Contacts of the strand formed by residues 265 - 270 (chain A) in PDB entry 3WF4
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 ILE 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.6 25.8 - - + -
50A TYR* 3.2 24.7 - - + +
218A PHE* 6.0 1.3 - - + -
237A TYR* 3.8 20.6 - - + -
239A THR* 3.6 24.2 - - + -
240A VAL* 3.4 24.6 + - - +
252A PHE* 3.7 5.8 - - - -
255A GLN* 3.0 15.1 + - - +
263A PRO* 3.9 9.4 - - + +
264A LEU* 1.3 79.6 - - - +
266A ASN* 1.3 61.6 + - - +
267A SER* 3.7 19.3 - - - +
302A SER* 3.2 18.8 - - - +
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Residues in contact with ASN 266 (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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240A VAL 3.4 4.7 - - - -
241A ASP* 3.6 0.9 - - - -
242A PHE* 2.9 67.3 + - + -
252A PHE* 4.2 5.8 - - + -
265A ILE* 1.3 72.8 - - - +
267A SER* 1.3 59.1 + - - +
268A GLU 2.9 24.6 + - - +
269A PHE* 3.5 17.6 - - - +
296A ILE* 4.1 3.5 - - + +
302A SER 3.1 6.6 + - - +
303A VAL* 3.4 9.7 - - + -
304A ASN 2.9 25.1 + - - +
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Residues in contact with SER 267 (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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50A TYR* 4.3 2.9 + - - -
81A GLN* 2.9 35.0 + - - -
184A GLN* 4.8 2.0 - - - -
218A PHE* 3.3 15.5 - - - -
220A THR* 3.3 27.0 + - - -
239A THR* 2.9 23.3 + - - -
240A VAL 3.0 6.9 + - - -
265A ILE* 3.7 9.4 - - - +
266A ASN* 1.3 72.2 - - - +
268A GLU* 1.3 60.4 + - - +
304A ASN* 3.2 14.6 + - - +
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Residues in contact with GLU 268 (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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83A TYR* 3.0 0.7 + - - -
121A ARG* 2.8 40.9 + - - +
187A ASN* 3.9 0.3 - - - +
220A THR* 4.7 2.2 - - + +
241A ASP* 3.6 16.0 - - + +
242A PHE 3.1 17.5 + - - +
266A ASN* 2.9 10.9 + - - +
267A SER* 1.3 86.0 - - - +
269A PHE* 1.3 61.5 + - - +
270A TYR* 2.6 47.3 + - + +
304A ASN 3.6 2.9 - - - -
306A TYR* 3.7 16.9 - - + -
706A 6DJ 2.7 34.8 + - - -
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Residues in contact with PHE 269 (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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242A PHE* 3.3 15.5 - + - -
243A GLY* 4.1 15.9 - - - -
244A THR* 4.1 11.0 - - + -
266A ASN* 3.1 12.8 + - - +
268A GLU* 1.3 68.9 - - - +
270A TYR* 1.3 64.3 + - - +
271A THR* 3.1 2.1 + - - +
289A VAL* 3.4 42.6 - - + -
292A SER* 3.5 27.1 - - - -
293A LEU* 3.7 28.3 - - + -
296A ILE* 3.6 16.4 - - + -
303A VAL* 3.5 16.4 - - + -
304A ASN 2.8 11.0 + - - +
305A LEU* 3.5 12.8 - - + -
306A TYR 3.0 20.5 + - - -
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Residues in contact with TYR 270 (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 GLU* 4.2 0.5 + - - -
241A ASP* 3.5 16.3 + - + -
242A PHE* 3.8 12.9 + - - -
243A GLY* 3.7 23.0 - - - -
244A THR* 4.4 13.0 + - - +
268A GLU* 2.6 46.4 + - + -
269A PHE* 1.3 75.8 - - - +
271A THR* 1.3 62.0 + - - +
272A GLY 3.5 15.2 + - - +
273A TRP* 3.9 34.8 - + + -
284A ILE* 4.9 4.1 - - + +
289A VAL* 4.3 8.3 - - - +
306A TYR* 3.3 26.0 - + + -
333A TYR* 4.8 0.4 - - - -
706A 6DJ 3.3 18.2 - - - +
709A EDO 4.6 10.1 - - - -
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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