Contacts of the strand formed by residues 241 - 246 (chain B) in PDB entry 3KG2
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 GLU 241 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B TYR* 5.2 3.5 - - - -
218B TYR 3.1 6.4 + - - +
219B HIS* 3.2 37.6 + - + +
220B TYR* 2.9 25.5 + - - +
239B GLY 3.5 6.5 + - - +
240B ALA* 1.3 71.7 - - - +
242B VAL* 1.3 59.3 + - - +
243B SER* 4.3 0.7 - - - +
362B GLU* 5.6 3.4 - - - +
363B LEU 5.1 5.4 - - - +
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B TYR* 3.4 25.6 - - + +
222B ILE* 4.2 13.7 - - + -
227B PHE* 3.7 22.5 - - + -
232B LEU* 5.2 1.3 - - + -
235B ILE* 3.8 34.8 - - + +
240B ALA* 3.5 11.8 + - + +
241B GLU* 1.3 78.5 - - - +
243B SER* 1.3 65.6 + - - +
362B GLU* 3.6 1.7 - - - +
363B LEU* 2.8 49.7 + - + +
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.4 9.0 - - - -
128B TYR* 2.7 32.8 + - - -
219B HIS* 3.3 20.5 + - - -
220B TYR 2.8 8.4 + - - +
221B ILE* 3.3 6.1 - - - -
222B ILE* 2.9 24.5 + - - +
227B PHE* 3.4 11.5 - - - -
241B GLU* 5.6 0.3 - - - +
242B VAL* 1.3 73.8 - - - +
244B GLY* 1.3 58.9 + - - +
361B MET 3.2 13.0 - - - -
362B GLU* 3.6 6.2 - - - +
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Residues in contact with GLY 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 4.8 1.3 - - - +
221B ILE* 4.9 0.9 - - - -
222B ILE 3.6 13.2 - - - -
227B PHE* 3.3 18.6 - - - -
243B SER* 1.3 77.2 - - - +
245B PHE* 1.3 76.8 + - - -
360B ILE* 3.9 3.5 - - - +
361B MET 3.0 28.7 + - - +
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Residues in contact with PHE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 3.6 25.4 - - + -
120B ALA* 3.4 29.4 - - + -
121B LEU* 3.6 26.7 - - + -
124B LEU* 3.6 23.6 - - + -
221B ILE* 4.2 13.5 - - + -
222B ILE 3.5 17.5 + - - -
223B ALA* 4.4 7.0 - - - -
224B ASN 3.1 21.8 + - - +
225B LEU* 3.3 4.8 - - - -
227B PHE* 3.0 27.7 + - - +
244B GLY* 1.3 79.3 - - - -
246B GLN* 1.3 61.1 + - - +
358B ILE* 3.9 17.5 - - + -
359B ASN 3.6 2.7 - - - -
360B ILE* 4.3 15.5 - - + -
361B MET* 4.4 0.2 - - - -
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Residues in contact with GLN 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B LEU 3.7 3.8 + - - -
226B GLY 3.8 0.3 - - - -
227B PHE* 3.1 26.4 + - + +
228B THR* 3.1 33.2 + - + +
229B ASP* 4.1 9.1 + - - -
245B PHE* 1.3 74.0 - - - +
247B ILE* 1.3 60.2 + - - +
248B VAL* 3.3 41.6 + - - +
249B ASP* 5.1 2.8 + - - +
250B TYR* 3.5 11.1 + - + -
280B TYR* 5.9 0.2 - - - +
357B THR 5.0 0.2 - - - +
358B ILE* 4.1 4.1 - - - +
359B ASN* 3.0 37.8 + - + +
361B MET* 3.6 27.6 - - + -
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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