Contacts of the strand formed by residues 243 - 249 (chain P) in PDB entry 2D2C
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 ASP 243 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32P ALA 3.6 21.1 + - - +
33P GLU* 4.5 2.1 - - - +
34P VAL* 3.5 30.3 + - + +
35P GLU* 3.6 20.6 - - - +
150P HIS* 3.9 0.7 - - - -
151P LEU* 3.2 27.7 + - - +
242P GLN* 1.3 75.9 - - - +
244P ASP* 1.3 77.9 + - - +
2S MET* 3.5 24.4 - - - +
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Residues in contact with ASP 244 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O LEU* 2.9 36.4 - - - +
74O GLU* 4.3 14.5 - - + +
14P ARG* 4.5 1.8 + - - -
149P ILE 3.3 5.6 - - - -
150P HIS* 3.6 32.5 - - + +
242P GLN* 3.9 16.5 - - - +
243P ASP* 1.3 94.1 + - - +
245P THR* 1.3 67.2 + - - +
2S MET* 4.6 10.4 - - - +
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Residues in contact with THR 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309O BNT 5.3 0.9 - - - +
34P VAL* 3.8 27.3 + - + +
35P GLU* 4.6 11.3 + - - +
36P VAL* 5.4 6.9 + - + +
148P ALA* 3.5 5.5 - - - +
149P ILE* 2.6 58.3 + - + +
150P HIS* 4.6 1.2 + - - -
244P ASP* 1.3 78.8 - - - +
246P GLU* 1.3 96.8 + - - +
2S MET* 6.1 2.0 - - - -
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Residues in contact with GLU 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58O ASP* 5.4 1.4 - - - +
1309O BNT 3.8 16.8 - - + -
36P VAL* 5.5 1.9 - - - +
37P PRO 5.1 1.6 - - - +
38P GLN* 4.8 2.6 - - - +
146P LYS* 3.6 34.3 - - + +
147P TYR 3.0 18.8 - - - +
149P ILE* 4.0 5.6 - - - -
245P THR* 1.3 108.5 + - - +
247P ILE* 1.3 58.0 + - - +
248P VAL* 5.6 0.3 - - - +
1R MET* 5.3 7.8 + - - +
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Residues in contact with ILE 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P VAL* 3.9 15.5 - - + -
37P PRO* 3.0 28.7 - - + +
38P GLN 3.1 6.7 - - - +
40P VAL* 3.0 46.9 - - + -
46P PHE* 4.3 6.1 - - + -
79P PRO* 4.5 18.6 - - + -
82P PHE* 4.7 7.9 - - + -
145P GLY 3.8 1.7 - - - +
146P LYS* 3.5 1.3 - - - -
147P TYR* 3.2 26.4 + - + +
149P ILE* 3.8 18.7 - - + +
246P GLU* 1.3 73.3 - - - +
248P VAL* 1.3 68.0 + - - +
249P LEU* 4.6 1.5 - - + +
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Residues in contact with VAL 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57O LEU 4.7 0.2 - - - +
58O ASP* 4.8 2.2 - - - +
59O PRO* 3.3 33.2 - - + -
38P GLN* 3.1 26.8 + - - +
39P SER* 3.2 4.6 - - - -
40P VAL* 2.9 29.8 + - - +
145P GLY* 3.8 5.6 - - - +
146P LYS* 3.3 33.2 - - + -
247P ILE* 1.3 80.3 - - - +
249P LEU* 1.3 77.4 - - - +
250P GLN* 4.0 13.2 - - + +
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Residues in contact with LEU 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P VAL* 3.3 10.1 - - - +
42P PRO* 5.5 6.1 - - + -
82P PHE* 3.5 37.5 - - + -
133P SER* 4.6 6.7 - - - +
134P PRO* 5.0 6.3 - - + +
136P PRO* 5.3 6.7 - - + -
142P ILE* 5.0 9.4 - - + -
143P HIS 4.1 12.8 - - - +
144P PHE* 3.4 42.7 - - + +
145P GLY 2.8 29.3 + - - +
147P TYR* 4.0 11.2 - - + -
247P ILE* 4.6 3.4 - - + +
248P VAL* 1.3 89.2 - - - +
250P GLN* 1.3 63.3 + - - +
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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