Contacts of the strand formed by residues 216 - 219 (chain A) in PDB entry 4J1O
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 PHE 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A VAL* 3.9 19.1 - - + -
191A LEU* 3.2 19.0 - - + +
193A VAL* 3.7 25.6 - - + -
207A LEU* 3.9 35.2 - - + -
208A SER* 4.3 2.5 - - - -
211A CYS* 3.8 17.9 - - + -
214A ILE* 2.9 26.0 + - + -
215A PRO* 1.3 77.0 - - - +
217A VAL* 1.3 76.2 + - - +
218A LEU* 4.1 11.0 - - + -
237A HIS* 3.3 61.7 - + + +
238A GLY 4.5 1.6 + - - -
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ARG* 4.1 2.9 - - - +
191A LEU 3.1 7.8 + - - +
192A ALA* 3.8 20.9 - - + -
193A VAL 2.9 26.0 + - - -
215A PRO 5.5 0.7 - - - +
216A PHE* 1.3 80.7 - - - +
218A LEU* 1.3 60.7 + - - +
219A GLU* 3.7 1.3 + - + +
238A GLY* 3.3 18.8 - - - +
240A TYR* 3.7 54.5 - - + +
318A GLU* 5.4 1.3 - - - +
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Residues in contact with LEU 218 (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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165A ILE* 5.2 0.2 - - + -
193A VAL* 3.6 19.3 - - + +
195A GLY 5.1 1.8 - - - +
199A LEU* 4.8 3.1 - - + -
204A ALA* 4.2 23.6 - - + +
207A LEU* 3.8 27.6 - - + -
208A SER* 5.0 4.7 - - - -
216A PHE* 4.1 11.5 - - + -
217A VAL* 1.3 70.3 - - - +
219A GLU* 1.3 61.1 + - - +
221A PRO* 3.6 36.5 - - + +
231A ILE* 5.3 1.8 - - + -
235A VAL* 4.7 15.7 - - + -
237A HIS* 5.0 3.1 - - + -
238A GLY 2.8 13.9 + - - +
239A ILE* 3.3 15.9 - - + +
240A TYR 2.9 21.6 + - - -
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Residues in contact with GLU 219 (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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135A TYR* 5.3 0.3 + - - -
160A ARG* 4.6 7.1 + - - -
162A GLN* 2.8 21.8 + - - +
192A ALA* 4.3 11.2 - - + +
193A VAL 2.8 15.9 + - - +
194A ASP* 3.0 10.9 - - - +
195A GLY 3.0 19.9 + - - -
217A VAL* 3.7 3.5 + - + +
218A LEU* 1.3 70.1 - - - +
220A GLN* 1.3 71.3 + - - +
221A PRO* 3.1 3.2 - - - +
240A TYR* 3.5 20.8 - - + +
241A LEU 5.0 0.4 - - - -
242A ASP* 2.9 19.2 - - + +
264A GLY* 4.5 11.0 - - - -
401A MG 2.1 33.4 - - - -
412A PBE 3.1 5.0 - - - +
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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