Contacts of the strand formed by residues 227 - 235 (chain A) in PDB entry 6PXC
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 VAL 227 (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* 3.8 27.6 - - + +
195A LEU* 3.8 26.2 - - + -
196A ARG* 3.8 26.6 - - + +
220A PHE 3.2 10.5 - - - +
221A LEU* 3.9 19.3 - - + -
226A VAL* 1.3 79.4 - - - +
228A ASN* 1.3 64.3 + - - +
229A HIS* 3.3 38.7 + - + +
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Residues in contact with ASN 228 (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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218A LEU 3.5 1.9 - - - +
219A SER* 3.4 4.3 - - - -
220A PHE* 2.8 37.1 + - + +
222A SER* 3.9 4.5 - - - -
226A VAL* 3.3 23.6 - - - +
227A VAL* 1.3 74.6 - - - +
229A HIS* 1.3 61.3 + - - +
230A PHE* 3.7 21.0 - - + -
263A LEU* 3.7 38.5 - - + +
1106U SER* 4.0 17.7 + - - +
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Residues in contact with HIS 229 (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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188A ARG* 3.3 54.0 - - + +
191A ALA* 4.7 1.6 - - + -
192A GLU* 2.8 28.5 + - + -
207A ARG* 3.1 16.4 + - - -
217A VAL* 3.8 9.9 - - + -
218A LEU 3.4 3.1 - - - -
219A SER* 2.8 27.5 + - - -
227A VAL* 3.3 30.2 - - + +
228A ASN* 1.3 72.9 - - - +
230A PHE* 1.3 57.6 + - - +
1104U ILE 4.9 1.5 + - - +
1105U PTR 3.5 6.2 - - + -
1106U SER* 2.8 35.2 + - - -
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Residues in contact with PHE 230 (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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217A VAL* 3.3 5.3 - - - +
218A LEU* 2.8 53.6 + - + +
220A PHE* 4.3 3.4 - + + -
228A ASN* 3.7 32.3 - - + -
229A HIS* 1.3 73.6 - - - +
231A ARG* 1.3 64.1 + - - +
232A ILE* 4.0 0.5 - - - +
241A ILE* 3.8 20.0 - - + -
262A LEU* 3.6 38.4 - - + -
263A LEU* 3.8 16.4 - - + -
1106U SER* 3.4 32.3 - - - +
1107U VAL 3.6 19.5 - - - -
1108U PRO* 3.6 21.3 - - + -
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Residues in contact with ARG 231 (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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209A SER* 4.7 4.0 + - - -
211A ARG* 6.3 0.2 - - - +
212A ARG* 3.7 61.6 - - - +
215A SER* 4.4 4.6 + - - +
216A PHE 3.5 7.9 - - - +
217A VAL* 4.6 1.4 - - - +
230A PHE* 1.3 74.0 - - - +
232A ILE* 1.3 59.5 + - - +
233A ILE* 4.1 15.8 - - + +
240A TYR 4.0 0.7 - - - +
241A ILE* 3.7 22.3 - - - +
242A GLY 4.7 1.7 + - - -
1102U GLU* 4.2 17.8 + - - -
1103U ASN 4.8 1.6 + - - -
1105U PTR 3.1 63.8 + - + +
1106U SER 4.3 4.8 + - - -
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Residues in contact with ILE 232 (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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206A ILE* 4.0 23.3 - - + -
216A PHE* 2.9 41.6 + - + +
217A VAL 4.4 2.2 - - - -
218A LEU* 4.0 25.1 - - + +
230A PHE 4.0 6.3 - - - +
231A ARG* 1.3 77.8 - - - +
233A ILE* 1.3 67.0 + - - +
234A ALA 3.8 1.6 + - - -
239A TYR* 3.8 39.3 - - + -
240A TYR 3.4 6.5 - - - +
241A ILE* 4.2 8.5 - - + -
249A LEU* 4.1 4.7 - - + -
252A LEU* 3.8 28.0 - - + -
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Residues in contact with ILE 233 (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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212A ARG* 4.2 20.6 - - - +
215A SER* 4.0 20.2 - - - -
231A ARG* 4.5 15.9 - - + -
232A ILE* 1.3 79.9 - - - +
234A ALA* 1.3 70.8 + - - +
235A MET* 4.5 13.0 - - + -
239A TYR* 3.5 2.5 - - - -
240A TYR* 2.8 52.7 + - + +
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Residues in contact with ALA 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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214A GLY 4.5 10.5 + - - +
215A SER* 5.2 1.0 - - - +
216A PHE* 3.6 29.6 - - + -
232A ILE 3.8 2.6 + - - -
233A ILE* 1.3 74.5 - - - +
235A MET* 1.3 66.5 + - - +
237A GLY* 5.4 1.8 - - - +
238A ASP 3.3 7.0 - - - +
239A TYR* 3.9 16.4 - - + -
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Residues in contact with MET 235 (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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233A ILE* 3.7 14.4 + - + +
234A ALA* 1.3 77.2 - - - +
236A SER* 1.3 89.0 + - - +
237A GLY 3.2 2.0 - - - +
238A ASP* 3.0 25.6 + - - +
240A TYR* 4.0 23.5 + - + +
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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