Contacts of the strand formed by residues 257 - 265 (chain A) in PDB entry 1XJV
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 THR 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A SER* 3.3 14.7 + - - +
251A MET* 4.1 14.3 - - - +
255A ASN 4.2 0.2 + - - -
256A GLN* 1.3 74.6 - - - +
258A MET* 1.3 72.8 + - - +
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Residues in contact with MET 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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249A GLN* 3.2 44.2 - - - +
250A SER* 2.9 25.9 + - - +
251A MET 3.7 4.3 - - - -
252A ASN* 3.7 33.9 - - + +
256A GLN* 3.5 10.1 - - + +
257A THR* 1.3 84.0 - - - +
259A LEU* 1.3 71.8 + - - +
260A SER* 3.5 26.9 - - - +
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Residues in contact with LEU 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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191A PHE* 4.1 26.9 - - + -
192A PRO* 4.1 15.7 - - + +
248A LEU* 3.8 28.7 - - + -
249A GLN 3.3 1.3 - - - -
250A SER* 4.4 11.0 - - - -
258A MET* 1.3 87.5 - - - +
260A SER* 1.3 63.7 + - - +
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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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191A PHE* 4.7 1.6 - - - -
192A PRO* 3.4 13.0 - - - -
193A SER 4.6 1.1 - - - -
194A TRP* 3.9 22.6 - - - +
248A LEU* 3.0 9.9 - - - +
249A GLN* 2.5 59.0 + - - +
258A MET* 3.5 15.1 - - - +
259A LEU* 1.3 75.9 - - - +
261A LEU* 1.3 59.2 + - - +
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Residues in contact with LEU 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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156A VAL* 3.7 21.5 - - + -
157A GLN 4.5 1.1 - - - +
158A PRO* 3.9 32.5 - - + +
189A THR* 3.9 15.3 - - - -
190A PRO* 4.4 8.1 - - + -
191A PHE* 4.1 15.2 - - + +
192A PRO 3.0 14.1 + - - +
193A SER* 3.5 4.0 - - - -
194A TRP* 2.9 24.2 + - - -
246A THR* 4.4 7.6 - - + -
247A LYS 3.7 5.8 - - - +
248A LEU* 4.0 12.8 - - + +
260A SER* 1.3 73.1 - - - +
262A GLU* 1.3 63.6 + - - +
263A PHE* 3.6 32.1 - - + -
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Residues in contact with GLU 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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194A TRP* 3.6 30.2 - - + -
246A THR* 3.2 7.1 - - - -
247A LYS* 2.7 57.9 + - + +
249A GLN* 2.4 47.2 + - + +
261A LEU* 1.3 76.3 - - - +
263A PHE* 1.3 63.5 + - - +
264A HIS* 2.8 33.3 + - + -
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Residues in contact with PHE 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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153A LEU* 4.2 9.6 - - + -
156A VAL* 4.5 2.0 - - + -
162A PHE* 4.3 4.9 - + - -
189A THR* 3.6 24.9 - - + -
193A SER* 4.3 4.9 - - - -
194A TRP* 3.2 13.2 - - - +
218A ILE* 3.8 37.0 - - + -
219A ASP 3.5 19.5 - - - +
220A ILE* 3.6 12.5 - - + -
221A LEU 3.0 22.5 + - - -
244A LEU* 3.9 17.7 - - + -
245A HIS 3.3 4.3 - - - -
246A THR* 3.6 27.6 - - + -
261A LEU* 3.6 35.0 - - + -
262A GLU* 1.3 76.4 - - - +
264A HIS* 1.3 60.7 + - - +
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Residues in contact with HIS 264 (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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194A TRP* 3.5 16.8 - + - -
221A LEU 3.4 3.6 - - - -
223A TYR* 2.7 34.8 + + + -
243A SER 4.5 0.9 - - - +
244A LEU* 3.4 5.2 - - - +
245A HIS* 2.8 49.4 + - - +
247A LYS* 4.5 13.1 - - + +
262A GLU* 2.8 46.5 + - + +
263A PHE* 1.3 74.4 + - - +
265A LEU* 1.3 59.9 + - - +
266A HIS* 3.4 33.7 + + + +
8B T 6.3 0.2 - - - -
10B G 4.6 7.6 - + - +
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Residues in contact with LEU 265 (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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220A ILE* 4.7 0.7 - - + -
221A LEU 2.9 9.1 + - - -
222A VAL* 3.8 19.5 - - + -
223A TYR* 3.1 26.2 + - - -
226A HIS* 3.5 31.7 - - + +
241A ILE* 4.1 12.8 - - + -
242A TYR 3.4 25.6 - - - +
243A SER 4.0 11.7 - - - +
244A LEU* 4.0 8.0 - - + +
264A HIS* 1.3 72.9 - - - +
266A HIS* 1.3 58.7 + - - +
273A ARG* 4.1 8.1 - - + -
274A GLY 4.1 8.1 - - - +
275A ILE* 3.8 33.4 - - + -
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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