Contacts of the helix formed by residues 82 - 97 (chain A) in PDB entry 2N5T
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 ASP 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A MET* 3.2 12.4 + - - +
79A LEU* 3.0 32.6 + - + +
80A LEU 3.1 0.8 - - - -
81A GLU* 1.3 78.5 - - - +
83A GLU* 1.3 83.3 + - - +
84A GLU* 3.0 32.1 + - - +
85A LEU* 3.0 22.7 + - + +
86A GLU* 3.4 8.5 + - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLU 3.1 7.4 + - - +
82A ASP* 1.3 79.1 + - - +
84A GLU* 1.3 61.8 + - + +
85A LEU 3.3 0.2 - - - -
86A GLU* 3.5 27.7 + - - +
87A GLN* 3.3 32.5 + - + +
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Residues in contact with GLU 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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82A ASP* 3.0 22.6 + - - +
83A GLU* 1.3 83.1 - - + +
85A LEU* 1.3 60.0 + - + +
87A GLN* 4.1 4.3 - - - +
88A GLU* 3.0 45.1 + - + +
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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
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47A ARG* 4.6 8.7 - - - +
79A LEU* 2.9 42.2 - - + +
80A LEU* 3.4 24.9 - - + +
82A ASP* 3.0 13.9 + - + +
84A GLU* 1.3 77.6 - - + +
86A GLU* 1.3 58.4 + - - +
88A GLU* 4.4 2.5 - - - -
89A ILE* 2.8 36.5 + - + +
107A VAL* 3.1 32.8 - - + +
108A ILE* 4.9 13.5 - - + -
111A GLN* 6.0 2.2 - - + +
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Residues in contact with GLU 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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43A PHE* 5.3 7.4 - - + -
47A ARG* 4.8 12.0 - - - +
81A GLU 5.7 0.9 - - - +
82A ASP 3.4 6.8 + - - +
83A GLU* 3.5 25.1 - - - +
84A GLU 3.3 0.4 - - - -
85A LEU* 1.3 79.5 - - - +
87A GLN* 1.3 87.4 + - - +
89A ILE* 3.4 5.6 - - - +
90A ILE* 2.6 61.4 + - + +
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Residues in contact with GLN 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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83A GLU* 3.3 26.1 + - + +
84A GLU* 4.1 4.7 - - - +
85A LEU 3.3 0.4 - - - -
86A GLU* 1.3 101.8 + - - +
88A GLU* 1.3 62.6 + - + +
90A ILE* 2.9 18.9 - - - +
91A ALA* 2.8 30.7 + - - +
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Residues in contact with GLU 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 GLU* 3.0 39.5 + - + +
85A LEU* 4.0 3.4 - - + +
87A GLN* 1.3 78.2 - - + +
89A ILE* 1.3 65.6 + - - +
91A ALA* 3.9 7.6 - - - +
92A LEU* 3.3 37.1 + - - +
107A VAL* 4.2 19.1 - - + -
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Residues in contact with ILE 89 (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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43A PHE* 4.1 34.5 - - + -
47A ARG* 5.7 2.5 - - - +
85A LEU* 2.8 24.4 + - + +
86A GLU 3.4 7.4 - - - +
88A GLU* 1.3 76.1 - - - +
90A ILE* 1.3 87.0 + - + +
92A LEU* 3.6 3.0 + - - +
93A ILE* 3.4 38.9 + - + +
100A ALA* 4.4 2.7 - - - +
103A ALA* 4.0 2.2 - - + -
104A ALA* 3.7 43.5 - - + +
107A VAL* 4.2 11.6 - - + +
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Residues in contact with ILE 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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40A VAL* 4.5 23.6 - - + -
43A PHE* 4.8 6.1 - - + -
86A GLU* 2.6 44.2 - - + +
87A GLN* 2.9 32.1 - - - +
89A ILE* 1.3 91.1 - - + +
91A ALA* 1.3 78.7 + - + +
93A ILE* 3.3 8.0 + - + +
94A LYS* 2.8 56.8 + - + +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A GLN 2.8 20.8 + - - +
88A GLU* 3.9 11.0 - - - +
89A ILE 3.3 0.2 - - - -
90A ILE* 1.3 85.9 - - + +
92A LEU* 1.3 55.1 + - + +
94A LYS* 4.5 3.4 - - - -
95A ASP* 2.4 43.3 + - + +
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Residues in contact with LEU 92 (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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88A GLU* 3.3 24.7 + - - +
89A ILE 4.0 2.9 - - - +
90A ILE 3.3 0.4 - - - -
91A ALA* 1.3 78.2 - - + +
93A ILE* 1.3 58.5 + - - +
95A ASP* 4.5 1.1 - - + -
96A LYS* 2.5 74.6 + - + +
97A HIS 3.2 0.9 + - - -
98A MET* 3.8 7.7 + - - -
103A ALA* 4.2 17.7 - - + +
106A GLU* 4.0 24.9 - - - +
107A VAL* 3.9 22.4 - - + -
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Residues in contact with ILE 93 (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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31A ILE* 3.6 24.9 - - + -
36A VAL* 3.9 8.3 - - + +
39A GLU* 4.2 5.8 - - + -
40A VAL* 4.2 32.3 - - + +
43A PHE* 5.1 3.1 - - + -
89A ILE* 3.4 33.9 - - + +
90A ILE* 3.3 7.3 + - + +
91A ALA 3.3 0.2 - - - -
92A LEU* 1.3 76.6 - - - +
94A LYS* 1.3 60.1 + - - +
97A HIS* 2.9 29.6 + - - -
98A MET 3.6 13.7 - - - +
99A THR 4.2 0.4 - - - +
100A ALA* 3.9 19.5 - - + -
103A ALA* 3.7 16.2 - - + -
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Residues in contact with LYS 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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36A VAL* 3.8 25.3 - - + +
37A ASP* 5.3 5.8 - - - -
40A VAL* 4.5 20.6 - - + -
90A ILE* 2.8 39.8 + - + +
91A ALA* 3.8 3.4 - - - +
93A ILE* 1.3 79.1 - - - +
95A ASP* 1.3 56.6 + - - +
97A HIS* 3.0 23.6 + - - -
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Residues in contact with ASP 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 ALA* 2.4 37.0 + - + +
92A LEU* 4.5 2.5 - - + -
94A LYS* 1.3 72.8 - - - +
96A LYS* 1.3 72.8 + - + +
97A HIS* 3.6 9.0 + - - -
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Residues in contact with LYS 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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30A LYS* 3.3 23.7 + - - +
92A LEU* 2.5 51.9 + - + +
95A ASP* 1.3 86.2 + - - +
97A HIS* 1.3 71.9 + - - +
98A MET* 3.1 29.3 + - + -
106A GLU* 5.4 6.1 - - - +
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Residues in contact with HIS 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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30A LYS* 3.2 12.6 - - + -
31A ILE* 2.8 47.5 + - + +
32A SER 5.9 0.4 - - - -
33A ALA* 5.7 9.6 + - + +
36A VAL* 3.8 16.4 - - + +
92A LEU 3.2 0.2 + - - -
93A ILE 2.9 17.4 + - - -
94A LYS 3.0 28.0 + - - -
95A ASP 4.0 7.2 + - - -
96A LYS* 1.3 80.7 - - - +
98A MET* 1.3 60.3 + - - +
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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