Contacts of the strand formed by residues 253 - 263 (chain A) in PDB entry 3URF
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 HIS 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A THR* 3.3 4.0 - - - -
244A LYS* 2.8 44.9 + - + +
249A ILE* 4.3 10.4 - - + +
251A SER* 3.2 32.5 + - - -
252A SER* 1.3 82.1 + - - +
254A THR* 1.3 65.1 + - - +
255A LEU* 3.5 1.9 + - + +
49Z TYR* 3.6 20.7 + - - -
60Z LEU* 4.0 14.3 - - + +
61Z TYR* 4.6 14.1 + - + -
63Z SER* 5.3 9.9 - - - +
81Z ASN* 5.3 2.9 + - - -
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Residues in contact with THR 254 (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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241A TYR* 4.2 25.6 - - + -
242A VAL 3.5 7.2 - - - +
243A THR* 4.1 9.0 - - + +
252A SER* 5.6 0.5 + - - -
253A HIS* 1.3 74.1 - - - +
255A LEU* 1.3 62.5 + - - +
256A MET 3.4 29.6 - - - +
257A LYS* 4.6 4.9 - - + -
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Residues in contact with LEU 255 (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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216A LEU* 3.5 30.5 - - + -
242A VAL* 2.7 20.4 + - + +
243A THR 4.3 3.4 - - - -
244A LYS* 3.8 51.8 - - + +
253A HIS* 4.7 2.0 - - + +
254A THR* 1.3 77.1 - - - +
256A MET* 1.3 67.5 + - + +
281A PHE* 3.9 37.0 - - + -
283A LEU* 5.2 1.1 - - + -
289A ILE* 4.2 10.8 - - + -
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Residues in contact with MET 256 (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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216A LEU* 3.7 37.9 - - + +
217A TYR* 4.3 1.8 - - - +
240A VAL 4.7 0.2 - - - -
241A TYR* 3.4 0.7 - - - -
242A VAL* 2.8 58.9 + - + +
254A THR* 3.4 8.1 - - - +
255A LEU* 1.3 85.5 - - + +
257A LYS* 1.3 62.4 + - - +
277A VAL* 4.1 14.6 - - + -
278A GLY* 3.2 43.7 - - - +
279A GLY 3.5 2.0 - - - -
281A PHE* 3.6 17.9 - - + -
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Residues in contact with LYS 257 (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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239A MET* 3.9 15.3 - - + -
240A VAL 3.4 7.4 - - - +
241A TYR* 3.8 15.0 - - + -
254A THR* 4.6 4.5 - - + -
256A MET* 1.3 77.2 - - - +
258A GLY* 1.3 62.3 + - - +
277A VAL* 3.6 14.0 - - - +
67Z LYS* 4.5 7.9 - - - +
95Z GLU* 3.1 39.9 + - - +
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Residues in contact with GLY 258 (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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239A MET* 3.1 14.3 - - - +
240A VAL* 2.7 39.3 + - - +
257A LYS* 1.3 78.4 - - - +
259A GLY* 1.3 56.4 + - - -
275A ILE* 3.7 17.3 - - - -
277A VAL* 4.1 5.2 - - - -
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Residues in contact with GLY 259 (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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238A LEU 3.0 11.7 - - - -
239A MET* 3.9 6.7 - - - +
258A GLY* 1.3 75.4 - - - -
260A SER* 1.3 65.3 + - - -
273A TYR* 3.1 14.3 + - - -
275A ILE* 3.6 12.5 - - - +
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Residues in contact with SER 260 (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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237A GLN* 4.9 0.7 - - - -
238A LEU* 2.9 34.3 + - - +
239A MET* 3.9 5.8 - - - -
259A GLY* 1.3 72.5 - - - -
261A THR* 1.3 79.2 + - - +
262A LYS* 3.7 10.3 + - - +
273A TYR* 3.1 31.8 + - - -
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Residues in contact with THR 261 (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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236A LEU 3.2 7.9 - - - +
237A GLN* 4.1 23.8 - - + +
239A MET* 6.4 0.9 - - - -
260A SER* 1.3 87.7 + - - +
262A LYS* 1.3 64.2 + - - +
96Z PHE* 4.2 21.1 - - + -
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Residues in contact with LYS 262 (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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234A GLU 3.4 1.4 - - - +
235A TYR* 3.4 6.8 - - - +
236A LEU* 2.8 41.7 + - + +
238A LEU* 4.2 11.4 - - + -
260A SER* 3.7 15.3 - - - +
261A THR* 1.3 74.9 - - - +
263A TYR* 1.3 61.6 + - - +
264A TRP* 3.7 26.4 - - + +
272A PHE 5.0 3.2 + - - -
273A TYR* 3.2 58.4 - - + +
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Residues in contact with TYR 263 (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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234A GLU* 3.4 34.1 + - + -
235A TYR* 3.4 53.8 + + + -
262A LYS* 1.3 73.3 - - - +
264A TRP* 1.3 65.8 + - - +
265A SER* 3.3 26.4 + - - -
267A ASN* 5.4 3.1 + - - -
271A HIS* 5.1 0.5 + - - -
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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