Contacts of the strand formed by residues 73 - 79 (chain V) in PDB entry 2J28
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 LYS 73 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56V PHE 5.8 0.4 - - - -
57V TYR 6.1 1.1 - - - -
58V SER* 3.7 21.7 + - - +
59V GLU 4.6 1.3 - - - +
60V VAL* 3.6 32.1 - - + +
61V LEU* 4.8 4.7 - - - -
72V VAL* 1.3 83.3 - - - +
74V ALA* 1.3 62.0 + - - +
91V PHE* 3.2 14.1 - - - -
92V VAL* 2.8 45.6 + - + +
93V ARG 6.1 0.4 - - - +
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Residues in contact with ALA 74 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56V PHE* 3.6 44.3 + - + +
57V TYR* 4.1 27.6 - - + +
61V LEU* 4.9 1.2 - - - +
73V LYS* 1.3 74.5 - - - +
75V GLN* 1.3 64.8 + - - +
77V VAL* 5.2 3.6 - - + -
89V ILE* 5.4 1.8 - - + -
90V ASP 3.6 6.3 - - - +
91V PHE* 4.1 6.3 - - + -
92V VAL* 4.5 3.3 - - - +
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Residues in contact with GLN 75 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A U 3.5 40.7 + - - +
104A A 5.2 5.1 + - - +
31V TYR* 3.9 10.5 - - + +
57V TYR* 5.0 4.9 - - - -
73V LYS 3.8 0.6 + - - -
74V ALA* 1.3 77.4 - - - +
76V ASP* 1.3 67.3 + - + +
77V VAL* 4.0 6.3 + - - +
90V ASP* 2.8 23.5 + - + +
91V PHE 4.7 0.2 - - - -
92V VAL* 3.8 29.3 - - + +
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Residues in contact with ASP 76 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A G 3.9 13.1 + - - -
102A G 5.5 5.4 + - - +
103A U 5.6 5.4 - - - +
75V GLN* 1.3 84.8 - - + +
77V VAL* 1.3 76.7 + - - +
78V GLN* 3.6 23.4 + - - +
88V HIS* 4.5 0.9 - - - -
89V ILE* 3.7 0.9 - - - +
90V ASP* 2.8 47.4 + - + +
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Residues in contact with VAL 77 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57V TYR* 3.4 40.8 - - + +
74V ALA* 5.2 4.5 - - + -
75V GLN 4.2 4.9 - - - +
76V ASP* 1.3 88.8 + - - +
78V GLN* 1.3 62.8 + - - +
79V ARG* 3.6 26.8 + - - +
86V LEU* 3.6 18.4 - - + -
89V ILE* 3.3 28.3 - - + -
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Residues in contact with GLN 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A G 4.1 7.1 + - - -
76A G 2.5 58.6 + - - +
77A U 3.7 11.9 + - - -
101A A 5.5 0.2 - - - +
76V ASP* 3.6 15.9 - - - +
77V VAL* 1.3 71.8 - - - +
79V ARG* 1.3 54.3 + - - +
86V LEU* 4.3 1.2 - - - +
87V GLN* 2.7 47.6 + - + +
88V HIS* 2.8 38.2 + - + +
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Residues in contact with ARG 79 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M ASP* 6.1 1.1 - - - -
131M VAL* 3.2 39.7 + - - +
132M THR* 5.2 1.6 - - - +
133M LYS 4.5 1.4 + - - -
134M THR* 5.8 2.2 - - - +
51V GLN* 4.0 18.4 - - - +
57V TYR* 3.7 21.0 + - - -
77V VAL* 4.1 22.9 - - - +
78V GLN* 1.3 75.5 - - - +
80V HIS* 1.3 69.6 + - - +
81V PRO* 3.6 3.1 - - - +
85V LYS 4.2 9.2 - - - +
86V LEU* 4.7 12.2 - - + +
87V GLN* 3.9 12.1 - - - +
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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