Contacts of the strand formed by residues 257 - 262 (chain E) in PDB entry 5W69
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 257 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E LEU* 3.9 5.1 - - + +
217E TRP* 3.6 19.9 - + + -
218E GLN 3.2 13.9 - - - -
219E ARG* 3.3 40.6 - - + -
224E GLN* 3.9 17.5 + - + -
247E VAL* 3.9 16.6 - - + -
248E VAL 4.7 2.9 + - - -
249E VAL* 3.6 37.3 - - + +
250E PRO* 3.8 19.6 - - + +
253E GLU* 3.4 25.0 + - + -
254E GLU 3.2 12.2 + - - +
256E ARG* 1.3 81.6 - - + +
258E THR* 1.3 61.2 + - - +
273E ARG* 3.3 26.0 - - - +
274E TRP 4.9 0.7 + - - -
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Residues in contact with THR 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E TRP* 3.2 7.4 - - - -
218E GLN* 2.9 40.9 + - - +
221E GLY 5.1 3.1 + - - -
256E ARG 4.8 2.0 + - - +
257E TYR* 1.3 78.1 - - - +
259E CYS* 1.3 59.5 + - - +
260E HIS* 2.9 29.0 + - - -
271E THR* 3.8 14.8 - - + -
272E LEU 3.4 6.5 - - - +
273E ARG* 3.3 43.7 - - - +
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Residues in contact with CYS 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E VAL* 4.7 0.4 - - + -
203E CYS* 2.0 53.6 - - + -
215E LEU* 3.8 15.0 - - - -
216E THR 3.3 11.4 - - - -
217E TRP* 3.5 15.8 - - + -
245E ALA* 5.4 0.2 - - - -
258E THR* 1.3 73.0 - - - +
260E HIS* 1.3 63.5 + - - +
261E VAL* 4.3 4.0 - - - -
270E LEU 3.8 0.3 - - - +
271E THR* 3.3 5.7 - - - -
272E LEU* 2.8 42.4 + - + +
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Residues in contact with HIS 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E THR 3.2 6.9 - - - +
215E LEU* 3.4 2.8 - - - -
216E THR* 2.7 45.7 + - - +
218E GLN* 3.3 39.0 + - + -
258E THR* 2.9 36.8 + - - -
259E CYS* 1.3 73.9 - - - +
261E VAL* 1.4 61.5 + - - +
262E GLN* 5.5 4.0 - - + +
269E PRO* 6.4 0.9 - - + -
270E LEU 3.4 4.6 + - - +
271E THR* 3.5 31.9 + - + -
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Residues in contact with VAL 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E PRO* 3.8 28.7 - - + -
187E THR* 3.8 12.6 - - + -
203E CYS* 4.6 0.2 - - - -
213E ILE* 4.1 16.2 - - + -
214E THR 3.4 4.0 - - - +
215E LEU* 3.7 21.3 - - + -
259E CYS* 4.3 1.6 - - - -
260E HIS* 1.4 76.8 - - - +
262E GLN* 1.3 64.2 + - - +
263E HIS 4.2 0.2 - - - -
266E LEU* 4.0 7.1 - - + +
269E PRO* 3.4 10.9 - - - +
270E LEU* 3.1 38.2 + - + -
272E LEU* 3.7 27.8 - - + -
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Residues in contact with GLN 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213E ILE* 3.4 7.3 - - - +
214E THR* 3.0 52.7 + - + +
260E HIS* 5.5 3.6 - - + -
261E VAL* 1.3 78.7 - - - +
263E HIS* 1.3 61.7 + - - +
266E LEU* 4.7 0.2 - - - -
269E PRO* 4.2 22.7 - - + +
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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