Contacts of the strand formed by residues 233 - 238 (chain A) in PDB entry 6N8P
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 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLU* 2.8 23.8 - - + +
193A ALA* 4.5 10.1 - - + -
207A GLY* 3.8 18.8 - - - -
208A TYR 3.2 26.9 - - - +
209A SER* 2.7 16.2 + - - +
211A GLY* 4.3 7.4 - - - -
212A LEU 5.1 0.2 - - - -
213A VAL* 3.7 28.5 - - + -
229A SER* 4.6 0.9 - - - +
231A GLN 3.5 1.4 + - - -
232A GLN* 1.3 75.4 - - - +
234A GLU* 1.3 61.6 + - - +
235A ASN 3.6 24.9 - - - +
236A ILE* 4.9 1.8 - - + -
247A SER* 3.8 21.1 - - - -
248A CYS 4.0 0.4 - - - +
249A HIS* 3.9 13.0 - - + +
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Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLU* 4.0 28.6 - - - +
232A GLN* 5.2 2.3 + - - -
233A LEU* 1.3 76.1 - - - +
235A ASN* 1.3 69.2 + - - +
248A CYS 3.0 10.8 + - - +
249A HIS 3.5 3.4 - - - -
250A SER* 2.5 45.4 + - - +
282A ALA* 4.0 13.7 - - + +
283A ILE 3.2 22.9 - - - +
284A THR* 3.9 18.3 - - - +
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Residues in contact with ASN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A GLU 3.8 19.0 + - - -
193A ALA* 5.1 2.9 - - - +
195A GLN* 4.5 5.6 + - - +
233A LEU* 3.6 9.2 - - - +
234A GLU* 1.3 80.1 + - - +
236A ILE* 1.3 83.1 + - - +
237A TRP* 5.2 1.7 - - - -
247A SER* 3.5 1.9 - - - -
248A CYS* 3.0 34.7 + - - +
284A THR 3.2 19.4 + - - +
285A ARG* 3.7 22.8 + - - +
286A ILE 4.2 5.0 + - - +
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ALA* 3.7 11.4 - - + +
195A GLN* 2.6 44.4 + - - +
205A LEU* 3.7 19.1 - - + -
213A VAL* 3.9 30.1 - - + -
227A PHE* 4.3 4.0 - - + -
233A LEU* 4.9 2.5 - - + -
235A ASN* 1.3 89.9 + - - +
237A TRP* 1.3 71.9 + - - +
245A LEU* 4.0 23.8 - - + -
246A VAL 3.3 18.4 - - - +
247A SER* 3.7 18.8 - - - -
286A ILE* 4.7 2.5 - - - -
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Residues in contact with TRP 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLN* 4.0 8.7 - - - -
235A ASN* 5.2 1.8 - - - -
236A ILE* 1.3 80.2 - - - +
238A TRP* 1.3 87.4 + - - +
244A LEU 4.1 0.3 - - - +
245A LEU* 3.6 8.8 - - - +
246A VAL* 2.9 36.8 + - + +
285A ARG* 4.1 20.0 - - - -
286A ILE* 3.5 25.4 - - + +
287A LEU* 3.7 34.1 - - + -
288A TRP* 3.2 43.0 + - + +
289A LEU* 4.1 11.7 - - + +
348A ASP* 5.4 1.2 + - - -
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Residues in contact with TRP 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLN* 3.7 21.2 + - + +
196A GLU 3.4 17.9 - - - +
197A HIS* 3.4 50.0 - + + -
198A PRO* 3.7 15.0 - - + +
204A ILE 4.6 0.9 - - - -
205A LEU* 3.5 35.9 - - + -
215A ILE* 3.7 31.2 - - + -
237A TRP* 1.3 95.5 + - - +
239A GLN* 1.3 67.1 + - - +
240A ARG 4.0 0.2 + - - -
242A GLY* 2.9 37.5 + - - -
244A LEU 3.6 4.5 - - - -
245A LEU* 3.4 23.7 - - + +
259A VAL* 4.4 1.2 - - + +
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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