Contacts of the strand formed by residues 234 - 239 (chain I) in PDB entry 6A3V
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 234 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I GLN* 3.6 31.0 - - + +
95I LEU 3.3 15.7 - - - +
96I VAL* 4.0 13.5 - - + -
109I TRP* 4.2 2.7 - - - -
144I PHE* 4.1 7.9 - - + +
145I PHE* 3.8 2.9 - - - -
146I GLN* 3.0 48.5 + - + +
231I GLY 3.8 18.8 - - - +
232I ALA 3.7 3.7 + - - +
233I THR* 1.3 81.4 - - - +
235I LEU* 1.3 72.4 + - - +
236I GLY 4.4 0.4 - - - +
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Residues in contact with LEU 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I GLN* 3.6 0.2 - - - -
95I LEU* 2.8 40.0 + - + +
109I TRP* 3.4 31.5 - - + +
133I LEU* 3.7 32.3 - - + -
143I VAL* 3.7 19.7 - - + -
144I PHE 3.7 7.6 - - - +
145I PHE* 3.6 28.0 - - + -
165I LEU* 3.8 6.3 - - + -
212I LEU* 5.1 2.2 - - + +
214I VAL* 4.1 19.3 - - + -
234I VAL* 1.3 75.6 - - - +
236I GLY* 1.3 68.8 + - - +
237I LEU* 6.0 2.0 - - + -
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Residues in contact with GLY 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I ALA 3.4 9.0 - - - -
94I GLN* 4.2 3.6 - - - -
143I VAL* 3.5 9.0 - - - +
144I PHE* 3.2 53.9 + - - -
235I LEU* 1.3 80.1 - - - +
237I LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I PHE* 3.2 6.1 - - - +
93I ALA* 2.6 46.4 + - + +
124I LEU* 4.4 13.7 - - + -
133I LEU* 4.5 11.7 - - + -
135I VAL* 4.1 24.7 - - + -
141I TYR* 3.4 37.9 - - + -
142I TYR 3.4 4.9 - - - -
143I VAL* 3.9 14.6 - - + -
144I PHE* 3.9 3.9 - - - -
206I LEU* 4.3 3.1 - - + -
212I LEU* 4.2 20.0 - - + -
235I LEU* 6.0 2.2 - - + -
236I GLY* 1.3 73.9 - - - +
238I PHE* 1.3 82.6 + - - +
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Residues in contact with PHE 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238G PHE* 4.0 27.1 - + - -
91I MET 3.8 1.1 - - - +
92I PHE* 3.5 20.2 - - + +
141I TYR* 3.5 2.3 - - - -
142I TYR* 2.9 75.3 + + + -
144I PHE* 4.2 15.3 - + - -
237I LEU* 1.3 84.0 - - - +
239I ARG* 1.3 71.8 + - - +
240I VAL* 4.7 3.6 - - + -
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Residues in contact with ARG 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I GLY 5.9 1.3 - - - +
91I MET* 3.1 37.5 + - + +
137I LYS* 3.5 16.8 - - - +
138I ALA 2.8 21.9 + - - -
139I GLY* 4.2 6.9 - - - -
140I VAL 4.5 1.1 - - - +
141I TYR* 2.8 50.2 + - + -
238I PHE* 1.3 86.0 - - - +
240I VAL* 1.3 64.5 + - - +
241I THR* 2.3 41.8 + - - +
242I PRO* 4.5 3.4 - - + +
243I GLU* 3.3 32.2 - - - +
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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