
413B ILE* 3.6 24.1 - - + +
423B VAL 3.2 5.7 + - - -
424B GLU* 3.2 10.4 - - - +
425B GLY 3.2 18.7 + - - -
1701B FAD 2.6 52.6 + - - -
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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