Contacts of the helix formed by residues 81 - 97 (chain B) in PDB entry 2GTL
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 GLN 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B SER 4.2 3.4 + - - -
78B THR* 3.0 17.2 + - - +
80B ASP* 1.3 103.7 + - - +
82B PRO* 1.3 71.6 - - - +
83B ALA* 2.8 6.2 + - + -
84B THR* 2.9 29.9 + - - +
85B LEU 3.0 9.2 + - - -
29C SER* 3.7 25.7 + - - -
30C LYS* 3.9 25.9 + - - +
33C ILE* 4.3 14.0 - - - +
68C SER* 5.8 0.2 - - - -
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Residues in contact with PRO 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B THR 4.2 0.2 - - - -
79B LEU 4.9 4.6 - - - +
80B ASP* 3.7 7.2 - - - +
81B GLN* 1.3 87.2 - - - +
83B ALA* 1.3 66.1 + - + +
85B LEU* 4.4 11.2 - - + -
86B LYS* 2.9 28.2 + - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLN* 2.8 6.8 + - + +
82B PRO* 1.3 82.9 - - + +
84B THR* 1.3 62.8 + - - +
86B LYS* 3.2 15.8 - - - +
87B GLU* 3.6 6.8 + - - +
65C PRO* 3.5 29.6 - - + +
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE* 6.2 0.7 - - + -
78B THR* 4.7 14.1 - - + -
81B GLN* 2.9 31.4 + - - +
83B ALA* 1.3 72.4 - - - +
85B LEU* 1.3 69.1 + - - +
87B GLU* 2.7 17.0 + - - +
88B GLU* 3.1 10.1 + - + +
33C ILE* 5.1 4.3 - - + -
65C PRO* 3.4 21.5 - - - +
68C SER* 4.0 10.9 - - - -
69C ALA* 3.6 35.2 - - + +
72C LEU* 5.1 0.9 - - + -
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ALA* 3.6 32.8 - - + +
78B THR* 3.4 28.5 + - - +
79B LEU* 3.9 26.9 - - + -
81B GLN 3.0 7.0 + - - +
82B PRO* 3.9 8.5 - - + +
84B THR* 1.3 76.7 - - - +
86B LYS* 1.3 67.6 + - - +
88B GLU* 2.9 7.1 + - + +
89B LEU* 2.8 59.3 + - + +
136B HIS* 4.2 17.9 - - + +
137B ILE* 5.1 0.9 - - + -
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PRO 2.9 21.7 + - - +
83B ALA* 3.2 9.2 - - - +
85B LEU* 1.3 77.0 - - - +
87B GLU* 1.3 67.0 + - - +
89B LEU* 3.4 7.3 + - - +
90B ASP* 2.9 60.3 + - - +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA 3.6 9.0 + - - +
84B THR 2.7 17.0 + - - +
86B LYS* 1.3 79.4 - - - +
88B GLU* 1.3 61.1 + - - +
90B ASP* 3.0 13.6 + - - +
91B HIS* 2.7 30.4 + - - +
65C PRO* 4.4 7.5 - - - +
66C LYS* 2.9 64.1 + - + +
69C ALA* 4.1 10.5 - - + -
73C ARG* 5.3 2.2 - - - +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLY* 4.3 4.2 - - - -
74B ILE* 3.6 43.6 - - + +
75B ALA* 4.3 10.5 - - + +
78B THR* 6.4 0.2 - - + -
84B THR* 3.1 6.4 + - + +
85B LEU* 2.9 15.6 + - + +
87B GLU* 1.3 74.6 - - - +
89B LEU* 1.3 64.8 + - - +
91B HIS* 3.0 10.3 + - - +
92B LEU* 2.9 55.3 + - + +
95B GLN* 5.4 0.2 + - - -
69C ALA* 4.3 8.7 - - + +
73C ARG* 3.0 32.7 + - - +
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA* 4.3 5.6 - - + -
85B LEU* 2.8 51.1 + - + +
86B LYS* 3.6 9.4 - - - +
88B GLU* 1.3 72.7 - - - +
90B ASP* 1.3 53.5 + - - +
92B LEU* 3.0 11.2 + - + +
93B GLN* 2.7 34.3 + - - +
136B HIS* 4.5 14.6 - - + +
137B ILE* 3.3 44.2 - - + +
140B GLY* 3.6 25.2 - - - +
141B ILE* 4.1 7.6 - - + -
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LYS* 2.9 48.4 + - - +
87B GLU* 3.4 18.6 - - - +
89B LEU* 1.3 76.1 - - - +
91B HIS* 1.3 65.5 + - - +
93B GLN* 3.1 37.2 + - - +
94B VAL* 3.2 12.9 + - + +
140B GLY 4.7 1.6 - - - +
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Residues in contact with HIS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLU 2.7 16.1 + - - +
88B GLU* 3.2 14.5 + - - +
90B ASP* 1.3 72.9 - - - +
92B LEU* 1.3 64.6 + - - +
94B VAL* 3.1 22.3 + - + +
95B GLN* 3.4 22.9 + - + +
56C ARG* 4.9 20.3 + - - +
73C ARG* 3.1 50.1 + - + +
160C HEM 3.4 39.7 + - - -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLY* 4.8 9.4 - - - +
75B ALA* 5.3 2.9 - - + -
88B GLU* 2.9 40.4 + - + +
89B LEU* 3.3 14.4 - - + +
91B HIS* 1.3 72.7 - - - +
93B GLN* 1.3 70.2 + - - +
95B GLN* 2.7 36.3 + - - +
96B HIS* 3.1 18.8 + - + +
141B ILE* 3.6 34.5 - - + -
160B HEM 3.9 39.7 - - + -
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Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU 2.7 15.4 + - - +
90B ASP* 3.1 28.5 + - - +
92B LEU* 1.3 72.4 - - - +
94B VAL* 1.3 61.3 + - - +
96B HIS* 3.2 2.1 + - - +
97B GLU* 2.8 37.9 + - + +
140B GLY* 3.6 17.7 + - - +
141B ILE* 3.4 27.6 - - - +
142B LYS 4.6 5.6 - - - +
143B GLY* 4.0 20.4 - - - -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP 3.4 14.8 - - - +
91B HIS* 3.3 12.1 - - + +
92B LEU 2.8 4.0 + - - -
93B GLN* 1.3 73.5 - - + +
95B GLN* 1.3 56.8 + - + +
96B HIS 2.7 15.2 + - - -
97B GLU* 3.3 38.1 + - + +
56C ARG* 6.2 1.8 - - - +
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLU* 5.4 0.4 + - - -
91B HIS* 3.4 38.0 + - + +
92B LEU* 2.7 34.8 + - - +
94B VAL* 1.3 73.9 - - + +
96B HIS* 1.3 65.0 + - - +
97B GLU 4.7 1.0 - - - +
99B ARG* 2.9 29.3 + - - +
160B HEM 3.5 41.4 + - + +
101C GLN* 4.9 1.2 + - - -
160C HEM 4.2 16.6 + - - +
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Residues in contact with HIS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 3.1 19.1 + - + +
93B GLN 3.7 6.1 - - - +
94B VAL 2.7 3.4 + - - -
95B GLN* 1.3 85.4 - - + +
97B GLU* 1.3 67.4 + - - +
99B ARG* 3.1 29.3 + - - +
101B ILE* 3.7 19.2 - - + +
106B PHE* 4.8 3.1 - + + -
141B ILE* 4.1 20.7 - - + +
160B HEM 2.0 94.9 + + + -
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B GLN* 2.8 26.0 + - + +
94B VAL* 3.4 34.5 - - + +
95B GLN 4.7 0.9 - - - +
96B HIS* 1.3 75.8 - - - +
98B GLY* 1.3 59.2 + - - +
99B ARG* 3.6 3.0 + - - +
141B ILE 5.5 0.4 + - - -
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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