Contacts of the strand formed by residues 75 - 81 (chain N) in PDB entry 1JJ2
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 THR 75 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56N GLU 5.0 2.8 + - - -
57N THR* 3.5 25.2 - - + +
58N VAL* 2.9 26.0 + - - +
74N VAL* 1.3 76.2 - - - +
76N VAL* 1.3 61.4 + - - +
77N ALA* 5.7 0.2 - - + -
94N GLU* 3.4 22.9 + - + +
96N VAL* 4.1 26.2 - - + -
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Residues in contact with VAL 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48N ILE* 4.1 28.3 - - + -
58N VAL* 3.5 16.2 - - + +
60N VAL* 4.3 3.6 - - + -
64N VAL* 4.0 18.2 - - + -
74N VAL* 4.1 20.6 - - + +
75N THR* 1.3 76.6 - - - +
77N ALA* 1.3 60.0 + - - +
81N PHE* 3.5 21.5 - - + -
89N ILE* 4.3 19.1 - - + -
94N GLU 2.9 10.0 + - - +
95N ALA 3.7 0.2 - - - -
96N VAL* 2.7 34.8 + - - +
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Residues in contact with ALA 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57N THR* 4.3 10.8 - - + -
58N VAL 2.8 14.4 + - - +
59N VAL* 3.4 5.9 - - + -
60N VAL* 2.8 26.9 + - - +
75N THR* 4.1 0.8 + - + -
76N VAL* 1.3 74.0 - - - +
78N ALA* 1.3 61.1 + - - +
96N VAL* 3.1 13.7 - - + +
97N SER 4.7 0.2 - - - +
98N LEU* 3.5 20.3 - - + +
101N ALA* 3.9 21.8 - - + -
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Residues in contact with ALA 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N VAL* 3.5 15.0 - - + -
62N GLY 3.8 2.7 - - - +
64N VAL* 3.7 30.3 - - + -
77N ALA* 1.3 76.5 - - - +
79N VAL* 1.3 65.2 + - - +
80N ASP* 3.2 13.0 - - - +
81N PHE* 3.7 9.9 - - + -
96N VAL 3.3 6.8 + - - +
97N SER* 3.9 5.7 - - - -
98N LEU* 3.2 25.5 + - - +
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Residues in contact with VAL 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N LEU* 4.5 16.2 - - + -
10N LEU* 4.4 16.7 - - + +
33N LEU* 3.7 28.7 - - + -
40N HIS* 6.0 0.2 - - - +
60N VAL 3.9 0.2 + - - -
62N GLY* 2.9 40.5 + - - +
63N LYS* 5.2 0.4 - - + -
78N ALA* 1.3 72.6 - - - +
80N ASP* 1.3 63.7 + - + +
97N SER* 5.8 2.1 - - - -
98N LEU* 4.2 11.7 - - + -
99N GLU* 5.2 4.9 - - - +
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Residues in contact with ASP 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6580 C 4.2 12.5 + - - -
6590 A 5.0 1.4 + - - -
62N GLY 3.6 0.8 + - - -
63N LYS* 3.2 29.9 + - + +
64N VAL 3.0 22.0 + - - -
78N ALA* 3.2 5.5 - - - +
79N VAL* 1.3 85.5 - - + +
81N PHE* 1.3 99.6 + - - +
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Residues in contact with PHE 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6590 A 4.3 1.2 + - - -
63N LYS* 4.0 4.9 - - - -
64N VAL* 3.5 24.9 - - + +
76N VAL* 3.5 33.0 - - + -
78N ALA* 3.7 19.7 - - + -
80N ASP* 1.3 100.1 + - - +
82N SER* 1.3 73.0 + - - +
83N GLY 3.9 0.2 + - - -
85N ALA* 4.2 0.2 - - + -
86N GLU* 3.9 31.5 - - + +
89N ILE* 4.3 10.1 - - + -
95N ALA* 3.9 17.3 - - + -
96N VAL 3.1 39.3 - - - -
97N SER* 4.6 2.2 - - - -
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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