Contacts of the strand formed by residues 59 - 68 (chain C) in PDB entry 2J2M
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 GLY 59 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C ALA 3.7 3.0 + - - -
58C ARG* 1.3 83.9 + - - +
60C PHE* 1.3 61.2 + - - +
93C ARG* 3.8 11.4 - - - +
94C PHE 3.0 13.0 - - - -
190C TYR* 4.1 6.1 - - - -
243C SER* 3.8 10.0 + - - -
306C TYR* 2.8 28.3 + - - -
310C THR* 4.5 2.7 - - - -
156D ASN* 4.9 2.4 + - - -
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Residues in contact with PHE 60 (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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59C GLY* 1.3 74.3 - - - -
61C GLY* 1.3 82.8 + - - +
62C ALA* 4.1 9.6 - - + -
92C ALA 4.0 0.2 - - - +
93C ARG* 3.2 3.1 - - - +
94C PHE* 2.9 44.9 + + - -
190C TYR* 3.6 14.1 - + + -
243C SER* 3.5 33.4 - - - +
246C THR* 3.3 36.3 - - + -
247C PHE* 3.9 24.9 - + + -
250C ILE* 4.4 1.6 - - + -
299C LEU* 5.9 0.7 - - + -
302C ASN* 3.7 20.6 - - - -
303C VAL* 6.3 1.1 - - + -
306C TYR* 4.6 7.9 - + - -
310C THR* 3.8 6.7 - - - -
155D THR 5.7 3.4 - - - -
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Residues in contact with GLY 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PHE* 1.3 93.0 - - - +
62C ALA* 1.3 65.4 + - - +
91C PHE* 4.0 3.8 - - - -
92C ALA 3.1 12.1 - - - -
93C ARG* 4.2 1.1 - - - -
94C PHE* 5.8 0.4 - - - -
302C ASN* 4.7 0.3 - - - +
303C VAL* 3.7 16.1 + - - +
306C TYR* 4.9 0.8 - - - -
310C THR* 3.3 27.7 + - - +
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Residues in contact with ALA 62 (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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60C PHE* 4.1 8.4 - - + -
61C GLY* 1.3 76.2 - - - +
63C HIS* 1.3 63.8 + - - +
91C PHE* 3.5 12.7 - - - -
92C ALA* 3.0 35.0 + - - +
94C PHE* 6.0 0.6 - - - -
250C ILE* 3.6 27.8 - - + -
299C LEU* 4.2 10.0 - - + +
301C LYS 3.3 14.1 - - - +
302C ASN* 4.3 2.2 - - - -
303C VAL* 4.3 3.1 - - - -
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Residues in contact with HIS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ALA* 1.3 75.2 - - - +
64C GLY* 1.3 60.3 + - - +
90C VAL 3.5 10.6 + - - +
91C PHE* 3.6 26.1 - + + +
118C TYR* 5.5 2.9 - + - -
299C LEU* 3.6 5.8 - - - +
300C ASN* 3.1 21.5 + - - +
301C LYS* 2.8 38.0 + - + +
302C ASN 4.5 2.7 - - - -
303C VAL* 4.2 8.7 - - - -
304C ASP 5.4 0.2 - - - -
309C GLU* 2.6 29.8 + - - -
356C ILE* 3.9 14.8 - - + -
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Residues in contact with GLY 64 (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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63C HIS* 1.3 78.2 - - - +
65C VAL* 1.3 61.1 + - - +
89C PRO* 3.7 6.1 - - - +
90C VAL* 3.0 33.3 + - - +
298C THR 3.1 14.6 - - - -
299C LEU* 4.1 1.6 - - - -
300C ASN* 3.2 13.9 - - - -
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Residues in contact with VAL 65 (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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64C GLY* 1.3 75.3 - - - +
66C PHE* 1.3 64.3 + - - +
67C LYS* 5.3 4.9 - - + +
87C GLU* 3.8 37.7 - - + +
88C VAL 3.5 12.8 - - - +
89C PRO* 4.9 1.3 - - + -
90C VAL* 3.6 4.6 - - - +
296C THR 3.8 0.9 - - - +
297C MET* 3.3 4.7 - - - +
298C THR* 2.9 50.0 + - - +
300C ASN* 4.5 13.2 - - - +
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Residues in contact with PHE 66 (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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65C VAL* 1.3 75.3 - - - +
67C LYS* 1.3 62.8 + - - +
68C VAL* 3.7 30.1 - - + -
80C PHE* 4.3 11.0 - + - -
86C THR 3.6 0.9 - - - +
87C GLU* 3.2 5.4 - - - -
88C VAL* 2.7 53.8 + - + +
90C VAL* 3.9 5.8 - - + +
117C PHE* 3.7 19.3 - + + -
217C TRP* 3.6 33.9 - + - -
260C LEU* 3.5 23.3 - - + -
294C VAL* 4.1 5.2 - - + -
295C GLY* 3.8 20.2 - - - -
296C THR 3.6 24.7 - - - -
297C MET* 3.8 3.8 - - + -
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Residues in contact with LYS 67 (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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65C VAL* 4.1 5.8 - - + -
66C PHE* 1.3 75.4 - - - +
68C VAL* 1.3 65.6 + - - +
69C LYS* 3.4 5.6 + - + +
85C GLY* 3.1 36.4 + - - +
86C THR 3.7 0.9 - - - -
87C GLU* 3.0 32.6 + - + +
295C GLY* 3.1 3.1 - - - -
296C THR* 2.9 51.4 + - + +
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Residues in contact with VAL 68 (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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66C PHE* 3.7 23.3 - - + +
67C LYS* 1.3 73.9 - - - +
69C LYS* 1.3 56.1 + - - +
70C ASN 4.2 11.2 - - - +
80C PHE* 3.3 30.7 - - + +
81C LEU* 4.2 13.9 - - + +
83C GLU 3.0 31.0 - - - +
84C GLU* 3.8 2.7 - - - -
85C GLY* 2.7 34.4 + - - +
86C THR* 3.0 17.2 + - - +
88C VAL* 5.1 0.7 - - + -
294C VAL 3.7 9.2 - - - +
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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