Contacts of the strand formed by residues 39 - 47 (chain A) in PDB entry 2P02
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLY* 1.3 81.2 - - - +
40A PHE* 1.3 64.7 + - - +
209A GLN* 3.4 25.0 + - - +
210A TYR 3.1 9.0 - - - +
211A MET* 3.7 26.9 - - + -
220A ILE* 3.8 17.9 - - + -
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Residues in contact with PHE 40 (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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39A THR* 1.3 79.0 - - - +
41A LEU* 1.3 76.6 + - - +
42A PHE* 4.3 9.2 - + + -
209A GLN* 3.4 3.9 - - - +
210A TYR* 2.8 63.5 + + + -
212A GLN* 3.7 42.2 - - + +
217A VAL* 3.8 24.7 - - + -
296A TRP* 3.9 19.1 - + - -
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Residues in contact with LEU 41 (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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40A PHE* 1.3 86.2 - - - +
42A PHE* 1.3 65.9 + - - +
43A THR* 5.5 0.4 - - - +
207A THR* 4.0 10.5 - - + -
208A VAL 3.4 3.6 - - - +
209A GLN* 3.8 29.2 - - + +
223A HIS* 3.6 50.5 - - + +
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Residues in contact with PHE 42 (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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40A PHE* 4.3 7.2 - + + -
41A LEU* 1.3 78.2 - - - +
43A THR* 1.3 79.3 + - - +
175A THR* 3.4 7.5 - - + +
207A THR* 3.3 0.9 - - - -
208A VAL 2.9 31.3 + - - -
210A TYR* 4.0 8.1 - - + -
294A GLY 3.7 13.9 - - - -
295A GLY* 3.6 24.2 - - - -
296A TRP* 3.2 70.9 - + + -
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Residues in contact with THR 43 (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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41A LEU* 5.5 0.3 - - - +
42A PHE* 1.3 82.6 - - - +
44A SER* 1.3 67.5 + - - +
205A GLN* 3.4 38.4 - - + +
206A VAL 3.3 4.5 - - - +
207A THR* 2.8 33.6 + - - +
294A GLY 3.5 8.1 - - - +
295A GLY* 5.3 0.2 - - - -
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Residues in contact with SER 44 (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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43A THR* 1.3 72.3 - - - +
45A GLU* 1.3 60.6 - - - +
175A THR* 2.7 32.0 + - - -
176A ILE* 3.8 16.2 + - - +
179A ALA* 4.1 3.1 - - - +
205A GLN* 3.4 5.4 - - - +
206A VAL* 2.9 32.4 + - - +
294A GLY* 2.6 35.8 + - - -
296A TRP* 4.0 3.3 - - - -
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Residues in contact with GLU 45 (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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44A SER* 1.3 75.6 - - - +
46A SER* 1.3 64.2 + - - +
47A VAL* 5.2 2.9 - - - -
176A ILE* 3.8 16.8 - - - +
179A ALA* 3.9 4.0 - - - -
203A LYS* 3.9 26.2 + - - +
204A THR 3.2 14.5 - - - +
205A GLN* 4.1 20.1 - - + +
287A LYS* 4.8 8.2 + - - +
289A ILE* 6.5 0.9 - - + -
290A VAL* 3.5 27.2 - - + +
294A GLY* 5.2 2.8 - - - -
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Residues in contact with SER 46 (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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45A GLU* 1.3 76.5 - - - +
47A VAL* 1.3 80.2 + - - +
176A ILE 4.9 0.2 - - - -
179A ALA* 3.5 18.1 - - - +
180A HIS* 2.7 36.9 + - - -
183A ASN* 3.2 17.5 + - - +
203A LYS* 3.5 0.9 - - - +
204A THR 2.9 28.9 + - - +
290A VAL* 3.9 8.9 - - - +
399A TYR* 5.0 1.4 - - - -
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Residues in contact with VAL 47 (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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45A GLU* 5.2 2.0 - - - -
46A SER* 1.3 88.6 + - - +
48A GLY* 1.3 62.9 + - - +
51A HIS* 3.6 39.0 - - + +
54A LYS* 3.6 31.9 - - + +
183A ASN* 3.5 11.4 + - - +
202A SER 3.4 9.6 - - - +
203A LYS* 3.9 14.8 - - + -
287A LYS* 3.8 24.5 - - + -
290A VAL* 4.1 7.7 - - + +
398A ALA* 5.6 0.5 - - - +
399A TYR* 4.8 10.7 + - - -
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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