Contacts of the strand formed by residues 396 - 405 (chain C) in PDB entry 5O67
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 396 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339B ASP* 3.7 27.6 - - + -
363B ASN* 4.1 6.1 - - - -
365B GLY* 4.6 0.4 - - - -
389B MET* 3.8 32.5 - - + -
390B THR* 3.9 19.7 - - + -
116C TYR* 3.8 21.1 - + - -
118C ARG* 3.0 54.8 + - + -
385C LEU* 4.5 3.1 - - + -
386C ALA 3.4 11.4 - - - +
394C PRO* 3.2 4.0 - - - +
395C ASP* 1.3 83.8 - - + +
397C THR* 1.3 69.8 + - - +
398C PHE* 3.3 39.5 - + - -
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Residues in contact with THR 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C THR* 3.3 34.1 - - + -
116C TYR 3.3 7.2 - - - +
117C ALA* 3.9 7.3 - - + +
366C TYR* 5.0 1.4 - - - -
384C ASN* 3.7 1.6 + - - +
385C LEU* 3.6 4.2 - - - +
386C ALA* 3.0 41.9 + - + +
394C PRO* 3.4 22.3 - - - +
396C PHE* 1.3 82.2 + - - +
398C PHE* 1.3 64.8 + - - +
399C SER* 4.9 3.9 + - - +
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Residues in contact with PHE 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B PHE* 3.7 35.9 - + - -
337B VAL* 4.0 27.1 - - + -
338B SER* 4.9 3.4 - - - -
339B ASP* 4.3 12.3 - - + -
389B MET* 4.6 1.6 - - + -
114C ILE 4.2 0.2 - - - +
115C THR* 3.5 3.1 - - - +
116C TYR* 2.9 49.3 + + + +
384C ASN 3.7 4.5 - - - -
385C LEU* 3.9 21.3 - - + -
396C PHE* 3.3 37.9 - + - -
397C THR* 1.3 75.8 - - - +
399C SER* 1.3 64.0 + - - +
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Residues in contact with SER 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ILE 3.4 6.3 - - - -
115C THR* 3.5 23.6 - - - +
382C VAL 4.1 0.9 - - - -
383C PRO* 3.3 5.2 - - - +
384C ASN* 3.0 52.4 + - - +
397C THR* 4.9 3.6 + - - +
398C PHE* 1.3 77.6 - - - +
400C LEU* 1.3 66.4 + - - +
401C LYS* 5.2 10.9 - - - +
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Residues in contact with LEU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C GLY* 3.4 1.6 - - - -
114C ILE* 2.9 47.2 + - + +
381C ILE* 4.0 20.6 - - + -
382C VAL 3.4 2.0 - - - -
383C PRO* 3.7 29.8 - - + -
399C SER* 1.3 74.6 - - - +
401C LYS* 1.3 62.8 + - - +
402C PHE* 4.0 22.4 - - + -
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Residues in contact with LYS 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU* 3.2 32.6 + - - -
111C GLU* 3.1 33.2 - - - +
112C THR 3.6 3.8 - - - +
113C GLY* 4.0 13.0 - - - -
114C ILE 5.1 0.2 - - - +
380C THR 3.5 5.0 - - - +
381C ILE* 3.5 2.8 - - - +
382C VAL* 2.9 48.4 + - + +
384C ASN* 6.3 1.8 - - + -
399C SER* 5.2 11.2 - - - +
400C LEU* 1.3 77.3 - - - +
402C PHE* 1.3 64.6 + - - +
403C PRO* 3.5 4.6 - - + +
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Residues in contact with PHE 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C PHE 3.7 1.2 - - - +
111C GLU* 3.6 1.3 - - - -
112C THR* 2.8 48.4 + - + +
113C GLY* 5.2 0.4 - - - -
114C ILE* 4.7 8.5 - - + -
379C LEU* 4.0 17.6 - - + +
380C THR 3.4 4.7 - - - -
381C ILE* 3.9 37.5 - - + -
400C LEU* 4.0 37.9 - - + -
401C LYS* 1.3 75.3 - - - +
403C PRO* 1.3 65.8 - - - +
404C TYR* 3.4 3.8 + - - +
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Residues in contact with PRO 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C SER* 6.0 2.0 - - - -
110C PHE 3.7 5.8 - - - +
111C GLU* 3.4 29.6 - - + +
157C ARG* 5.3 1.1 - - - +
378C ASN 3.6 2.8 - - - +
379C LEU* 3.3 16.5 - - - +
380C THR* 3.3 40.2 + - + +
382C VAL* 4.4 7.4 - - + -
401C LYS* 3.5 8.7 - - + +
402C PHE* 1.3 86.7 - - - +
404C TYR* 1.3 59.2 + - - +
405C TYR* 3.7 25.5 - - + +
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Residues in contact with TYR 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C SER* 3.3 5.6 - - - -
110C PHE* 2.8 41.3 + - + +
376C SER* 5.5 0.9 - - - -
378C ASN* 3.4 42.5 + - + -
379C LEU* 4.4 20.9 - - + -
402C PHE 3.4 2.2 + - - +
403C PRO* 1.3 73.7 - - - +
405C TYR* 1.3 62.0 + - - +
406C PHE* 3.7 43.8 + + + -
502C LDA 3.4 33.3 - - + +
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Residues in contact with TYR 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ASN* 5.8 2.2 - - - -
97C ASN* 3.1 29.6 + - - +
103C ALA* 4.0 23.0 - - + +
104C GLY 5.0 0.4 - - - -
105C ASN 4.4 17.7 - - - +
106C GLY* 4.8 9.4 - - - -
108C PHE 4.2 6.3 - - - +
109C SER* 4.0 17.9 - - - -
157C ARG* 5.6 2.5 + - - -
377C GLU 5.3 2.7 - - - +
378C ASN* 2.9 51.0 + - - +
380C THR* 5.0 8.7 - - - -
403C PRO* 3.7 31.9 - - + +
404C TYR* 1.3 75.3 - - - +
406C PHE* 1.3 63.8 + - - +
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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