Contacts of the strand formed by residues 251 - 257 (chain B) in PDB entry 4Y2H
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 GLN 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192B PHE* 3.3 4.2 - - - -
193B ILE* 2.8 44.2 + - + +
249B ARG* 2.8 37.9 + - - +
250B PRO* 1.3 76.4 + - - +
252B ARG* 1.3 66.1 + - - +
253B PHE 3.5 0.5 + - - -
275B PHE* 4.1 24.7 - - + -
276B ARG 3.3 25.6 + - - +
277B CYS* 3.5 20.1 - - + +
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Residues in contact with ARG 252 (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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190B GLU* 2.6 52.2 + - - -
191B LEU 3.3 16.6 - - - +
192B PHE* 3.6 22.6 - - + -
250B PRO 4.2 0.6 + - - -
251B GLN* 1.3 79.4 + - - +
253B PHE* 1.3 59.9 + - - +
254B ALA 3.6 12.3 - - - +
255B GLN* 3.9 23.0 - - - +
274B ARG 4.7 4.9 - - - +
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Residues in contact with PHE 253 (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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191B LEU* 2.9 42.6 + - + -
192B PHE 3.4 39.7 - - - -
193B ILE* 3.8 20.6 - - + -
251B GLN 3.5 1.3 + - - +
252B ARG* 1.3 74.4 - - - +
254B ALA* 1.3 63.5 + - + +
271B VAL 4.7 0.2 - - - -
272B GLY* 3.3 36.2 - - - +
273B GLY* 3.6 11.8 + - - +
274B ARG 4.5 10.5 - - - +
275B PHE* 5.0 2.5 - - + -
290B ILE* 4.1 7.9 - - + -
341B ILE* 3.5 37.7 - - + -
343B LEU* 4.2 12.8 - - + -
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Residues in contact with ALA 254 (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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190B GLU* 3.4 3.2 - - - -
191B LEU* 2.9 35.9 + - + -
252B ARG* 3.6 10.4 - - - +
253B PHE* 1.3 90.8 - - + +
255B GLN* 1.3 62.9 + - - +
256B LEU* 5.4 3.1 - - + -
271B VAL* 4.0 27.4 - - + -
272B GLY 4.4 7.2 - - - +
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Residues in contact with GLN 255 (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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188B SER* 3.6 17.8 + - - -
189B ALA 3.2 24.8 + - - -
190B GLU* 3.9 9.4 - - + +
252B ARG* 3.9 32.3 - - - +
254B ALA* 1.3 75.1 - - - +
256B LEU* 1.3 76.2 + - - +
257B GLU* 3.9 20.4 + - - +
260B ARG* 3.5 20.6 + - - -
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Residues in contact with LEU 256 (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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156B TRP* 5.3 0.7 - - + -
161B LEU* 3.9 27.8 - - + -
162B LEU* 4.2 7.4 - - + -
167B LEU* 4.2 22.0 - - + -
188B SER* 3.2 6.6 - - - -
189B ALA* 2.7 44.0 + - + +
191B LEU* 5.2 1.1 - - + -
254B ALA* 5.4 3.1 - - + -
255B GLN* 1.3 81.8 - - - +
257B GLU* 1.3 60.5 + - - +
258B LEU* 3.6 12.4 + - + +
260B ARG* 4.2 6.1 - - - +
263B LEU* 3.8 26.5 - - + -
266B GLU* 5.1 1.3 - - + +
267B LEU* 4.7 3.6 - - + -
271B VAL* 4.5 30.1 - - + -
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Residues in contact with GLU 257 (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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187B ALA* 4.3 10.2 - - - +
188B SER* 3.6 15.6 - - - -
255B GLN* 3.9 12.6 + - - +
256B LEU* 1.3 69.8 - - - +
258B LEU* 1.3 62.5 + - - +
259B SER* 3.8 20.8 + - - +
260B ARG* 3.0 51.1 + - + +
263B LEU* 3.6 7.0 - - - +
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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