Contacts of the strand formed by residues 235 - 240 (chain A) in PDB entry 3R2W
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 TYR 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LYS 3.1 10.0 + - - +
97A LEU* 3.2 13.6 - - + +
98A VAL* 2.7 34.0 + - - +
234A GLU* 1.3 107.2 - - + +
236A ILE* 1.3 55.7 + - - +
253A LEU* 6.0 1.6 - - + -
256A LEU* 3.3 50.9 + - + +
257A MET* 4.1 14.8 - - + -
264A ARG 4.7 0.2 + - - -
265A CYS 2.6 40.8 + - - -
266A GLU 5.4 0.7 - - - -
267A PHE 5.6 0.2 - - - -
322A TRP* 4.5 3.6 - - + -
323A ILE* 3.0 35.2 - - - -
324A SER* 4.0 5.4 - - - -
325A LEU* 3.7 5.1 - - - +
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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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97A LEU* 4.0 0.7 - - - -
98A VAL* 3.4 22.4 - - + +
100A VAL* 3.3 24.5 - - + -
215A ILE* 5.8 1.1 - - + -
219A PHE* 3.7 22.7 - - + -
228A PHE* 5.3 0.7 - - + -
235A TYR* 1.3 74.9 - - - +
237A PHE* 1.3 60.4 + - - +
238A VAL* 3.6 23.3 - - + +
322A TRP* 3.2 8.5 - - - +
323A ILE* 2.9 55.5 + - + +
325A LEU* 3.6 33.8 - - + +
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Residues in contact with PHE 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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97A LEU* 3.5 19.7 - - + -
98A VAL 2.8 11.8 + - - +
99A VAL* 4.2 11.3 - - + +
100A VAL 2.9 20.9 + - - +
101A LYS* 5.5 1.3 - - - -
236A ILE* 1.3 75.2 - - - +
238A VAL* 1.3 70.4 + - - +
239A SER* 3.6 17.7 + - - -
246A ALA* 4.3 9.2 - - + -
247A THR 3.4 33.9 - - - -
248A VAL* 4.0 23.1 - - + -
270A GLU* 3.9 9.9 - - - -
320A ASN* 4.6 1.3 - - + -
321A LEU 3.3 15.3 - - - -
322A TRP* 3.5 39.0 - + - +
380A ARG* 4.6 0.4 - - - -
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Residues in contact with VAL 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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100A VAL* 3.4 17.3 - - + +
102A LEU* 3.8 33.7 - - + -
215A ILE* 3.6 26.2 - - + -
236A ILE* 3.6 22.1 - - + +
237A PHE* 1.3 73.6 - - - +
239A SER* 1.3 65.1 + - - +
319A ASN 5.2 0.2 - - - +
320A ASN* 3.7 0.3 - - - -
321A LEU* 2.8 58.4 + - + +
323A ILE* 4.9 7.2 - - + -
361A VAL* 5.0 6.5 - - + -
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Residues in contact with SER 239 (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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100A VAL 3.2 4.4 + - - -
101A LYS* 3.0 36.4 - - - +
102A LEU* 3.0 31.9 + - - +
237A PHE* 4.2 13.9 + - - -
238A VAL* 1.3 76.4 - - - +
240A ASN* 1.3 60.5 + - - +
246A ALA* 3.9 15.1 + - - +
319A ASN 3.9 11.0 - - - -
320A ASN* 3.8 14.4 - - - -
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Residues in contact with ASN 240 (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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101A LYS* 4.2 7.9 + - - +
102A LEU* 3.3 42.4 + - + +
212A HIS* 5.9 0.7 - - - -
239A SER* 1.3 78.0 + - - +
241A ILE* 1.3 67.3 + - - +
242A ASP* 3.0 35.0 + - + +
243A ASN* 3.2 28.8 + - + +
246A ALA* 4.3 0.5 - - - +
319A ASN* 4.5 15.6 + - + +
320A ASN* 4.6 3.4 - - - +
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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