Contacts of the strand formed by residues 72 - 79 (chain C) in PDB entry 4J2X
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 GLN 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C ASP* 1.3 69.2 - - - +
73C THR* 1.3 60.5 + - - +
105C GLY* 3.5 34.0 + - - -
106C TRP* 3.7 29.1 - - + +
109C LYS* 4.1 14.2 - - - +
173C TYR* 3.5 20.8 + - - -
366C PHE* 3.0 73.0 + - + +
367C TYR* 5.0 3.0 - - - +
368C GLU* 4.6 22.2 - - - +
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Residues in contact with THR 73 (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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71C ASP* 4.5 4.5 - - - +
72C GLN* 1.3 75.2 - - - +
74C VAL* 1.4 67.4 + - - +
75C LEU* 4.5 4.0 - - + -
101C LEU* 3.5 1.2 - - - -
102C MET* 2.8 56.2 + - + +
103C GLY* 4.7 2.4 + - - -
106C TRP* 3.0 12.6 + - - -
363C GLU* 3.9 23.8 - - + -
364C TYR 3.2 5.4 - - - +
365C THR* 3.1 30.6 + - - +
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C THR* 1.4 77.7 - - - +
75C LEU* 1.3 69.7 + - - +
76C ILE* 4.5 8.3 - - + -
99C VAL* 4.5 4.7 - - + -
100C TYR 3.5 5.2 - - - +
101C LEU* 4.3 1.6 - - + -
106C TRP* 3.9 15.7 - - + -
171C MET* 3.5 31.6 - - + -
182C PHE* 3.6 44.4 - - + -
362C ALA 3.9 0.2 - - - +
363C GLU* 3.3 4.9 - - - -
364C TYR* 2.9 33.4 + - + +
366C PHE* 4.0 5.6 - - + -
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Residues in contact with LEU 75 (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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73C THR* 4.5 2.9 - - + -
74C VAL* 1.3 75.0 - - - +
76C ILE* 1.3 64.0 + - - +
77C LEU* 4.0 14.8 - - + -
98C CYS 4.1 0.2 - - - -
99C VAL* 3.3 9.2 - - - +
100C TYR* 2.8 50.4 + - + +
102C MET* 3.5 32.3 - - + -
361C LYS* 3.7 25.6 - - + +
362C ALA 3.4 14.4 - - - +
363C GLU* 3.6 26.7 - - + +
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Residues in contact with ILE 76 (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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74C VAL* 4.5 8.3 - - + +
75C LEU* 1.3 77.6 - - - +
77C LEU* 1.3 63.3 + - - +
78C HIS* 3.5 10.8 + - - +
98C CYS 3.2 9.2 - - - +
99C VAL* 4.4 9.0 - - + -
129C ILE* 5.2 1.1 - - + -
167C LEU* 4.4 13.7 - - + +
169C VAL* 3.7 21.3 - - + -
182C PHE* 3.5 35.7 - - + +
183C LEU 4.0 17.7 - - - +
184C SER* 3.9 18.4 - - - +
361C LYS* 3.3 5.0 - - - -
362C ALA* 3.0 39.6 + - + -
364C TYR* 4.7 1.6 - - + -
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Residues in contact with LEU 77 (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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75C LEU* 4.2 18.2 - - + -
76C ILE* 1.3 72.3 - - - +
78C HIS* 1.3 59.8 + - - +
97C PRO* 3.3 3.5 - - - +
98C CYS* 2.6 46.3 + - + +
100C TYR* 3.6 38.8 - - + -
212C LYS* 5.9 1.8 - - - +
243C TRP* 3.7 20.1 - - + -
360C ASP 3.8 4.0 - - - +
361C LYS* 3.5 35.2 - - + -
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Residues in contact with HIS 78 (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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76C ILE* 3.5 18.2 + - + +
77C LEU* 1.3 73.5 - - - +
79C ALA* 1.3 77.7 + - - +
80C LYS* 4.5 0.6 - - - -
95C PRO 5.8 0.4 - - - -
97C PRO* 4.2 10.3 - - + -
167C LEU* 4.0 19.3 - - + -
184C SER* 3.5 11.4 - - - -
185C LYS* 3.2 52.7 + - + +
186C ARG 4.2 2.8 + - - -
187C ILE* 3.5 18.7 - - + +
243C TRP* 3.9 10.8 - - - -
359C THR* 3.3 8.6 - - - -
360C ASP* 2.9 47.7 + - + +
362C ALA 4.8 0.2 - - - -
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Residues in contact with ALA 79 (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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78C HIS* 1.3 95.7 - - - +
80C LYS* 1.3 57.6 + - - +
81C VAL 3.3 11.2 + - - +
94C CYS 5.2 0.9 - - - +
95C PRO* 4.1 20.9 + - + +
97C PRO* 5.8 0.6 - - - +
187C ILE* 3.6 9.5 - - - +
243C TRP* 4.9 0.8 - - - -
357C ILE* 3.6 31.0 - - + -
358C SER 3.4 9.0 - - - +
359C THR* 3.9 4.2 - - + +
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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