Contacts of the strand formed by residues 386 - 391 (chain B) in PDB entry 2G9Y
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 LEU 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LYS* 4.3 13.5 - - - +
273B ALA* 3.6 22.9 - - + +
274B THR* 3.5 20.0 - - - -
275B TYR* 3.9 5.6 - - + +
333B ALA* 3.8 22.7 - - + -
385B GLY* 1.3 78.4 - - - +
387B THR* 1.3 67.4 + - - +
401B SER* 3.4 0.9 + - - -
402B TYR* 2.8 43.5 + - + +
405B SER 5.8 1.1 - - - +
410B GLN* 3.9 17.3 - - - +
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Residues in contact with THR 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ALA* 3.5 3.3 - - - -
274B THR* 2.8 32.4 + - - +
276B HIS* 3.6 5.6 + - - +
277B GLY* 3.0 20.3 + - - -
278B ASN* 2.8 29.7 + - - +
381B THR* 5.1 4.5 - - + -
383B ALA* 4.2 20.8 + - + +
385B GLY 5.1 1.3 - - - +
386B LEU* 1.3 80.2 - - - +
388B GLN* 1.3 65.9 + - - +
399B VAL* 4.4 5.2 - - + -
400B MET 3.3 13.9 - - - +
401B SER* 3.8 17.0 - - - +
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Residues in contact with GLN 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO* 2.8 43.1 + - - +
272B LYS 3.8 8.9 + - - -
273B ALA* 4.3 6.0 - - + +
277B GLY 4.4 2.2 - - - -
278B ASN* 4.0 10.7 - - - +
281B LYS* 5.8 0.8 - - - +
282B PRO 5.6 0.4 - - - +
284B VAL* 3.9 18.5 - - + +
335B PRO* 3.5 35.3 - - + +
336B CYS* 4.7 2.6 + - - -
387B THR* 1.3 81.7 - - - +
389B ALA* 1.3 71.6 + - - +
390B LEU* 3.8 13.1 - - + +
398B MET 3.7 0.7 - - - +
399B VAL* 3.3 3.6 - - - -
400B MET* 3.1 28.7 + - - +
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Residues in contact with ALA 389 (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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277B GLY 4.8 1.0 + - - -
278B ASN* 4.0 26.2 - - + +
281B LYS 5.1 0.7 - - - +
282B PRO 4.8 3.0 + - - +
283B ALA* 3.3 19.2 - - + +
284B VAL* 2.7 30.3 + - - +
388B GLN* 1.3 81.6 - - - +
390B LEU* 1.3 56.4 + - - +
397B VAL* 3.7 19.7 - - + -
398B MET 3.5 4.5 - - - -
399B VAL* 4.2 3.6 - - + -
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Residues in contact with LEU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.9 22.2 - - + -
283B ALA* 4.5 0.7 - - - -
284B VAL* 3.4 16.4 - - + +
286B CYS* 4.2 0.9 - - - -
335B PRO* 3.7 13.5 - - + -
336B CYS* 4.0 19.3 - - - -
339B ILE* 4.2 5.8 - - + -
388B GLN* 3.8 20.0 - - - +
389B ALA* 1.3 77.4 - - - +
391B ASN* 1.3 63.1 + - - +
392B THR* 3.5 1.3 + - - +
396B ALA 3.5 1.7 - - - +
397B VAL* 3.2 7.0 - - - -
398B MET* 2.7 52.2 + - + +
400B MET* 3.6 34.3 - - + -
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.1 22.4 + - - -
283B ALA* 3.4 37.2 - - - +
284B VAL 2.8 9.2 + - - +
285B THR* 3.1 28.3 + - + +
390B LEU* 1.3 69.1 - - - +
392B THR* 1.3 65.9 + - - +
395B GLY* 6.2 2.1 - - - -
396B ALA 3.8 5.6 + - - +
397B VAL* 4.0 12.1 - - - +
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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