Contacts of the strand formed by residues 275 - 279 (chain B) in PDB entry 3GW5
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 LYS 275 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191B HIS* 3.5 48.6 - - + +
270B PHE 3.4 2.3 - - - +
271B HIS* 3.4 7.5 - - - -
272B LEU 2.9 32.8 + - - +
273B GLY 3.9 1.8 - - - +
274B GLY* 1.3 84.8 - - - +
276B GLU* 1.3 61.0 + - - +
277B TYR* 3.6 8.6 + - + -
504B GOL 4.5 19.8 - - - -
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Residues in contact with GLU 276 (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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207B GLY 5.0 0.2 - - - +
209B SER* 4.6 10.6 + - - -
214B THR* 5.6 0.5 + - - -
269B SER* 3.5 23.8 - - - +
270B PHE 3.7 12.0 - - - -
271B HIS* 3.0 30.3 + - + +
275B LYS* 1.3 72.0 - - - +
277B TYR* 1.3 63.9 + - - +
278B THR* 3.7 13.9 + - - +
504B GOL 3.4 16.5 + - - -
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Residues in contact with TYR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B HIS* 2.7 27.5 + - - +
269B SER* 3.3 1.4 - - - -
270B PHE* 2.8 52.0 + - + +
272B LEU* 3.8 32.3 - - + -
275B LYS* 3.7 17.5 - - + -
276B GLU* 1.3 71.7 - - - +
278B THR* 1.3 60.0 + - - +
279B LEU* 5.6 0.2 - - - -
319B PHE* 3.8 29.2 - + + -
323B PHE* 3.6 30.5 - + + -
336B PHE* 3.3 40.1 - + + +
504B GOL 3.2 28.0 - - - -
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Residues in contact with THR 278 (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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267B ASP* 3.6 35.7 - - + +
268B ILE 3.3 3.4 - - - +
269B SER* 2.7 23.4 + - - +
276B GLU* 3.7 13.5 + - - +
277B TYR* 1.3 76.0 - - - +
279B LEU* 1.3 63.7 + - - +
280B THR* 4.7 2.7 - - + +
322B LYS* 2.7 37.3 + - - +
323B PHE* 4.1 5.3 - - - -
504B GOL 5.5 0.4 + - - -
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Residues in contact with LEU 279 (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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232B ILE* 3.5 31.6 - - + -
267B ASP* 3.5 1.0 - - - -
268B ILE* 2.7 41.8 + - + +
270B PHE* 4.0 15.7 - - + -
277B TYR 5.2 0.2 - - - +
278B THR* 1.3 81.1 - - - +
280B THR* 1.3 63.9 + - - +
283B ASP* 3.5 19.1 - - + -
284B TYR* 3.8 13.2 - - + -
300B ILE* 6.1 0.9 - - + -
318B THR* 4.2 21.8 - - + +
319B PHE* 4.5 7.0 - - + -
322B LYS* 3.8 29.8 - - + -
323B PHE* 4.3 8.7 - - + -
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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