Contacts of the strand formed by residues 216 - 220 (chain B) in PDB entry 2G1Y
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 CYS 216 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B GLN* 3.3 9.3 + - - +
200B MET* 2.9 41.2 + - - +
212B CYS* 2.0 45.8 - - + -
215B GLY* 1.3 74.6 - - - +
217B LEU* 1.3 69.1 + - - +
307B THR* 6.3 0.2 - - - -
308B TRP* 3.8 26.9 - - + +
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Residues in contact with LEU 217 (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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191B ILE* 5.4 9.6 - - + -
197B GLN* 3.7 19.3 - - + +
198B ILE 3.7 6.5 - - - +
199B GLN* 4.0 15.9 - - - +
216B CYS* 1.3 84.8 - - - +
218B ALA* 1.3 61.6 + - - +
304B THR 4.5 2.7 - - - +
305B GLY* 5.6 1.6 - - - -
306B PRO 4.3 6.5 + - - +
307B THR* 3.1 34.3 - - + +
308B TRP* 2.8 32.1 + - - +
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Residues in contact with ALA 218 (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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197B GLN* 3.4 4.7 - - - +
198B ILE* 2.8 55.9 + - + +
200B MET* 4.2 29.2 - - + -
217B LEU* 1.3 76.0 - - - +
219B LEU* 1.3 59.9 + - - +
220B VAL* 3.7 1.3 + - - +
267B LEU* 4.6 0.9 - - + -
308B TRP* 3.6 7.2 - - + -
310B LEU* 4.4 16.6 - - + -
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Residues in contact with LEU 219 (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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34B THR 4.9 0.7 - - - +
35B GLY* 4.8 13.9 - - - +
195B VAL* 4.9 5.6 - - + -
196B TRP* 3.1 29.2 - - + +
197B GLN* 4.0 10.2 - - + +
217B LEU 4.3 0.2 - - - -
218B ALA* 1.3 71.8 - - - +
220B VAL* 1.3 71.6 + - - +
221B ASP* 3.2 22.9 + - + +
300B ILE* 4.7 13.9 - - + -
304B THR* 4.1 26.5 - - + -
307B THR* 4.1 7.1 + - - +
308B TRP 2.9 15.3 + - - +
309B ALA* 3.4 4.0 - - + -
310B LEU* 2.8 28.0 + - - +
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Residues in contact with VAL 220 (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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34B THR* 2.8 18.7 + - - -
196B TRP* 3.0 9.8 + - - +
198B ILE* 4.3 15.0 - - + -
218B ALA 4.4 3.1 - - - +
219B LEU* 1.3 76.3 - - - +
221B ASP* 1.3 57.9 + - - +
310B LEU* 3.8 19.5 - - + +
314B PHE* 5.8 0.2 - - + -
315B ILE* 4.9 8.1 - - + -
320B THR* 4.3 8.1 - - + +
322B PHE* 3.6 25.2 - - + -
329B ILE* 3.3 30.5 - - + -
331B PHE* 4.2 27.8 - - + -
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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