Contacts of the strand formed by residues 232 - 237 (chain A) in PDB entry 4J1K
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 GLY 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ASP* 4.8 4.5 - - - -
67A LEU* 3.3 18.8 - - - -
68A ARG* 4.2 0.9 - - - -
75A TYR* 3.3 13.9 - - - -
216A CYS* 2.9 32.5 + - - +
230A SER 4.0 0.2 + - - -
231A VAL* 1.3 74.6 - - - +
233A GLY* 1.3 58.6 + - - -
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Residues in contact with GLY 233 (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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65A ASP* 3.1 27.7 + - - -
67A LEU* 3.2 20.9 + - - -
214A GLN* 2.9 14.6 - - - -
216A CYS* 3.9 12.2 - - - -
232A GLY* 1.3 74.6 - - - -
234A SER* 1.3 64.5 + - - -
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Residues in contact with SER 234 (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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63A MET 4.2 0.7 - - - -
64A VAL* 3.7 7.8 - - - +
65A ASP* 2.8 25.2 + - - +
66A ASN* 3.4 6.1 - - - -
67A LEU* 3.7 8.4 - - - +
212A SER 3.7 0.3 - - - +
213A LEU* 3.4 4.7 - - - -
214A GLN* 2.8 42.9 + - - +
233A GLY* 1.3 73.0 - - - -
235A MET* 1.3 58.1 + - - +
236A ILE* 4.0 11.2 - - - +
244A LEU* 3.8 25.8 - - - +
403A TYR* 5.6 0.2 - - - -
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Residues in contact with MET 235 (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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63A MET* 3.8 4.9 - - - +
66A ASN* 2.8 28.1 + - - +
67A LEU* 3.9 12.0 - - + +
77A VAL* 3.9 35.2 - - + -
92A VAL* 4.1 8.3 - - + -
148A ILE* 4.9 4.9 - - + -
180A LEU* 4.5 11.0 - - + -
182A LEU* 4.2 24.2 - - - -
211A PHE* 4.8 8.1 - - + -
212A SER 3.4 5.4 - - - +
213A LEU* 3.5 24.2 - - + -
234A SER* 1.3 71.5 - - - +
236A ILE* 1.4 62.2 + - - +
237A ILE* 3.7 35.3 + - + +
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Residues in contact with ILE 236 (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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60A PHE* 3.6 33.0 - - + -
63A MET* 3.8 32.8 - - + +
64A VAL* 4.2 4.3 - - + +
211A PHE* 3.1 6.7 - - - +
212A SER* 2.9 48.4 + - - +
234A SER* 4.2 4.7 - - - -
235A MET* 1.4 74.1 - - - +
237A ILE* 1.3 59.7 + - - +
238A GLY 3.6 0.7 + - - -
239A GLY 3.3 25.6 - - - +
240A ILE* 4.1 1.3 - - - +
241A ASP* 4.2 9.2 - - + -
244A LEU* 3.8 22.4 - - + -
403A TYR* 3.8 10.1 - - + +
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Residues in contact with ILE 237 (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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60A PHE* 4.5 2.6 - - - -
63A MET* 3.5 22.9 - - - +
66A ASN* 4.8 1.6 - - - +
148A ILE* 4.2 15.3 - - + -
151A GLY* 4.4 8.1 - - - -
152A PRO* 3.6 36.0 - - + +
197A PHE* 6.3 0.4 - - + -
198A PHE* 4.0 9.9 - - + -
201A LEU* 3.6 31.0 - - + -
207A VAL* 3.9 6.9 - - + +
211A PHE* 4.1 8.5 - - + -
235A MET* 3.7 47.8 - - + +
236A ILE* 1.3 71.8 - - - +
238A GLY* 1.3 63.1 + - - +
239A GLY 3.5 0.6 + - - -
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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