Contacts of the strand formed by residues 254 - 260 (chain A) in PDB entry 5D7I
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 254 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU* 6.0 0.9 - - + -
214A TRP* 4.0 15.0 - - + -
215A MET 3.3 14.8 - - - +
216A LYS* 4.3 18.6 - - + -
222A VAL* 4.8 9.0 - - + -
244A ILE* 3.4 27.1 - - + -
245A GLU 4.8 2.2 + - - -
246A LEU* 3.7 56.8 + - + -
253A LEU* 1.3 82.4 - - - +
255A SER* 1.3 61.4 + - - +
268A GLN* 3.2 8.1 - - - +
269A VAL* 2.9 40.6 + - + +
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Residues in contact with SER 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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214A TRP* 3.4 8.2 - - - -
215A MET* 2.9 38.9 + - - +
217A ASN* 5.8 0.5 + - - -
218A GLY 5.3 2.9 + - - -
254A TYR* 1.3 78.1 - - - +
256A CYS* 1.3 60.9 + - - +
257A HIS* 3.1 19.9 + - - -
266A VAL* 4.1 13.7 - - - -
267A LEU 3.2 12.3 - - - -
268A GLN* 3.8 20.4 + - - -
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Residues in contact with CYS 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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186A VAL* 4.0 13.0 - - + -
200A CYS* 2.0 55.0 - - + -
212A MET* 4.6 2.5 - - - -
213A THR 3.5 12.1 - - - -
214A TRP* 3.6 11.1 - - + -
242A ALA* 6.0 0.4 - - - -
255A SER* 1.3 72.9 - - - +
257A HIS* 1.3 64.3 + - - +
258A VAL* 3.8 14.6 - - - -
265A MET 3.8 0.5 - - - +
266A VAL* 3.4 5.0 - - - -
267A LEU* 2.8 40.9 + - + +
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Residues in contact with HIS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR* 3.7 3.2 - - + +
212A MET* 3.3 4.7 - - - -
213A THR* 2.8 49.0 + - + +
215A MET* 4.0 35.4 - - + +
218A GLY 5.8 0.8 + - - -
255A SER* 3.1 32.5 + - - -
256A CYS* 1.3 76.9 - - - +
258A VAL* 1.3 64.3 + - - +
259A GLU 4.3 0.2 - - - -
264A HIS* 3.1 28.1 + - + +
265A MET 3.4 3.1 - - - -
266A VAL* 3.8 21.7 - - + +
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Residues in contact with VAL 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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182A PRO* 4.4 7.6 - - + -
184A VAL* 4.0 29.2 - - + -
210A ILE* 3.7 31.0 - - + -
211A TYR 3.2 5.6 - - - +
212A MET* 4.1 13.2 - - + -
256A CYS* 3.8 19.7 - - - -
257A HIS* 1.3 80.3 - - - +
259A GLU* 1.3 65.4 + - - +
260A HIS 4.8 0.2 - - - +
263A VAL 3.8 0.7 - - - +
264A HIS* 3.4 5.9 + - - -
265A MET* 2.7 48.0 + - + +
267A LEU* 4.7 4.0 - - + -
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Residues in contact with GLU 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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210A ILE* 3.5 3.1 - - - +
211A TYR* 2.8 54.1 + - + +
258A VAL* 1.3 75.9 - - - +
260A HIS* 1.3 70.7 + - - +
261A SER 5.0 0.7 - - - +
262A GLY* 4.4 15.5 + - - +
263A VAL 3.4 12.3 - - - +
264A HIS* 3.9 19.9 + - - +
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Residues in contact with HIS 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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179A THR* 4.1 4.3 - - + +
180A GLU 3.5 13.7 - - - -
181A PRO* 4.3 3.0 - - - +
182A PRO* 3.6 32.8 - - + +
205A PHE* 3.9 9.5 - + + +
206A TYR 3.3 23.9 - - - -
207A PRO* 2.8 32.2 + - + +
209A GLU 3.1 25.8 + - - -
210A ILE* 4.1 13.2 - - + -
258A VAL* 4.2 1.3 - - + +
259A GLU* 1.3 75.8 - - - +
261A SER* 1.3 79.3 + - - +
262A GLY 3.3 1.8 - - - -
263A VAL* 3.0 26.3 + - - +
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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