Contacts of the strand formed by residues 53 - 59 (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 VAL 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MSE 3.9 6.0 - - - +
2C ILE* 3.2 10.5 - - + +
4C THR* 3.6 30.7 - - + -
43C THR* 4.1 34.1 - - + +
46C LEU* 3.9 16.6 - - + -
47C ALA* 4.3 13.7 - - + +
51C GLU 3.4 12.1 + - - +
52C PRO* 1.3 75.8 - - - +
54C LEU* 1.3 63.6 + - - +
55C ALA 4.3 0.2 - - - -
76C ILE* 5.1 4.9 - - + -
77C LYS* 4.0 25.9 + - - +
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Residues in contact with LEU 54 (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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1C MSE 4.4 19.1 - - + -
2C ILE 2.9 10.0 + - - +
3C LEU* 3.3 16.6 - - + +
4C THR* 3.0 25.2 + - - -
53C VAL* 1.3 75.6 - - - +
55C ALA* 1.3 65.4 + - - +
77C LYS* 3.6 22.4 - - + +
78C HIS* 3.8 21.5 - - - +
79C ALA* 3.8 8.5 - - + +
124C MSE 3.8 35.9 - - + -
128C VAL* 5.7 3.6 - - + -
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Residues in contact with ALA 55 (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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4C THR* 3.4 15.7 - - - +
40C LEU* 3.9 24.5 - - + -
43C THR* 3.9 12.1 - - + +
53C VAL* 4.3 0.6 - - - +
54C LEU* 1.3 73.4 - - - +
56C SER* 1.3 60.9 + - - +
71C LEU* 4.7 2.5 - - + -
77C LYS 3.0 16.1 + - - +
78C HIS* 3.2 11.8 - - + +
79C ALA 2.8 28.4 + - - -
80C PHE* 4.3 5.0 + - + -
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Residues in contact with SER 56 (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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3C LEU* 4.1 3.1 - - - -
4C THR 2.9 10.5 + - - +
5C LEU* 4.0 14.6 - - - -
6C THR* 3.0 25.8 + - - +
40C LEU* 5.7 0.2 - - - +
54C LEU 4.0 0.2 + - - -
55C ALA* 1.3 74.6 - - - +
57C GLY* 1.3 63.9 + - - +
79C ALA 2.8 22.8 + - - -
80C PHE* 3.7 12.7 - - - -
117C PHE* 3.6 8.3 - - - -
120C HIS* 3.9 1.0 + - - -
124C MSE 3.3 34.2 - - - +
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Residues in contact with GLY 57 (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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6C THR 3.2 17.7 - - - -
7C LEU* 4.1 5.4 - - - -
56C SER* 1.3 81.4 + - - +
58C PHE* 1.3 64.0 + - - -
80C PHE* 3.6 8.0 - - - -
81C TYR* 2.9 28.9 + - - +
117C PHE* 4.0 13.5 - - - -
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Residues in contact with PHE 58 (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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6C THR 3.6 4.8 + - - -
7C LEU* 3.6 41.5 - - + +
9C PRO* 2.9 27.8 - - - +
57C GLY* 1.3 73.5 - - - -
59C ILE* 1.3 60.8 + - - +
81C TYR* 3.4 15.5 - + + -
83C ILE* 3.5 29.2 - - + -
87C THR* 4.4 1.4 + - - -
107C PRO* 5.9 1.4 - - + +
109C ILE* 3.8 40.4 - - + -
113C GLU 3.7 12.1 - - - -
114C ALA* 4.4 0.9 - - - -
117C PHE* 3.5 35.0 - + + -
138C PRO* 4.3 0.9 - - + -
141C LEU* 4.3 15.0 - - + -
145C TYR* 4.0 9.4 - + - -
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Residues in contact with ILE 59 (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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9C PRO* 3.7 24.7 - - + -
57C GLY 4.1 0.2 + - - -
58C PHE* 1.3 72.3 - - - +
60C GLY* 1.3 58.3 + - - +
64C GLY* 3.5 27.6 - - - +
67C ILE* 3.9 33.0 - - + -
68C ALA* 6.0 1.3 - - + -
80C PHE* 3.7 38.8 - - + -
81C TYR 3.0 7.5 + - - +
82C ASN* 3.3 26.6 - - - +
83C ILE* 2.8 28.9 + - - -
87C THR* 3.6 3.6 - - - +
96D GLU* 6.0 0.4 - - - -
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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