Contacts of the strand formed by residues 267 - 273 (chain A) in PDB entry 2AY5
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 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A PHE* 3.8 24.2 - - + -
105A THR 4.1 1.3 - - - -
107A GLY* 3.6 10.0 - - - +
108A GLY 4.3 0.2 + - - -
255A SER* 4.0 1.2 + - - -
256A CYS* 3.1 35.3 + - + +
257A SER* 4.1 5.8 + - - +
262A ILE* 3.7 18.1 + - - +
265A GLU* 4.1 2.4 + - - +
266A ARG* 1.3 75.7 + - - +
268A GLY* 1.3 61.1 + - - +
299A PRO 5.4 1.1 + - - -
302A GLY* 3.0 30.0 - - - -
303A ALA* 3.3 20.1 + - + +
306A VAL* 4.0 2.2 - - + -
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Residues in contact with GLY 268 (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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79A PHE* 3.8 12.5 - - - -
83A MET* 6.0 0.2 - - - -
104A ALA* 4.6 0.3 - - - +
105A THR* 3.0 33.0 + - - +
107A GLY 3.7 6.3 - - - +
254A ALA 3.2 17.0 - - - -
255A SER* 4.3 0.7 - - - -
256A CYS* 4.6 4.0 - - - -
267A THR* 1.3 78.2 - - - +
269A CYS* 1.3 63.6 + - - +
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Residues in contact with CYS 269 (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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79A PHE* 4.0 13.9 - - + -
83A MET* 3.9 31.2 - - - -
87A ILE* 4.9 0.7 - - - -
102A THR* 4.6 6.7 - - + -
103A LEU 3.1 15.7 - - - +
105A THR* 3.1 4.3 + - - -
111A ALA* 3.6 6.7 - - - +
252A ILE 3.5 1.9 - - - +
254A ALA* 2.9 43.7 + - - +
268A GLY* 1.3 76.3 - - - +
270A LEU* 1.3 59.4 + - - +
271A LEU* 4.3 22.8 - - - +
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Residues in contact with LEU 270 (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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102A THR* 3.5 2.1 - - - +
103A LEU* 2.8 43.5 + - + +
105A THR* 4.1 9.9 - - + +
111A ALA* 3.8 16.2 - - + +
114A GLN* 4.0 12.8 - - + +
115A ALA* 3.7 30.3 - - + +
118A LEU* 4.4 9.9 - - + -
251A LEU* 4.2 15.0 - - + -
252A ILE 3.3 15.3 - - - +
269A CYS* 1.3 72.7 - - - +
271A LEU* 1.3 84.7 + - - +
287A MET* 3.3 26.4 - - + +
290A LEU* 6.0 0.4 - - + -
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Residues in contact with LEU 271 (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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84A GLY* 4.3 23.3 - - - +
87A ILE* 3.9 29.4 - - + -
88A LEU* 4.6 10.5 - - + -
100A THR* 4.2 9.0 - - + -
101A ALA 3.5 2.2 - - - +
102A THR* 3.2 38.8 - - + +
250A VAL 3.6 1.6 - - - +
251A LEU* 3.4 4.9 - - - -
252A ILE* 2.8 57.6 + - + +
269A CYS* 4.3 11.2 - - - +
270A LEU* 1.3 76.7 - - - +
272A ALA* 1.3 61.0 + - - +
273A LEU* 4.0 8.7 - - + +
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Residues in contact with ALA 272 (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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99A THR 3.5 1.4 - - - +
100A THR* 3.5 3.1 - - - -
101A ALA* 2.8 49.2 + - + +
118A LEU* 4.7 3.6 - - + -
250A VAL 3.7 3.8 - - - -
251A LEU* 3.9 15.9 - - + -
270A LEU 4.1 0.4 - - - -
271A LEU* 1.3 72.3 - - - +
273A LEU* 1.3 64.8 + - - +
274A CYS* 3.6 3.0 + - - -
283A ALA* 4.5 5.8 - - + -
287A MET* 3.9 18.2 - - + -
6B LEU* 4.5 10.5 - - + -
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Residues in contact with LEU 273 (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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88A LEU* 4.3 19.7 - - + -
99A THR 3.8 4.5 - - - -
100A THR* 4.1 20.9 - - + +
244A ALA* 3.4 42.8 - - + +
247A ILE 5.5 0.7 - - - +
248A PRO 3.7 5.6 - - - +
249A GLU* 3.0 26.7 - - - +
250A VAL* 2.8 36.6 + - + +
252A ILE* 4.4 7.9 - - + -
271A LEU* 4.2 15.9 - - + +
272A ALA* 1.3 74.4 - - - +
274A CYS* 1.3 61.8 + - - +
6B LEU* 4.4 3.3 - - - +
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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