Contacts of the strand formed by residues 10 - 17 (chain C) in PDB entry 2JG1
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 SER 10 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C PRO* 1.3 76.0 - - - +
11C VAL* 1.3 56.1 + - - +
12C ASP* 2.9 23.8 + - - -
36C GLY* 2.7 42.0 + - - -
37C GLY* 3.7 9.4 - - - -
67C ILE* 3.8 7.8 - - - +
87C THR* 4.3 0.9 - - - -
88C ARG* 3.3 22.0 - - - -
89C ASN 3.2 2.6 - - - -
90C CYS* 2.9 28.1 + - - -
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Residues in contact with VAL 11 (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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10C SER* 1.3 71.2 - - - +
12C ASP* 1.3 60.8 + - - +
13C ILE* 3.9 2.2 + - + -
33C LYS* 4.4 16.4 - - + -
34C THR 3.5 4.5 - - - +
63C LEU* 3.5 46.7 - - + +
66C PHE* 3.6 37.0 - - + -
67C ILE* 3.8 8.2 - - + +
88C ARG 3.0 10.0 + - - +
89C ASN* 2.9 47.2 + - - +
90C CYS 3.3 2.4 + - - +
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Residues in contact with ASP 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C SER* 2.9 16.3 + - - -
11C VAL* 1.3 72.8 - - - +
13C ILE* 1.3 61.3 + - - +
32C SER 3.7 0.7 - - - +
33C LYS* 3.2 6.4 - - - -
34C THR* 3.0 43.8 + - - +
36C GLY* 3.3 7.9 - - - -
37C GLY 3.1 17.0 + - - -
41C ASN* 4.1 4.7 + - - +
90C CYS* 3.4 11.3 - - - +
290C THR* 4.7 4.8 - - + +
1312C TA6 2.7 48.1 + - - +
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Residues in contact with ILE 13 (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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13B ILE* 4.7 4.3 - - + -
89B ASN* 3.4 28.5 - - + +
11C VAL* 4.2 8.5 - - + +
12C ASP* 1.3 77.9 - - - +
14C SER* 1.3 61.4 + - - +
15C TYR* 3.4 29.7 + - + +
31C VAL* 3.4 28.3 - - + -
32C SER 3.6 1.8 - - - -
33C LYS* 4.0 16.4 - - + -
89C ASN* 4.0 16.4 - - - +
90C CYS 2.9 9.4 + - - +
91C ILE* 3.4 21.5 - - + +
92C ALA* 2.9 29.7 + - - +
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Residues in contact with SER 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP 4.2 0.4 - - - -
13C ILE* 1.3 72.1 - - - +
15C TYR* 1.3 61.5 + - - +
16C PRO* 3.5 13.1 - - - +
31C VAL* 3.6 19.1 - - - +
32C SER* 3.0 28.9 + - - -
92C ALA* 3.6 9.1 + - - +
94C LEU* 3.7 23.4 - - - +
248C ASN* 3.8 16.7 + - - -
288C ALA 4.3 4.4 + - - -
290C THR* 4.4 8.7 - - - -
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Residues in contact with TYR 15 (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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89B ASN* 4.1 0.9 + - - +
91B ILE* 3.4 39.6 - - + +
102B ILE* 3.7 41.3 - - + -
104B GLU* 2.6 34.1 + - + +
13C ILE* 3.4 26.5 - - + +
14C SER* 1.3 77.4 + - - +
16C PRO* 1.3 65.3 - - - +
17C LEU* 3.4 4.3 + - + +
28C VAL* 3.9 16.2 - - + -
31C VAL* 3.8 12.6 - - + -
91C ILE* 4.2 21.5 - - + -
92C ALA 2.8 16.5 + - - +
93C ILE* 3.5 10.0 - - + +
94C LEU* 3.0 22.9 + - - -
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Residues in contact with PRO 16 (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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14C SER* 3.5 19.0 - - - +
15C TYR* 1.3 83.2 - - - +
17C LEU* 1.3 66.4 + - - +
28C VAL* 4.6 5.2 - - + +
30C GLU 6.1 1.3 - - - +
31C VAL* 6.1 3.1 - - + -
32C SER 6.1 0.4 - - - +
94C LEU* 3.5 22.7 - - + +
247C LEU 5.6 1.8 - - - +
288C ALA* 6.3 2.9 - - + -
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Residues in contact with LEU 17 (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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102B ILE* 4.7 6.5 - - + -
15C TYR* 3.8 9.4 - - + +
16C PRO* 1.3 77.5 - - - +
18C THR* 1.3 64.3 - - - +
19C ALA 3.6 21.3 - - - +
20C LEU* 3.6 32.5 - - + -
26C ASN* 4.3 16.4 - - + +
27C ARG 4.5 7.2 - - - +
28C VAL* 3.3 34.1 - - + -
93C ILE* 3.6 13.7 - - + -
94C LEU 2.8 20.1 + - - +
95C HIS* 3.6 8.1 - - + -
96C GLU 4.4 1.2 + - - -
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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