Contacts of the strand formed by residues 311 - 318 (chain A) in PDB entry 1B70
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 THR 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A VAL* 3.3 8.3 - - - +
225A GLY 2.9 36.9 + - - -
226A GLU* 4.3 0.8 - - - +
227A GLY 4.4 5.5 + - - -
228A ILE* 2.8 32.8 + - - +
285A MET* 3.3 20.6 - - + -
291A PHE* 4.0 8.3 - - - -
310A VAL* 1.3 74.3 + - - +
312A GLY* 1.3 70.8 + - - +
410B TYR* 5.5 4.7 + - - -
414B LEU* 3.5 16.0 - - + +
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Residues in contact with GLY 312 (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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223A VAL 3.2 13.9 - - - -
224A VAL* 4.1 9.2 - - - -
228A ILE* 3.9 6.7 - - - -
285A MET* 3.3 12.5 - - - +
286A VAL* 2.8 29.4 + - - +
291A PHE* 4.2 3.4 - - - -
311A THR* 1.3 85.3 - - - +
313A PHE* 1.3 61.1 + - - -
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Residues in contact with PHE 313 (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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119A TYR* 3.5 20.4 - - - -
222A LEU* 3.5 3.9 - - - +
223A VAL* 2.9 57.7 + - + -
228A ILE* 3.4 22.9 - - + -
229A ALA 3.8 3.1 - - - -
232A HIS* 3.5 18.4 - - + -
233A LEU* 3.5 55.6 - - + -
236A ALA* 4.1 2.9 - - + -
284A GLY 3.1 13.7 - - - +
285A MET* 3.6 12.8 - - - -
286A VAL* 4.0 2.9 - - - +
312A GLY* 1.3 75.0 - - - +
314A ALA* 1.3 65.7 + - - +
315A PHE* 4.3 11.4 - + - -
477B PRO* 5.1 3.8 - - + -
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Residues in contact with ALA 314 (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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183A GLN* 3.7 29.8 - - - +
221A GLY 2.9 14.6 - - - +
222A LEU* 3.8 10.3 - - + -
261A VAL* 5.1 2.5 - - + -
283A ALA* 3.1 4.2 - - - +
284A GLY 3.0 29.7 + - - +
286A VAL* 4.3 5.1 - - + +
313A PHE* 1.3 79.6 - - - +
315A PHE* 1.3 63.1 + - - +
352A PHE* 3.7 9.1 - - + -
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Residues in contact with PHE 315 (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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114A PHE* 3.4 45.8 - + - -
119A TYR* 4.5 12.8 - + - -
197A VAL* 4.7 2.7 - - + -
219A LEU* 4.2 7.2 - - + -
220A GLU* 3.3 6.8 - - - +
221A GLY* 2.6 63.1 + - - +
233A LEU* 4.3 3.4 - - + -
236A ALA* 5.1 1.6 - - + -
237A ILE* 4.1 18.6 - - + -
267A PHE* 4.2 6.1 - + + -
282A GLY 3.1 8.3 - - - +
283A ALA* 3.2 23.6 - - + -
313A PHE* 4.3 17.5 - + - -
314A ALA* 1.3 72.0 - - - +
316A GLY* 1.3 61.3 + - - +
317A LEU* 4.1 19.1 - - + -
352A PHE* 3.5 8.7 - - - -
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Residues in contact with GLY 316 (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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218A GLN* 5.7 3.1 - - - -
219A LEU 3.2 11.0 - - - -
220A GLU* 4.1 8.1 - - - -
267A PHE* 5.0 0.4 - - - -
281A GLY* 3.2 2.4 - - - -
282A GLY 2.8 31.8 + - - +
315A PHE* 1.3 76.8 - - - +
317A LEU* 1.3 62.1 + - - -
352A PHE* 3.4 22.3 - - - +
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Residues in contact with LEU 317 (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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110A LEU* 4.7 13.2 - - + -
114A PHE* 5.1 0.2 - - + -
218A GLN* 3.3 9.5 - - - +
219A LEU* 3.1 58.6 + - + +
240A LEU* 4.3 22.7 - - + -
267A PHE* 4.4 9.2 - - + -
280A LEU* 3.2 29.8 - - + +
281A GLY* 4.1 1.3 - - - -
315A PHE* 4.1 25.1 - - + -
316A GLY* 1.3 73.4 - - - +
318A GLY* 1.3 66.2 + - - +
319A VAL* 3.4 6.9 + - + -
322A LEU* 5.9 3.6 - - + -
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Residues in contact with GLY 318 (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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216A PHE* 5.8 4.3 - - - -
217A HIS 4.0 6.7 - - - -
218A GLN* 4.7 5.6 - - - +
280A LEU* 3.5 13.8 + - - +
317A LEU* 1.3 77.2 - - - +
319A VAL* 1.3 62.6 + - - +
320A GLU* 3.7 1.6 - - - -
321A ARG* 4.1 11.2 - - - +
322A LEU* 3.9 16.6 + - - +
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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