Contacts of the strand formed by residues 214 - 218 (chain J) in PDB entry 1S7X
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 THR 214 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213J ILE* 1.3 81.2 + - - +
215J LEU* 1.3 70.7 + - - +
216J THR* 4.2 19.3 - - + -
243J LYS* 5.8 1.1 - - - +
260J ARG 3.8 0.5 - - - +
262J TYR* 3.2 45.0 + - + -
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Residues in contact with LEU 215 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203J CYS* 3.7 21.8 - - - +
205J ALA* 4.1 10.3 - - + -
213J ILE* 3.8 29.8 - - + -
214J THR* 1.3 85.0 - - - +
216J THR* 1.3 63.9 + - - +
228J MET* 4.0 16.1 - - - +
243J LYS* 3.7 40.8 - - + +
244J TRP* 3.9 4.0 - - - -
245J ALA* 3.8 26.1 - - + +
259J CYS* 5.2 1.6 - - - -
260J ARG 3.6 6.1 - - - +
261J VAL* 4.2 13.9 - - + -
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Residues in contact with THR 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214J THR* 4.2 14.8 - - + -
215J LEU* 1.3 77.7 - - - +
217J TRP* 1.3 71.0 + - - +
218J GLN* 3.9 11.2 + - - -
224J LEU 5.6 0.9 - - - -
228J MET* 4.0 7.6 - - + -
259J CYS* 3.4 9.7 - - - -
260J ARG* 3.1 44.7 + - - +
262J TYR* 3.8 19.3 + - + -
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Residues in contact with TRP 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189J VAL* 4.6 13.2 - - + -
201J LEU* 3.6 35.7 - - + -
203J CYS* 3.6 20.5 - - + +
216J THR* 1.3 80.6 - - - +
218J GLN* 1.3 75.6 + - - +
224J LEU* 3.1 39.8 + - + +
228J MET* 3.9 31.0 - - + +
245J ALA* 3.0 24.9 + - + +
247J VAL* 3.8 22.8 - - + +
257J TYR* 3.8 28.9 - + + -
258J THR 3.5 12.1 - - - -
259J CYS* 3.1 41.1 - - + -
272J LEU 4.9 0.9 - - - -
273J ARG* 5.3 1.6 - - - -
274J TRP 5.9 0.4 - - - -
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Residues in contact with GLN 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216J THR* 3.9 12.3 + - - -
217J TRP* 1.3 85.9 + - - +
219J LEU* 1.3 57.5 + - - +
220J ASN* 3.3 8.2 + - - +
221J GLY 3.2 25.8 + - - +
222J GLU 3.1 26.7 + - - -
223J GLU* 4.5 2.5 - - - +
224J LEU* 4.0 5.1 - - - +
257J TYR* 3.4 11.3 - - - -
258J THR* 3.1 43.9 + - - +
260J ARG* 3.3 29.3 - - - +
262J TYR* 5.0 1.0 + - - -
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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