Contacts of the helix formed by residues 78 - 87 (chain A) in PDB entry 2JFF
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 HIS 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A THR* 5.2 5.8 - - + +
57A LEU* 3.5 26.2 - - + +
74A ILE* 4.0 22.7 - - + -
75A ALA* 3.0 24.6 + - + +
77A ALA* 1.3 75.0 - - - +
79A PRO* 1.4 81.5 - - + +
80A SER* 3.0 35.5 + - - -
81A LEU* 2.8 18.9 + - + +
82A SER 2.9 10.4 + - - -
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Residues in contact with PRO 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA 3.3 6.9 - - - +
78A HIS* 1.4 95.9 - - + +
80A SER* 1.3 56.8 + - - +
82A SER* 3.5 8.6 - - - -
83A ALA* 2.9 29.6 + - - +
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 3.8 17.4 - - - +
59A ASP* 2.6 34.7 + - - +
62A LEU* 3.8 11.7 - - - +
63A MET* 5.0 2.3 - - - +
78A HIS* 3.0 24.9 + - - -
79A PRO* 1.3 76.7 - - - +
81A LEU* 1.3 59.5 + - - +
83A ALA* 3.5 6.8 + - - +
84A ALA* 3.1 24.6 + - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.8 24.2 - - + -
57A LEU* 5.4 2.7 - - + -
62A LEU* 4.9 3.1 - - + -
68A ILE* 3.9 24.2 - - + -
70A ALA* 4.3 8.3 - - + -
74A ILE* 3.9 28.9 - - + +
75A ALA 3.5 20.2 - - - +
76A LEU* 3.7 23.8 - - + +
78A HIS* 2.8 11.3 + - + +
80A SER* 1.3 76.6 - - - +
82A SER* 1.3 61.5 + - - +
83A ALA 3.2 0.2 - - - -
84A ALA* 3.3 1.0 + - + +
85A ALA* 2.9 30.9 + - - +
91A ILE* 3.6 23.4 - - + +
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LEU 3.7 9.5 + - - -
77A ALA* 4.5 6.3 - - - -
78A HIS 2.9 15.9 + - - -
79A PRO* 3.5 10.5 - - - -
81A LEU* 1.3 77.6 - - - +
83A ALA* 1.3 56.0 + - - -
85A ALA* 3.4 5.8 + - - +
86A ASP* 2.9 44.1 + - - +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASP* 6.6 0.2 - - - -
63A MET* 4.1 16.4 - - + +
79A PRO 2.9 18.6 + - - +
80A SER* 3.5 8.3 - - - +
82A SER* 1.3 74.0 - - - +
84A ALA* 1.3 65.0 + - - +
86A ASP* 3.4 10.3 + - - +
87A ALA* 3.1 22.0 + - - +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 4.7 4.0 - - + +
63A MET* 3.8 15.1 - - - -
68A ILE* 3.5 32.5 - - + -
80A SER 3.1 14.4 + - - +
81A LEU* 3.3 6.9 + - - +
83A ALA* 1.3 74.4 - - - +
85A ALA* 1.3 66.1 + - - +
87A ALA* 3.0 12.5 + - - +
88A GLY 3.3 0.2 + - - -
89A ILE* 3.1 31.2 + - + +
91A ILE* 4.6 2.0 - - + -
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU 2.9 17.4 + - - +
82A SER* 3.7 7.2 - - - +
84A ALA* 1.3 75.3 - - - +
86A ASP* 1.3 60.5 + - - +
88A GLY* 2.9 21.0 + - - -
89A ILE 4.2 10.3 - - - -
91A ILE* 4.0 11.3 - - + +
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A SER* 2.9 30.0 + - - +
83A ALA* 3.6 9.4 - - - +
85A ALA* 1.3 78.2 - - - +
87A ALA* 1.3 58.4 + - - +
88A GLY 3.4 2.9 + - - -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A MET* 3.7 22.2 - - + -
83A ALA 3.1 11.9 + - - +
84A ALA 3.0 11.1 + - - +
86A ASP* 1.3 75.4 - - - +
88A GLY* 1.3 59.7 + - - +
89A ILE* 3.6 11.8 + - + +
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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