Contacts of the strand formed by residues 222 - 226 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B VAL* 3.8 26.0 - - + -
109B LEU* 4.0 24.0 - - + -
197B LEU 3.6 2.0 + - - +
198B PHE* 3.5 7.8 - - + -
199B VAL 3.0 23.2 + - - -
220B ALA* 3.2 2.2 - - - +
221B HIS* 1.3 92.4 - - + +
223B VAL* 1.3 69.5 + - - +
239B ILE* 3.8 27.4 - - + -
240B LEU 3.8 6.1 - - - +
241B ALA* 4.6 0.4 - - - +
248B LEU* 4.5 8.3 - - + -
252B LEU* 4.0 21.5 - - + -
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 3.1 15.7 - - + +
201B MET* 3.8 31.2 - - + -
216B PRO* 4.2 6.3 - - + +
217B VAL* 3.9 30.1 - - + +
220B ALA* 3.9 18.8 - - + +
222B VAL* 1.3 78.9 - - - +
224B THR* 1.3 75.7 + - - +
239B ILE* 3.5 4.5 - - - +
240B LEU* 2.7 53.9 + - + +
241B ALA* 5.6 1.1 - - - -
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Residues in contact with THR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLY* 6.5 0.2 - - - -
101B ALA* 4.0 19.5 - - + +
102B ASN* 2.7 25.9 + - - +
105B VAL* 3.5 32.3 - - + -
198B PHE* 3.2 14.0 - - + -
199B VAL 2.9 4.6 + - - -
200B ASP* 3.5 9.4 - - - -
201B MET* 2.8 28.8 + - - +
223B VAL* 1.3 78.6 - - - +
225B THR* 1.3 65.5 + - - +
238B LEU 3.3 8.5 - - - +
239B ILE* 4.3 4.7 - - + -
240B LEU* 6.0 0.4 - - - -
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Residues in contact with THR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 5.3 0.7 - - + -
98B GLY* 5.3 2.5 - - - -
101B ALA* 4.9 1.2 - - - +
200B ASP* 4.5 1.1 + - - -
201B MET* 3.9 23.3 - - + -
202B ALA* 3.4 14.1 - - - +
205B ALA* 3.0 23.2 - - + +
224B THR* 1.3 79.0 - - - +
226B THR* 1.3 76.9 + - - +
231B LEU* 5.0 2.9 - - + -
237B GLY* 3.5 2.4 - - - -
238B LEU* 2.9 57.3 + - + +
240B LEU* 4.6 4.3 - - + -
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Residues in contact with THR 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLY* 3.5 29.8 - - - +
202B ALA* 3.6 15.4 + - + +
205B ALA* 4.4 1.9 - - - +
225B THR* 1.3 93.9 + - - +
227B THR* 1.3 62.1 + - - +
228B HIS* 3.2 19.6 + - + -
229B LYS* 3.1 44.8 + - - +
231B LEU* 4.0 8.3 - - - +
236B GLY 3.1 6.1 - - - -
2291B PLP 3.5 8.3 - - - +
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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