Contacts of the helix formed by residues 70 - 84 (chain A) in PDB entry 2BHT
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 GLY 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A THR* 3.0 7.9 + - - -
69A SER* 1.3 80.5 + - - +
71A ASN* 1.3 54.1 + - - +
72A THR 3.4 1.6 - - - -
73A GLY* 2.8 4.3 + - - -
74A ILE* 2.5 41.0 + - - +
91A MET* 3.7 0.2 - - - -
99A ARG* 3.6 16.6 - - - -
103A MET* 3.6 16.7 - - - +
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Residues in contact with ASN 71 (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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39A SER* 3.4 25.1 + - - +
40A VAL* 5.3 0.2 - - - +
41A LYS* 3.3 19.5 - - + +
69A SER* 3.9 2.2 + - - +
70A GLY* 1.3 74.0 - - - +
72A THR* 1.3 52.2 + - - +
74A ILE* 3.0 8.5 + - - +
75A ALA* 2.6 35.9 + - - +
99A ARG* 4.1 11.9 + - - +
280A CYS* 5.0 0.4 + - - +
281A ASP* 3.5 14.9 + - - +
285A ARG* 3.5 23.4 + - - -
320A PLP 3.1 42.5 + - - +
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Residues in contact with THR 72 (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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41A LYS* 3.3 38.5 + - + +
44A ALA* 5.4 6.7 - - + -
45A ALA* 5.8 1.6 - - + +
48A MET* 5.7 3.4 - - + -
66A GLU* 6.1 0.2 - - - -
68A THR* 3.0 15.5 + - - -
69A SER* 4.6 3.6 + - - -
71A ASN* 1.3 76.3 - - - +
73A GLY* 1.3 61.0 + - - +
75A ALA* 3.8 6.1 - - + -
76A LEU* 2.9 42.2 + - + +
140A GLN* 3.5 39.8 + - + +
146A ASN* 5.7 2.0 - - - +
175A THR* 5.8 0.2 - - - +
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Residues in contact with GLY 73 (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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68A THR* 2.5 26.0 + - - -
70A GLY 2.8 6.6 + - - -
72A THR* 1.3 75.2 - - - +
74A ILE* 1.3 62.5 + - - -
75A ALA 3.1 0.2 + - - -
76A LEU* 4.1 0.5 - - - +
77A ALA* 3.1 21.5 + - - +
89A LEU* 3.8 13.6 - - - +
103A MET* 3.6 23.0 - - - +
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Residues in contact with ILE 74 (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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37A ALA* 3.8 25.1 - - + +
70A GLY 2.5 26.3 + - - +
71A ASN* 3.6 8.5 - - - +
73A GLY* 1.3 71.2 - - - -
75A ALA* 1.3 63.6 + - - +
77A ALA* 3.7 4.6 - - - +
78A MET* 3.3 18.7 + - - +
99A ARG* 4.3 15.7 - - + +
102A ALA* 3.6 22.2 - - + -
103A MET* 3.7 16.1 - - + +
106A TYR* 4.0 20.9 - - + -
285A ARG* 3.5 39.9 - - - +
251B PHE* 6.4 0.2 - - + -
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 4.3 0.4 - - - -
39A SER* 5.2 0.2 - - - +
41A LYS* 3.7 13.7 - - + +
42A ASP* 3.4 24.2 - - - +
45A ALA* 3.7 18.6 - - + -
71A ASN 2.6 19.7 + - - +
72A THR* 3.3 9.9 - - - +
74A ILE* 1.3 72.9 - - - +
76A LEU* 1.3 64.0 + - - +
78A MET* 3.0 21.3 + - - +
79A ILE* 3.3 13.7 + - - +
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Residues in contact with LEU 76 (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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45A ALA* 3.6 25.8 - - + +
48A MET* 3.8 24.2 - - + -
49A ILE* 4.5 14.4 - - + +
64A LEU* 6.0 2.0 - - + -
66A GLU* 3.3 38.6 - - + -
72A THR* 2.9 37.3 + - + +
73A GLY 4.3 0.2 - - - +
75A ALA* 1.3 68.5 - - - +
77A ALA* 1.3 65.8 + - - +
79A ILE* 4.5 4.0 - - - -
80A ALA* 3.1 27.0 + - - +
87A MET* 3.5 20.3 - - + +
89A LEU* 4.1 8.7 - - + -
138A LEU* 5.6 2.9 - - + -
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Residues in contact with ALA 77 (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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73A GLY 3.1 18.0 + - - +
74A ILE* 3.7 7.9 - - - +
76A LEU* 1.3 77.9 - - - +
78A MET* 1.3 61.5 + - - +
80A ALA* 3.4 2.9 - - - +
81A ALA* 3.1 21.7 + - - +
87A MET* 4.2 11.0 - - - +
89A LEU* 5.4 0.2 - - - +
103A MET* 4.3 5.8 - - + +
106A TYR* 3.6 29.8 - - + +
108A ALA* 4.0 20.0 - - + -
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Residues in contact with MET 78 (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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4A LEU* 3.6 14.4 - - - -
8A ILE* 4.7 3.8 - - + -
36A PRO* 4.2 13.2 - - + -
37A ALA* 3.0 28.9 - - + +
42A ASP* 3.2 19.1 - - + +
74A ILE 3.3 8.8 + - - +
75A ALA 3.0 10.6 + - - +
77A ALA* 1.3 78.1 - - - +
79A ILE* 1.3 69.0 + - + +
81A ALA* 2.8 23.7 + - - +
82A LEU* 3.1 35.6 + - + +
106A TYR* 3.7 37.0 - - + +
249B GLY 3.9 9.6 - - - +
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Residues in contact with ILE 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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5A GLU* 5.0 1.1 - - + -
8A ILE* 5.0 5.8 - - + -
42A ASP* 4.1 7.2 - - + +
45A ALA* 3.3 34.3 - - + -
46A LEU* 3.7 22.0 - - + +
49A ILE* 3.7 25.4 - - + -
75A ALA* 3.3 17.8 + - - +
76A LEU* 4.4 4.0 - - - +
78A MET* 1.3 93.3 - - + +
80A ALA* 1.3 63.5 + - - +
82A LEU* 2.9 27.2 + - + +
83A LYS* 2.9 39.2 + - + +
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Residues in contact with ALA 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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49A ILE* 6.0 0.4 - - - +
64A LEU* 6.1 0.4 - - + -
76A LEU 3.1 21.1 + - - +
77A ALA 3.4 4.5 - - - +
79A ILE* 1.3 77.4 - - - +
81A ALA* 1.3 54.8 + - - +
83A LYS 3.0 0.2 + - - -
84A GLY* 2.7 33.1 + - - -
85A TYR* 3.0 40.5 + - + +
87A MET* 3.5 21.5 - - + +
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Residues in contact with ALA 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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77A ALA 3.1 11.2 + - - +
78A MET* 2.8 15.7 + - - +
80A ALA* 1.3 73.1 - - - +
82A LEU* 1.3 61.3 + - - +
83A LYS 3.4 0.3 + - - -
84A GLY* 3.7 3.2 + - - -
85A TYR 4.5 2.2 + - - -
106A TYR* 4.3 7.9 - - + +
18B ARG* 3.4 16.8 + - - -
245B ALA 3.9 5.2 - - - +
246B VAL 3.4 24.7 - - - +
247B ARG 4.3 6.1 - - - +
248B GLU 5.0 0.2 - - - -
249B GLY* 3.9 21.1 - - - +
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Residues in contact with LEU 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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4A LEU* 3.5 27.1 - - + -
5A GLU* 3.3 37.7 - - + +
78A MET* 3.5 28.7 - - - +
79A ILE* 2.9 29.8 + - + +
81A ALA* 1.3 78.9 - - - +
83A LYS* 1.3 57.8 + - - +
17B GLN* 6.2 0.2 - - - +
18B ARG* 3.9 12.9 + - - +
248B GLU 3.1 28.5 - - - +
249B GLY* 4.3 1.8 - - - -
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Residues in contact with LYS 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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5A GLU* 3.6 22.3 + - - +
46A LEU* 3.9 11.0 - - - +
49A ILE* 3.3 22.7 - - + -
50A VAL* 3.0 31.1 - - - +
53A GLU* 3.8 8.3 + - - +
60A PRO* 3.8 17.8 - - + +
79A ILE* 2.9 30.3 + - + +
80A ALA 3.5 0.2 - - - -
82A LEU* 1.3 80.4 - - - +
84A GLY* 1.3 66.5 + - - +
85A TYR* 3.7 14.4 - - + -
18B ARG* 5.0 3.6 - - - +
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Residues in contact with GLY 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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60A PRO* 3.5 4.0 - - - +
61A GLY* 3.0 24.9 + - - -
80A ALA 2.7 8.6 + - - -
81A ALA* 3.7 5.3 + - - -
82A LEU 3.6 1.6 - - - -
83A LYS* 1.3 81.3 - - - +
85A TYR* 1.3 59.7 + - - -
18B ARG* 4.5 7.0 - - - +
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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