Contacts of the helix formed by residues 70 - 84 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68D THR* 2.6 21.0 + - - -
69D SER* 1.3 76.0 - - - +
71D ASN* 1.3 55.4 + - - +
73D GLY* 2.5 29.3 + - - -
74D ILE* 3.3 7.2 + - - +
103D MET* 3.4 10.9 - - - +
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Residues in contact with ASN 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D SER* 3.2 28.7 + - - +
41D LYS* 4.1 4.9 - - + +
69D SER* 4.5 1.9 + - - +
70D GLY* 1.3 73.1 - - - +
72D THR* 1.3 56.5 + - - +
74D ILE* 3.3 14.4 + - - +
75D ALA* 2.8 31.9 + - - +
281D ASP* 3.0 27.3 + - - +
285D ARG* 3.7 19.7 + - - +
286D TYR* 5.2 2.9 + - - -
320D PLP 3.8 26.1 + - + +
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Residues in contact with THR 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LYS* 3.4 23.7 - - + +
45D ALA* 6.1 0.9 - - + -
48D MET* 5.8 3.6 - - + -
66D GLU* 4.9 1.1 - - + -
67D ALA 4.5 1.8 - - - +
68D THR* 2.8 16.5 + - - -
69D SER* 3.1 17.3 + - - -
71D ASN* 1.3 75.2 - - - +
73D GLY* 1.3 66.8 + - - +
75D ALA* 4.4 4.9 - - + -
76D LEU* 3.3 38.8 + - + +
89D LEU* 5.0 0.6 - - - +
140D GLN* 3.5 35.6 + - + +
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Residues in contact with GLY 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D THR* 2.5 23.2 + - - -
70D GLY 2.5 10.8 + - - -
72D THR* 1.3 73.9 - - - +
74D ILE* 1.3 61.3 + - - -
76D LEU* 4.0 1.6 - - - +
77D ALA* 3.3 21.5 + - - +
89D LEU* 4.1 12.0 - - - +
103D MET* 3.3 24.2 - - - +
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Residues in contact with ILE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C PHE* 6.3 0.7 - - + -
37D ALA* 3.8 23.6 - - + +
70D GLY 3.3 8.6 + - - +
71D ASN* 3.3 16.3 + - - +
73D GLY* 1.3 74.3 - - - +
75D ALA* 1.3 64.7 + - - +
77D ALA* 3.4 3.7 + - - +
78D MET* 3.2 21.8 + - - +
98D GLU* 4.9 1.1 - - - +
102D ALA* 3.6 35.9 - - + +
103D MET* 3.6 7.7 - - - +
106D TYR* 3.8 23.6 - - + +
285D ARG* 3.1 40.6 - - - +
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ALA* 4.5 4.5 - - - -
39D SER* 4.7 0.7 - - - +
41D LYS* 3.5 37.5 - - + +
42D ASP* 3.9 17.5 - - - +
45D ALA* 3.9 5.6 - - + -
71D ASN 2.8 21.5 + - - +
72D THR* 4.3 3.6 - - - +
74D ILE* 1.3 75.2 - - - +
76D LEU* 1.3 63.5 + - - +
78D MET* 3.5 4.9 + - - +
79D ILE* 3.2 23.4 + - - +
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ALA* 3.4 28.9 - - + -
48D MET* 5.3 6.1 - - + -
49D ILE* 3.8 19.0 - - + +
66D GLU* 3.3 42.6 - - + -
72D THR* 3.3 26.3 + - + +
73D GLY 4.0 1.8 - - - +
74D ILE 3.3 0.6 - - - -
75D ALA* 1.3 78.4 - - - +
77D ALA* 1.3 52.1 + - - +
79D ILE* 2.7 10.9 + - - +
80D ALA* 2.7 33.4 + - - +
87D MET* 3.7 23.4 - - + +
89D LEU* 4.6 2.0 - - + -
138D LEU* 3.5 14.4 - - + -
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Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D GLY 3.3 15.0 + - - +
74D ILE* 3.4 4.2 + - - +
76D LEU* 1.3 78.4 - - - +
78D MET* 1.3 57.2 + - - +
80D ALA* 3.3 9.8 + - - +
81D ALA* 2.8 28.9 + - - +
87D MET* 4.6 3.7 - - - +
103D MET 4.0 4.0 - - - +
106D TYR* 3.3 30.0 - - + +
108D ALA* 3.7 26.2 - - + +
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Residues in contact with MET 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C GLY 3.9 2.5 - - - +
4D LEU* 3.7 17.9 - - + -
5D GLU* 5.9 0.9 - - - -
8D ILE* 4.4 8.1 - - + -
36D PRO* 3.3 15.7 - - + -
37D ALA* 3.3 19.5 - - + +
42D ASP* 3.2 32.1 - - - +
74D ILE 3.2 7.4 + - - +
75D ALA 3.6 7.6 - - - +
76D LEU 3.2 0.4 - - - -
77D ALA* 1.3 77.8 - - - +
79D ILE* 1.3 69.2 + - + +
81D ALA* 2.7 21.9 + - - +
82D LEU* 2.8 44.9 + - + +
106D TYR* 3.3 34.3 - - + +
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Residues in contact with ILE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLU* 5.2 4.9 - - + -
8D ILE* 4.2 11.9 - - + -
42D ASP* 4.5 2.2 - - - +
45D ALA* 3.9 21.3 - - + +
46D LEU* 4.1 35.2 - - + +
49D ILE* 3.9 28.7 - - + -
50D VAL* 5.9 1.3 - - + -
75D ALA 3.2 16.2 - - - +
76D LEU* 2.7 11.9 + - - +
78D MET* 1.3 89.5 - - + +
80D ALA* 1.3 62.5 + - - +
82D LEU* 3.3 6.9 + - + +
83D LYS* 3.1 34.8 + - + +
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Residues in contact with ALA 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ILE* 5.0 1.0 - - - +
64D LEU* 5.0 1.1 - - + -
76D LEU 2.7 15.1 + - - +
77D ALA* 3.6 11.4 - - - +
79D ILE* 1.3 73.6 - - - +
81D ALA* 1.3 53.0 + - - +
84D GLY* 2.5 28.4 + - - -
85D TYR* 2.8 46.8 + - + +
87D MET* 4.1 21.3 - - + -
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG* 2.7 31.5 + - - -
245C ALA 3.7 3.4 - - - +
246C VAL 2.9 24.6 - - - +
247C ARG 3.4 3.8 - - - +
249C GLY* 3.7 17.0 - - - -
77D ALA 2.8 11.4 + - - +
78D MET* 2.7 17.0 + - - +
80D ALA* 1.3 69.0 - - - +
82D LEU* 1.3 56.0 + - - +
83D LYS 3.0 2.8 + - - -
84D GLY* 3.5 4.3 + - - -
106D TYR* 4.2 9.6 - - + +
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG* 2.6 25.7 + - - +
248C GLU* 2.7 30.1 - - - +
249C GLY* 4.4 0.9 - - - -
3D THR* 6.2 1.8 - - + -
4D LEU* 3.3 32.5 - - + +
5D GLU* 2.8 33.6 - - + +
78D MET* 2.8 61.0 + - + +
79D ILE* 3.7 7.6 - - - +
81D ALA* 1.3 76.6 - - - +
83D LYS* 1.3 58.6 + - - +
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Residues in contact with LYS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG* 4.4 3.6 - - - +
5D GLU* 3.0 42.0 - - + +
46D LEU* 5.5 2.0 - - - -
49D ILE* 6.5 0.2 - - + -
50D VAL* 4.2 23.4 - - - +
53D GLU* 4.5 13.6 + - - +
60D PRO* 4.9 9.4 - - - +
79D ILE* 3.1 22.6 + - + +
80D ALA 3.6 0.7 - - - -
82D LEU* 1.3 77.9 - - + +
84D GLY* 1.3 63.9 + - - +
85D TYR* 3.5 24.0 + - + -
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Residues in contact with GLY 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ARG* 4.7 4.5 - - - +
60D PRO 5.1 0.2 - - - -
61D GLY* 4.1 16.6 - - - +
80D ALA 2.5 17.7 + - - -
81D ALA* 3.5 7.1 + - - -
83D LYS* 1.3 76.3 - - - +
85D TYR* 1.3 62.0 + - - -
86D ARG* 4.9 9.5 + - - -
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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