Contacts of the strand formed by residues 307 - 313 (chain X) in PDB entry 2AE0
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 PHE 307 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87X MET* 3.5 38.4 - - + -
96X VAL* 3.6 23.3 - - + -
97X GLN 3.0 4.9 + - - -
98X PHE* 3.5 28.7 - + + -
99X THR 3.0 24.6 + - - +
258X VAL* 3.7 17.9 - - + -
259X ALA 3.6 0.9 - - - -
260X SER* 3.6 31.0 - - - -
265X ILE* 3.7 18.6 - - + -
271X LEU* 3.7 24.5 - - + -
293X MET* 5.9 0.2 - - + -
302X ILE* 4.6 0.4 - - - -
305X GLN 4.2 2.9 - - - -
306X HIS* 1.3 85.5 - - - +
308X ASP* 1.3 59.8 + - - +
309X ILE 3.9 0.4 - - - -
330X VAL* 4.0 10.8 - - + -
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Residues in contact with ASP 308 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99X THR* 3.0 20.4 + - - -
100X GLY 3.2 24.8 - - - +
101X TYR* 3.2 30.6 - - + +
258X VAL* 3.2 2.3 - - - -
259X ALA* 2.8 51.7 + - + +
302X ILE* 3.6 23.2 - - + +
307X PHE* 1.3 73.0 - - - +
309X ILE* 1.3 60.5 + - - +
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Residues in contact with ILE 309 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X PHE* 3.3 43.5 - - + -
99X THR 2.9 13.4 + - - +
100X GLY* 3.4 2.9 - - - -
101X TYR* 3.0 23.0 + - - -
255X ARG* 4.3 11.0 - - + -
257X SER 3.9 5.6 - - - +
258X VAL* 4.0 7.0 - - + -
275X VAL* 3.6 32.8 - - + -
291X ARG* 6.5 0.2 - - - -
293X MET* 4.0 18.2 - - - -
308X ASP* 1.3 71.8 - - - +
310X TYR* 1.3 73.9 + - - +
311X GLN* 3.2 20.9 + - - +
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Residues in contact with TYR 310 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X TYR* 3.5 42.0 - + + +
102X TYR* 4.0 1.6 - - - -
103X THR* 2.7 35.0 + - - -
244X VAL* 3.7 22.9 - - + +
252X LEU* 3.5 38.6 - - + -
253X VAL 4.1 6.1 - - - -
254X GLY* 4.1 2.0 - - - -
255X ARG* 2.7 34.1 + - - -
257X SER* 3.0 26.6 + - - +
308X ASP 3.5 3.2 + - - -
309X ILE* 1.3 70.2 - - - +
311X GLN* 1.3 53.5 + - - +
312X GLY* 3.4 33.3 + - - -
313X ILE* 4.1 3.5 + - - +
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Residues in contact with GLN 311 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X GLY* 4.8 2.3 - - - -
101X TYR 2.8 17.3 + - - +
102X TYR* 4.2 0.4 - - + -
254X GLY* 3.8 10.3 - - - -
255X ARG* 3.2 23.7 + - - +
275X VAL* 5.4 5.5 - - - +
309X ILE* 3.9 27.1 - - - +
310X TYR* 1.3 73.2 - - - +
312X GLY* 1.3 56.5 + - - +
317X ALA* 3.4 28.7 - - + +
320X ARG* 2.9 72.3 + - - +
321X ALA* 3.9 15.2 - - - +
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Residues in contact with GLY 312 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X TYR* 3.3 6.6 - - - +
103X THR 2.9 23.6 + - - -
254X GLY* 4.0 8.3 - - - -
310X TYR* 3.4 28.2 + - - -
311X GLN* 1.3 79.2 - - - +
313X ILE* 1.3 58.8 + - - -
317X ALA* 3.5 5.2 - - - -
320X ARG* 5.1 0.2 - - - -
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Residues in contact with ILE 313 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X THR* 3.4 33.4 - - + +
105X VAL* 3.6 21.3 - - + -
166X TYR* 4.9 4.7 - - + -
175X LEU* 4.2 18.4 - - + -
241X PHE* 6.0 2.0 - - + -
244X VAL* 5.1 5.8 - - + -
310X TYR* 4.4 3.8 - - - +
312X GLY* 1.3 73.5 - - - -
314X GLY* 1.3 65.7 + - - +
316X GLU* 5.4 0.3 + - - +
317X ALA* 3.8 6.2 + - - +
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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