Contacts of the strand formed by residues 214 - 217 (chain A) in PDB entry 1G24
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 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A TYR* 4.2 5.8 - - - -
80A THR* 4.9 1.5 - - - +
174A SER* 2.8 33.3 + - - -
175A THR 3.2 14.8 - - - +
202A TYR* 3.5 5.4 - - - -
203A ILE* 3.1 54.4 + - + +
204A ASP* 3.6 5.1 + - - +
210A ALA* 3.5 8.0 - - + -
211A GLY* 2.7 48.0 + - - +
212A GLN 3.0 2.4 - - - -
213A LEU* 1.3 76.4 - - - +
215A MET* 1.3 66.9 + - - +
216A LEU* 4.2 1.2 - - - +
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Residues in contact with MET 215 (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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58A TRP* 3.6 31.0 - - + -
62A GLN* 5.7 1.6 - - + -
66A TYR* 5.0 2.5 - - - +
120A THR* 4.7 4.7 - - - -
124A ILE* 3.9 16.8 - - + -
126A LEU* 4.0 23.3 - - + -
173A ILE 3.9 0.7 - - - +
175A THR* 2.8 48.7 + - - +
177A LEU* 3.9 11.4 - - + -
200A ALA* 4.3 21.5 - - + +
201A GLY 3.2 6.1 - - - +
202A TYR* 3.6 35.2 - - + +
213A LEU 3.3 4.4 + - - +
214A GLU* 1.3 75.4 - - - +
216A LEU* 1.3 63.1 + - - +
217A LEU* 4.6 0.7 - - - +
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Residues in contact with LEU 216 (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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76A ILE* 5.5 1.6 - - + -
79A TYR* 3.6 43.7 - - + +
111A LEU* 4.0 32.8 - - + -
115A PHE* 3.3 15.5 - - + -
118A MET* 6.0 0.9 - - + -
172A TYR* 3.9 10.3 - - + -
173A ILE 3.7 11.2 - - - +
174A SER* 3.7 14.4 - - - +
200A ALA* 3.4 3.8 - - - -
201A GLY* 2.7 38.2 + - - +
203A ILE* 4.1 23.8 - - + -
214A GLU* 4.0 3.0 - - - +
215A MET* 1.3 72.0 - - - +
217A LEU* 1.3 66.7 + - - +
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Residues in contact with LEU 217 (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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115A PHE* 3.7 3.6 - - - -
126A LEU* 3.8 21.8 - - + -
172A TYR* 3.6 10.0 - - - +
173A ILE* 2.9 44.4 + - + +
175A THR* 4.0 21.5 - - + -
192A PHE* 4.8 2.5 - - + -
194A VAL* 4.6 10.8 - - + -
199A LYS 3.6 7.6 - - - +
200A ALA* 3.5 30.1 - - + -
215A MET 4.6 0.4 - - - +
216A LEU* 1.3 75.7 - - - +
218A PRO* 1.3 73.5 - - + +
221A SER* 5.2 1.6 - - - +
243A MET* 3.8 33.7 - - + -
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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