Contacts of the helix formed by residues 81 - 99 (chain A) in PDB entry 4JF7
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A TYR* 3.1 41.9 + - + +
80A ALA* 1.3 82.4 - - + +
82A ALA* 1.3 63.1 + - - +
83A LEU 3.6 0.7 - - - -
84A PRO* 3.8 3.5 - - - +
85A LEU* 3.1 37.6 + - + +
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Residues in contact with ALA 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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77A TYR* 3.1 28.8 + - + +
78A ASN* 3.6 27.8 - - - +
81A VAL* 1.3 81.0 - - - +
83A LEU* 1.3 65.7 + - + +
85A LEU* 3.6 6.4 + - - +
86A GLN* 3.4 19.9 + - - +
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Residues in contact with LEU 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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78A ASN 2.8 23.5 + - - +
79A SER* 5.1 1.8 - - - +
82A ALA* 1.3 73.8 - - + +
84A PRO* 1.4 71.4 - - + +
85A LEU 3.1 1.8 - - - -
86A GLN* 3.4 22.0 + - - +
87A LEU* 3.1 28.1 + - + +
83B LEU* 4.4 23.8 - - + -
79D SER* 3.3 37.0 - - - +
83D LEU* 4.4 22.2 - - + -
84D PRO* 4.3 10.5 - - + -
87D LEU* 4.7 9.9 - - + +
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Residues in contact with PRO 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER 3.6 18.4 - - - +
80A ALA* 3.2 30.3 - - - +
81A VAL* 3.8 3.8 - - - +
83A LEU* 1.4 94.8 - - + +
85A LEU* 1.3 55.4 + - - +
87A LEU* 3.2 6.1 + - + +
88A ASP* 3.0 33.0 + - - +
83B LEU* 3.9 6.7 - - + -
86B GLN* 3.4 29.8 + - - +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 3.1 27.0 + - + +
82A ALA* 3.7 7.2 - - - +
83A LEU 3.1 0.8 - - - -
84A PRO* 1.3 75.8 - - - +
86A GLN* 1.3 59.1 + - - +
87A LEU 3.1 1.6 - - - -
88A ASP* 3.2 14.0 + - + +
89A THR* 3.0 39.7 + - - +
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA 3.4 10.0 + - - +
83A LEU* 3.4 14.6 + - - +
85A LEU* 1.3 78.8 - - - +
87A LEU* 1.3 58.5 + - - +
89A THR* 3.9 8.4 - - + -
90A LEU* 3.0 28.7 + - + +
84D PRO* 3.1 44.4 + - - +
87D LEU* 3.7 19.2 - - + +
88D ASP* 3.1 28.4 + - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.1 18.3 + - + +
84A PRO* 3.3 10.8 - - + +
85A LEU 3.1 0.6 - - - -
86A GLN* 1.3 77.1 - - - +
88A ASP* 1.3 61.3 + - - +
90A LEU* 3.7 7.9 - - + +
91A GLU* 3.1 27.9 + - - +
83B LEU* 4.5 12.1 - - + -
86B GLN* 3.4 33.9 - - + +
87B LEU* 3.9 31.0 - - + -
90B LEU* 3.7 17.4 - - + +
87D LEU* 3.7 37.2 - - + -
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Residues in contact with ASP 88 (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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84A PRO* 3.0 22.0 + - - +
85A LEU* 3.2 16.9 + - + +
87A LEU* 1.3 73.8 - - - +
89A THR* 1.3 66.4 + - - +
91A GLU* 3.4 15.4 + - - +
92A SER* 3.1 24.6 + - - -
86B GLN* 3.5 14.0 + - - -
90B LEU* 6.0 0.3 - - - +
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Residues in contact with THR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.0 25.8 + - - +
86A GLN* 3.9 8.7 - - + -
88A ASP* 1.3 77.0 - - - +
90A LEU* 1.3 61.3 + - - +
92A SER* 2.6 23.2 + - - +
93A THR* 3.1 25.4 - - + +
91D GLU* 6.0 1.3 - - - +
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Residues in contact with LEU 90 (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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86A GLN* 3.0 20.8 + - + +
87A LEU* 3.7 9.4 - - + +
88A ASP 3.3 0.2 - - - -
89A THR* 1.3 76.5 - - - +
91A GLU* 1.3 67.1 - - - +
93A THR* 2.9 23.0 + - - -
94A LEU* 3.4 29.6 + - + +
90B LEU* 4.6 15.0 - - + -
94B LEU* 5.4 2.9 - - + -
87D LEU* 3.6 49.1 - - + +
90D LEU* 4.4 15.3 - - + -
91D GLU* 3.9 25.8 - - + +
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Residues in contact with GLU 91 (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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87A LEU 3.1 15.0 + - - +
88A ASP* 3.4 15.9 + - - +
90A LEU* 1.3 84.7 - - - +
92A SER* 1.3 58.3 + - - +
94A LEU* 3.6 5.8 - - - +
95A LEU* 2.9 43.4 + - + +
90B LEU* 3.6 25.9 - - + +
93B THR* 3.2 33.0 + - - +
94B LEU* 3.7 16.6 - - + -
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASP 3.1 13.7 + - - -
89A THR* 2.6 26.5 + - - +
91A GLU* 1.3 77.7 - - - +
93A THR* 1.3 56.6 + - - +
95A LEU* 3.5 6.6 + - - -
96A THR* 2.5 39.4 + - - -
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Residues in contact with THR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 3.1 26.5 + - + +
90A LEU 2.9 15.1 + - - -
92A SER* 1.3 84.0 + - - +
94A LEU* 1.3 59.1 + - - +
96A THR* 3.6 19.0 - - - +
97A ALA* 3.6 6.1 - - - +
91D GLU* 3.1 30.4 + - - +
95D LEU* 4.8 9.7 - - - +
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Residues in contact with LEU 94 (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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90A LEU* 3.4 31.6 - - + +
91A GLU* 3.6 9.9 - - - +
92A SER 3.2 0.2 - - - -
93A THR* 1.3 79.3 + - - +
95A LEU* 1.3 64.5 + - - +
96A THR 3.1 0.9 - - - -
97A ALA* 3.6 6.5 - - + +
98A ILE* 3.0 38.8 + - + +
94B LEU* 3.5 37.7 - - + -
91D GLU* 4.9 5.4 - - + -
94D LEU* 4.2 26.0 - - + -
95D LEU* 3.6 26.0 - - + -
98D ILE* 5.0 2.0 - - + +
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Residues in contact with LEU 95 (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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91A GLU* 2.9 34.2 + - + +
92A SER* 4.0 6.1 - - - +
94A LEU* 1.3 77.4 - - - +
96A THR* 1.3 58.8 + - - +
97A ALA 3.2 0.4 - - - -
98A ILE* 4.1 3.5 - - + +
99A LYS* 3.2 40.5 + - + +
93B THR* 3.7 31.4 - - + +
94B LEU* 4.0 13.2 - - + -
97B ALA* 3.5 32.1 - - + -
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Residues in contact with THR 96 (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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92A SER* 2.5 24.9 + - - -
93A THR* 3.6 9.5 - - - +
94A LEU 3.1 0.2 - - - -
95A LEU* 1.3 75.6 - - - +
97A ALA* 1.3 60.8 + - - +
99A LYS* 5.1 3.4 - - - +
100A SER* 4.6 9.7 - - - -
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Residues in contact with ALA 97 (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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93A THR 3.6 14.1 - - - +
94A LEU* 3.6 9.0 - - + +
95A LEU 3.2 0.6 + - - -
96A THR* 1.3 78.1 - - - +
98A ILE* 1.3 63.8 + - - +
99A LYS 3.7 1.6 - - - +
100A SER* 3.6 21.4 + - - +
101A LEU* 4.0 11.4 - - - +
95D LEU* 4.9 9.0 - - + -
98D ILE* 3.5 27.4 - - + +
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Residues in contact with ILE 98 (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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94A LEU* 3.0 26.1 + - + +
95A LEU* 4.1 6.5 - - - +
97A ALA* 1.3 76.0 - - - +
99A LYS* 1.3 67.5 + - - +
100A SER 3.1 1.2 + - - -
101A LEU* 3.3 12.1 - - + +
94B LEU* 4.1 22.7 - - + +
97B ALA* 3.7 34.3 - - + +
98B ILE* 3.7 28.9 - - + +
101B LEU* 3.1 31.7 - - + +
98D ILE* 4.6 15.0 - - + -
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Residues in contact with LYS 99 (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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95A LEU* 3.2 23.6 + - + +
96A THR* 5.1 2.2 - - - -
98A ILE* 1.3 81.8 - - + +
100A SER* 1.3 53.1 + - - +
101A LEU 2.6 15.1 + - - -
102A GLN 3.2 21.5 + - - +
97B ALA* 4.4 19.7 - - + +
100B SER* 3.6 28.3 + - - -
101B LEU* 4.9 9.6 - - + +
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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
------------------------------------------------------------
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