Contacts of the strand formed by residues 427 - 432 (chain B) in PDB entry 2DB3
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 427 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279B ILE* 3.0 24.7 + - - +
282B GLY* 3.2 35.5 - - - +
283B ARG 3.1 20.2 - - - +
284B ASP* 3.2 7.9 - - - +
306B LYS* 5.5 2.8 - - - +
394B ARG 2.9 13.5 + - - +
395B PHE* 3.1 40.7 - - + -
396B VAL 3.0 24.9 + - - -
426B HIS* 1.3 80.8 + - - +
428B THR* 1.3 60.3 + - - +
429B LEU* 4.1 6.6 - - + +
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Residues in contact with THR 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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284B ASP* 3.0 16.8 + - - +
285B LEU 3.1 21.5 + - - -
396B VAL* 3.4 8.3 - - + +
398B LEU* 5.2 4.0 - - + -
417B MET* 4.0 12.5 - - + +
426B HIS* 3.1 27.2 - - - -
427B GLN* 1.3 72.0 - - - +
429B LEU* 1.3 63.4 + - - +
430B MET* 3.8 17.7 - - + -
446B PHE* 3.3 30.1 + - + +
447B LEU* 3.7 13.8 - - + +
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Residues in contact with LEU 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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279B ILE* 3.8 30.7 - - + -
283B ARG 3.5 23.1 - - - +
284B ASP* 4.3 0.2 - - - -
285B LEU* 3.5 17.9 - - + +
299B PHE* 4.8 1.1 - - + -
303B ILE* 3.7 30.3 - - + -
395B PHE* 4.3 9.2 - - + -
396B VAL 3.0 9.6 + - - +
397B VAL* 3.5 10.6 - - + +
398B LEU* 2.8 28.1 + - - +
427B GLN* 4.4 7.4 - - + +
428B THR* 1.3 85.2 - - - +
430B MET* 1.3 65.9 + - - +
431B PHE* 4.1 15.7 - - + -
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Residues in contact with MET 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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285B LEU 2.8 16.3 + - - +
286B MET* 3.5 3.5 - - - -
287B ALA* 2.8 28.1 + - - +
398B LEU* 3.6 24.2 - - + -
401B ALA* 3.4 16.8 - - + -
405B LEU* 3.8 18.2 - - + -
428B THR* 3.8 13.7 - - + -
429B LEU* 1.3 77.7 - - - +
431B PHE* 1.3 66.8 + - - +
435B PHE* 4.4 12.3 - - + -
443B ALA* 3.8 25.1 - - - +
446B PHE* 3.8 16.8 - - + -
447B LEU* 3.7 31.6 - - + -
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Residues in contact with PHE 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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271B ILE* 4.2 2.0 - - + -
275B SER* 3.8 6.7 - - - -
279B ILE* 4.2 5.4 - - + -
285B LEU* 3.7 21.5 - - + -
287B ALA* 3.4 26.5 - - + -
295B LYS* 3.8 27.8 - - + -
298B ALA* 3.7 24.0 - - + -
299B PHE* 3.5 40.6 - + + -
397B VAL* 4.7 3.1 - - + -
398B LEU 3.1 7.5 + - - +
399B ASP* 4.1 14.1 - - - +
400B GLU 2.9 24.8 + - - -
401B ALA* 2.9 9.7 + - - -
429B LEU* 4.1 20.2 - - + -
430B MET* 1.3 80.3 - - - +
432B SER* 1.3 60.6 + - - +
435B PHE* 5.0 0.9 - - - -
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Residues in contact with SER 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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287B ALA 3.2 4.7 + - - +
288B CYS* 3.2 27.4 - - - +
289B ALA 3.3 2.4 + - - -
295B LYS* 3.8 15.7 - - - +
399B ASP* 5.4 0.2 - - - -
400B GLU* 3.9 8.5 + - - +
401B ALA 4.0 4.9 - - - -
402B ASP* 2.6 29.6 + - - -
431B PHE* 1.3 79.2 - - - +
433B ALA* 1.3 67.8 + - - +
434B THR* 3.0 16.9 + - - -
435B PHE* 4.3 7.6 - - - -
551B ARG* 3.6 8.7 + - - -
575B HIS* 4.0 0.5 - - - -
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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