Contacts of the strand formed by residues 96 - 103 (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 VAL 96 (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* 3.9 24.9 - - + +
89X GLY* 4.0 12.3 - - - -
94X GLY 3.8 11.0 - - - +
95X ASN* 1.3 70.5 - - - +
97X GLN* 1.3 68.6 + - - +
98X PHE* 3.4 5.9 + - + -
305X GLN* 3.3 20.2 - - - +
307X PHE* 3.6 26.0 - - + -
327X TYR* 3.3 5.4 - - - -
328X GLY 2.8 34.7 + - - +
330X VAL* 3.9 28.3 - - + +
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Residues in contact with GLN 97 (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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90X ALA* 4.5 14.7 - - + +
95X ASN 3.6 3.2 + - - -
96X VAL* 1.3 75.6 - - - +
98X PHE* 1.3 60.8 + - - +
204X GLU 4.9 2.8 + - - -
305X GLN 4.2 2.9 + - - +
306X HIS* 3.2 47.8 + - + +
307X PHE* 3.0 26.5 + - - -
325X ASN* 2.9 40.9 + - + +
327X TYR* 3.6 22.4 - - + -
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Residues in contact with PHE 98 (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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96X VAL* 3.4 19.7 + - + -
97X GLN* 1.3 74.9 - - - +
99X THR* 1.3 65.6 + - - +
273X ALA* 4.1 12.6 - - + -
274X GLU 4.2 7.4 - - - -
275X VAL* 4.6 2.2 - - + -
276X PRO* 3.9 16.4 - - + -
293X MET* 4.4 8.1 - - + -
307X PHE* 3.5 29.4 - + + -
309X ILE* 3.3 38.1 - - + -
324X TYR 4.3 1.0 - - - +
325X ASN* 3.9 0.5 - - - -
326X HIS* 2.8 42.5 + - + +
328X GLY* 3.7 23.6 - - - -
330X VAL* 3.4 33.0 - - + -
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Residues in contact with THR 99 (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* 1.3 75.5 - - - +
100X GLY* 1.3 61.2 + - - +
207X SER* 6.0 4.0 - - - +
302X ILE* 4.3 0.9 - - - +
306X HIS* 2.7 32.2 + - + +
307X PHE 3.0 4.9 + - - +
308X ASP* 3.0 17.8 + - - +
309X ILE* 2.9 28.4 + - - +
321X ALA 4.3 1.8 - - - -
324X TYR* 4.5 7.2 - - - +
325X ASN* 3.2 34.3 - - - +
326X HIS* 6.1 0.4 - - - -
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Residues in contact with GLY 100 (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* 1.3 77.6 - - - +
101X TYR* 1.3 59.2 + - - +
209X GLN* 3.7 20.4 - - - +
308X ASP* 3.2 8.6 - - - +
309X ILE* 3.4 11.2 - - - -
311X GLN* 4.8 2.5 - - - -
321X ALA* 3.3 32.0 + - - +
322X GLY 4.8 0.2 - - - +
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Residues in contact with TYR 101 (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* 1.3 75.0 - - - +
102X TYR* 1.3 70.1 + - - +
209X GLN* 5.1 3.8 - - + -
252X LEU* 3.6 11.2 - - + +
258X VAL 4.5 1.0 - - - -
259X ALA* 4.0 8.5 + - + +
297X ASP* 2.9 38.9 + - - +
308X ASP* 3.2 49.1 - - + +
309X ILE 3.0 14.1 + - - +
310X TYR* 3.5 34.4 - + + +
311X GLN* 2.8 27.6 + - - +
321X ALA* 4.0 4.0 - - - +
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Residues in contact with TYR 102 (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* 1.3 83.8 - - - +
103X THR* 1.3 68.0 + - - +
104X PRO* 3.3 33.4 - - + +
209X GLN* 3.3 28.7 - - - -
212X ARG* 3.1 37.9 + - - -
310X TYR* 4.0 7.6 - - - -
311X GLN* 4.2 0.7 - - + -
312X GLY 3.3 13.2 - - - +
314X GLY 3.4 24.0 - - - -
315X PRO* 5.3 0.9 - - + -
317X ALA* 3.8 15.3 - - + +
318X GLY* 3.5 29.5 - - - -
321X ALA* 4.1 6.7 - - + -
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Residues in contact with THR 103 (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* 1.3 73.5 - - - +
104X PRO* 1.3 68.4 - - + +
166X TYR* 3.5 38.8 - - + -
244X VAL* 3.3 16.8 - - + +
310X TYR* 2.7 31.6 + - - -
312X GLY 2.9 8.8 + - - -
313X ILE* 3.4 17.0 - - + +
314X GLY 3.0 25.1 + - - -
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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