Contacts of the strand formed by residues 289 - 292 (chain B) in PDB entry 2X1L
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 289 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B PHE* 2.8 52.9 + - + +
186B ILE* 3.4 3.8 - - - +
187B GLY 2.9 25.8 + - - +
260B HIS* 3.5 25.8 - - + +
262B ILE* 3.7 32.8 - - + -
267B ILE* 4.6 2.5 - - + -
270B HIS* 3.9 18.4 - - + +
271B THR* 3.8 18.6 - - + -
286B PRO* 4.0 15.7 - - + -
288B ARG* 1.3 76.3 - - - +
290B PHE* 1.3 63.9 + - - +
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Residues in contact with PHE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLY* 3.3 8.7 - - - -
188B PRO* 3.5 26.7 - - + -
259B LEU* 4.0 18.9 - - + +
260B HIS 3.1 8.9 + - - +
261B MET* 3.9 6.0 - - - +
262B ILE* 3.2 26.4 + - - +
288B ARG* 3.4 29.4 - - - +
289B ILE* 1.3 73.0 - - - +
291B ALA* 1.3 67.2 + - - +
292B HIS* 3.7 1.4 + - - -
334B PHE* 3.4 53.2 - + - -
335B GLY* 3.9 13.0 - - - -
406B VAL* 4.0 1.1 - - + -
407B PRO* 3.6 25.4 - - + -
603B 2HP 3.7 10.8 - - - -
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLY 2.9 11.2 + - - +
188B PRO* 3.5 18.9 - - - +
191B ARG* 4.2 11.3 + - + +
262B ILE* 3.2 9.2 - - + -
263B GLY 4.0 3.6 - - - +
264B LYS* 3.9 24.1 - - - +
267B ILE* 3.7 27.6 - - + -
289B ILE 4.1 1.0 + - - -
290B PHE* 1.3 71.8 - - - +
292B HIS* 1.3 64.9 + - - +
335B GLY* 3.9 5.9 - - - +
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Residues in contact with HIS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TYR* 3.9 11.8 - + + -
25B GLU* 2.7 47.7 + - + +
261B MET* 5.0 3.8 - - + -
262B ILE 2.9 29.6 + - - -
263B GLY* 3.6 10.7 - - - -
264B LYS* 3.2 25.6 + - - +
290B PHE* 3.7 4.6 + - - -
291B ALA* 1.3 73.9 - - - +
293B GLY* 1.3 78.6 + - - +
334B PHE* 3.6 39.3 - + + -
335B GLY* 3.9 7.6 - - - +
601B ADN 3.3 29.4 - + - -
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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