Contacts of the strand formed by residues 387 - 395 (chain B) in PDB entry 3K72
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 ILE 387 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B VAL 3.8 8.4 - - - +
96B THR* 4.1 5.4 + - - +
97B PHE* 3.0 35.4 + - + +
345B VAL* 3.4 26.7 - - + -
363B PHE 4.6 11.7 - - - +
364B CYS* 5.3 2.0 - - - -
365B SER 5.2 1.1 - - - +
378B CYS* 5.4 4.0 - - + -
381B VAL* 3.7 33.0 - - + -
385B VAL 3.9 3.6 - - - +
386B PRO* 1.3 82.9 - - - +
388B THR* 1.3 69.9 + - - +
389B PHE* 3.2 37.2 - - + -
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Residues in contact with THR 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASN* 4.9 18.4 - - + +
95B VAL 4.0 3.6 - - - +
361B ASP* 4.3 0.6 - - + -
362B SER* 3.7 5.4 + - - -
363B PHE* 3.2 55.0 + - + +
387B ILE* 1.3 82.8 + - - +
389B PHE* 1.3 71.1 + - - +
390B GLN* 4.3 4.4 + - + +
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Residues in contact with PHE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ASN* 3.6 1.8 - - - -
95B VAL* 3.0 44.5 + - + +
97B PHE* 4.7 2.7 - - + -
345B VAL* 3.8 14.6 - - + -
347B LEU* 3.3 39.7 - - + -
360B TYR* 4.9 2.5 - - + -
361B ASP 3.3 19.1 - - - +
362B SER* 4.0 5.6 - - - -
363B PHE 5.6 0.2 - - - -
375B ARG 4.8 1.3 - - - -
376B GLY* 3.3 44.0 - - - -
378B CYS* 4.5 10.3 - - - -
387B ILE* 3.2 39.5 - - + -
388B THR* 1.3 79.6 - - - +
390B GLN* 1.3 59.5 + - - +
391B VAL* 3.5 6.2 + - + -
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Residues in contact with GLN 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ALA* 3.8 19.8 - - + +
93B PHE 5.1 0.7 - - - +
94B ASN* 3.8 21.4 + - - +
360B TYR* 3.4 5.6 - - - -
361B ASP* 2.9 51.0 + - + +
363B PHE* 5.8 4.3 - - + -
388B THR* 4.2 5.2 + - + +
389B PHE* 1.3 69.8 - - - +
391B VAL* 1.3 62.6 + - - +
392B LYS* 3.2 35.7 + - + +
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Residues in contact with VAL 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ALA 3.5 2.1 - - - +
92B ALA* 3.5 3.8 - - - -
93B PHE* 3.2 64.0 + - + +
95B VAL* 3.6 28.9 - - + -
347B LEU* 4.5 3.1 - - + -
358B VAL* 4.2 3.4 - - + -
359B THR 3.7 12.1 - - - +
360B TYR* 3.7 26.5 - - + +
389B PHE 4.3 1.3 - - - +
390B GLN* 1.3 70.3 - - - +
392B LYS* 1.3 62.6 + - - +
393B VAL* 4.1 9.9 - - + -
406B ILE* 3.9 17.0 - - + -
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Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ALA* 4.8 14.4 - - + -
91B ALA 3.5 5.4 - - - +
92B ALA* 4.3 9.2 - - + -
357B LYS 4.1 0.9 - - - +
358B VAL* 4.0 1.0 - - - -
359B THR* 3.2 43.5 + - - +
361B ASP* 3.9 15.3 + - - +
372B ASN* 3.9 17.9 + - - +
390B GLN* 3.2 43.5 + - + +
391B VAL* 1.3 74.4 - - - +
393B VAL* 1.3 63.2 + - - +
394B THR* 3.9 5.1 + - - +
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LEU* 4.1 20.4 - - + -
85B LEU* 3.5 25.8 - - + +
91B ALA* 3.1 30.9 + - - +
93B PHE* 3.8 27.4 - - + -
356B LEU* 4.8 9.9 - - + -
357B LYS 4.1 2.7 - - - -
358B VAL* 4.2 23.6 - - + +
391B VAL* 4.1 8.3 - - + -
392B LYS* 1.3 73.0 - - - +
394B THR* 1.3 66.9 + - - +
404B PHE* 4.4 16.6 - - + -
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Residues in contact with THR 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU* 3.7 6.7 - - - -
88B GLY* 4.0 25.8 - - - +
89B GLN 4.3 2.9 - - - +
90B ALA* 3.3 23.4 - - - +
356B LEU* 4.0 5.2 - - - +
357B LYS* 3.3 39.3 + - - +
392B LYS* 3.9 3.9 + - - +
393B VAL* 1.3 73.3 - - - +
395B ALA* 1.3 75.0 + - - +
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Residues in contact with ALA 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU* 3.6 25.9 - - + +
87B PRO* 4.3 7.2 - - + -
88B GLY* 3.1 21.8 + - - +
355B THR 4.1 5.8 - - - -
356B LEU* 3.9 12.8 - - + -
394B THR* 1.3 83.5 - - - +
396B THR* 1.3 66.0 + - - +
397B GLU 3.7 17.3 - - - +
399B ILE* 4.2 7.6 - - + -
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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