Contacts of the strand formed by residues 261 - 267 (chain A) in PDB entry 5E6J
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 CYS 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ALA* 4.4 7.6 - - - -
123A GLN* 3.5 29.4 - - - +
124A LEU* 5.3 0.7 - - - -
259A PHE* 3.3 11.0 - - - -
260A LEU* 1.3 89.5 - - - +
262A ALA* 1.3 61.0 + - - +
276A HIS* 3.8 17.9 - - - +
277A ILE 3.1 15.9 - - - +
278A THR* 4.1 0.2 - - - -
305A PHE* 2.7 54.9 + - - -
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Residues in contact with ALA 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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254A LEU* 3.8 25.8 - - + -
259A PHE* 4.1 4.0 - - + -
261A CYS* 1.3 78.0 - - - +
263A ASN* 1.3 66.7 + - - +
276A HIS* 3.3 7.8 + - - -
277A ILE* 2.7 35.4 + - + -
301A VAL* 5.5 2.5 - - + -
303A ASP 3.1 15.0 - - - +
304A VAL* 3.8 15.9 - - + +
305A PHE* 4.5 2.9 - - - +
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Residues in contact with ASN 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 3.4 23.1 + - - -
120A ALA* 4.8 3.0 - - - +
166A VAL* 3.7 19.0 - - - +
262A ALA* 1.3 73.8 - - - +
264A GLU* 1.3 59.2 + - - +
274A TYR* 4.3 13.7 - - + -
275A THR 3.6 2.2 - - - +
276A HIS* 3.0 27.3 + - - -
277A ILE* 5.6 0.7 - - - -
301A VAL* 3.6 5.9 - - - +
302A THR* 2.9 26.9 + - + +
303A ASP* 2.6 30.0 + - + +
305A PHE* 3.5 30.5 - - - -
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Residues in contact with GLU 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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262A ALA 4.4 0.2 + - - -
263A ASN* 1.3 73.6 - - - +
265A TYR* 1.3 61.2 + - - +
266A THR* 3.1 29.1 - - + +
274A TYR* 3.2 9.2 - - - -
275A THR* 2.6 59.0 + - + +
277A ILE* 4.9 5.8 - - + +
285A ARG* 2.9 14.2 + - - -
297A TYR* 2.3 43.6 + - + -
300A PRO* 3.5 20.3 - - - +
301A VAL* 4.0 12.8 - - + +
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Residues in contact with TYR 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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249A PRO* 3.8 26.2 - - + +
263A ASN 4.2 0.8 + - - -
264A GLU* 1.3 73.2 - - - +
266A THR* 1.3 60.1 + - - +
267A GLY 3.9 8.1 + - - +
268A ASN 2.9 31.4 + - - -
269A TYR* 4.6 0.6 - - - -
271A CYS 3.9 0.2 - - - -
272A GLY* 3.5 14.2 + - - -
273A HIS 3.5 5.2 - - - -
274A TYR* 3.5 28.7 - + + -
300A PRO* 3.1 26.6 + - - +
302A THR* 4.0 19.2 - - + +
73B LEU* 4.0 18.8 - - + -
74B ARG* 3.0 30.4 + - - +
75B GLY* 3.4 27.6 - - - -
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Residues in contact with THR 266 (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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264A GLU* 3.1 31.2 - - - +
265A TYR* 1.3 72.1 - - - +
267A GLY* 1.3 58.7 + - - +
272A GLY* 3.1 3.4 - - - -
273A HIS* 2.8 58.4 + - - +
275A THR* 5.3 4.0 - - - +
285A ARG* 5.1 4.3 - - - +
300A PRO* 3.7 16.4 - - + -
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Residues in contact with GLY 267 (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 PRO* 6.0 1.4 - - - +
265A TYR* 3.9 8.2 + - - +
266A THR* 1.3 74.9 - - - +
268A ASN* 1.3 61.4 + - - +
271A CYS 3.9 7.4 - - - -
272A GLY* 4.2 0.7 - - - -
300A PRO* 5.7 0.2 - - - +
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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