Contacts of the strand formed by residues 222 - 226 (chain A) in PDB entry 1EQB
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A VAL* 3.8 26.9 - - + -
109A LEU* 4.0 24.0 - - + -
197A LEU 3.6 2.6 + - - +
198A PHE* 3.5 7.4 - - + -
199A VAL 3.0 23.6 + - - -
220A ALA* 3.2 2.6 - - - +
221A HIS* 1.3 91.7 - - + +
223A VAL* 1.3 70.1 + - - +
239A ILE* 3.8 26.5 - - + -
240A LEU 3.8 5.8 - - - +
241A ALA* 4.9 0.4 - - + +
248A LEU* 4.5 8.7 - - + -
252A LEU* 4.0 21.3 - - + -
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Residues in contact with VAL 223 (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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199A VAL* 3.1 15.3 - - + +
201A MET* 3.8 30.3 - - + -
216A PRO* 4.2 7.0 - - + +
217A VAL* 3.9 30.1 - - + +
220A ALA* 3.9 18.8 - - + +
222A VAL* 1.3 78.6 - - - +
224A THR* 1.3 77.2 + - - +
239A ILE* 3.5 4.7 - - - +
240A LEU* 2.7 51.1 + - + +
241A ALA* 5.6 0.7 - - - -
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Residues in contact with THR 224 (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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98A GLY 5.5 0.2 - - - -
101A ALA* 4.0 19.7 - - + +
102A ASN* 2.7 26.2 + - - +
105A VAL* 3.5 31.4 - - + -
198A PHE* 3.2 15.5 - - + -
199A VAL 2.9 4.2 + - - -
200A ASP* 3.5 9.4 - - - +
201A MET* 2.8 28.8 + - - +
223A VAL* 1.3 78.4 - - - +
225A THR* 1.3 64.4 + - - +
238A LEU 3.2 8.7 - - - +
239A ILE* 4.2 4.7 - - + -
240A LEU* 5.9 0.4 - - - -
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Residues in contact with THR 225 (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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86A PHE* 5.3 0.9 - - + -
98A GLY* 5.3 2.5 - - - -
101A ALA* 5.0 0.7 - - - +
200A ASP* 4.5 0.9 + - - -
201A MET* 3.9 23.3 - - + -
202A ALA* 3.4 14.4 - - - +
205A ALA* 3.0 28.4 - - + +
224A THR* 1.3 79.5 - - - +
226A THR* 1.3 72.4 + - - +
231A LEU* 5.0 2.9 - - + -
237A GLY* 3.4 1.7 - - - -
238A LEU* 2.8 57.7 + - + +
240A LEU* 4.7 4.0 - - + -
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Residues in contact with THR 226 (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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98A GLY* 3.5 18.2 - - - +
202A ALA* 3.7 15.3 + - + +
205A ALA* 4.4 1.9 - - - +
225A THR* 1.3 94.3 + - - +
227A THR* 1.3 62.3 + - - +
228A HIS* 3.3 20.9 + - + -
229A LYS* 3.1 45.4 + - - +
231A LEU* 4.0 7.1 - - - +
236A GLY 3.0 6.1 - - - -
1291A PLP 3.5 19.3 - - + +
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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