Contacts of the helix formed by residues 41 - 59 (chain B) in PDB entry 1BO1
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 PRO 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B SER 3.8 6.5 - - - +
40B GLU* 1.3 83.6 - - + +
42B ILE* 1.3 57.7 + - - +
44B SER* 3.3 8.7 + - - +
45B VAL* 3.0 32.2 + - - +
88B ASN 5.2 2.7 - - - +
90B PRO* 3.8 21.4 - - + +
191B VAL* 4.4 12.6 - - + -
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Residues in contact with ILE 42 (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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40B GLU* 3.0 25.5 - - + +
41B PRO* 1.3 78.6 - - - +
43B LEU* 1.3 73.6 + - + +
45B VAL* 3.1 1.6 + - - +
46B LEU* 2.9 25.3 + - - +
138B ARG* 4.5 7.9 - - - +
189B LEU* 3.4 22.1 - - + +
191B VAL* 4.3 18.0 - - + +
196B THR* 3.4 43.5 - - + +
198B MET* 3.7 15.3 - - + -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA* 3.5 21.8 - - + -
39B SER* 4.6 9.0 - - - +
40B GLU* 2.9 29.8 + - + +
42B ILE* 1.3 94.0 - - + +
44B SER* 1.3 57.6 + - - +
46B LEU* 3.6 7.5 + - + +
47B MET* 3.0 32.9 + - - +
125B ALA* 5.3 0.9 - - + -
126B PRO* 3.4 38.0 - - + +
128B ASN* 5.2 2.9 - - - +
138B ARG* 5.7 1.1 - - - +
140B LEU* 3.3 30.5 - - + -
198B MET* 4.9 8.1 - - + -
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 2.9 24.6 - - - +
38B ALA* 2.9 31.0 + - - +
39B SER 5.0 0.2 + - - -
40B GLU 3.2 6.1 + - - -
41B PRO* 3.6 9.3 - - - +
42B ILE 3.1 0.4 - - - -
43B LEU* 1.3 77.6 - - - +
45B VAL* 1.3 60.2 + - - +
46B LEU 3.1 0.4 - - - -
47B MET* 3.6 0.6 + - - -
48B TRP* 3.0 28.9 + - - +
88B ASN 3.2 19.9 + - - -
89B LEU* 3.4 11.6 - - - +
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Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO 3.0 20.2 + - - +
42B ILE* 3.1 6.3 + - - +
44B SER* 1.3 76.2 - - - +
46B LEU* 1.3 57.9 + - - +
48B TRP* 3.8 5.9 - - - +
49B GLY* 2.9 24.3 + - - -
89B LEU* 4.6 0.7 - - + -
90B PRO* 3.6 18.6 - - + -
93B PHE* 3.6 47.3 - - + -
94B LYS 4.0 14.6 - - - +
95B PHE* 3.6 8.0 - - + -
189B LEU* 3.7 16.2 - - + -
191B VAL* 4.2 8.5 - - + -
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE 2.9 15.7 + - - +
43B LEU* 3.7 11.7 - - + +
44B SER 3.1 0.2 - - - -
45B VAL* 1.3 74.5 - - - +
47B MET* 1.3 60.7 + - + +
49B GLY* 2.8 3.5 + - - -
50B VAL* 2.8 48.3 + - + +
95B PHE* 4.1 11.7 - - + -
121B VAL* 4.3 9.6 - - + -
126B PRO* 4.8 8.5 - - + -
140B LEU* 5.2 0.4 - - + -
149B ILE* 3.4 35.2 - - + -
187B TYR* 4.4 13.5 - - + -
189B LEU* 3.3 12.1 - - + +
198B MET* 3.9 26.9 - - + -
200B VAL* 5.4 0.9 - - + -
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Residues in contact with MET 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE 4.4 13.5 - - - +
37B ARG* 3.4 17.3 - - - +
38B ALA* 3.9 17.5 - - - -
43B LEU 3.0 19.9 + - - +
44B SER 4.0 2.5 - - - +
46B LEU* 1.3 76.0 - - + +
48B TRP* 1.3 61.6 + - - +
51B ASN* 3.1 10.7 + - - +
121B VAL* 3.2 27.6 - - + +
122B THR* 3.1 51.8 - - + +
123B ARG 5.0 0.2 - - - +
124B SER* 3.8 1.1 - - - -
125B ALA* 3.5 37.7 - - + +
126B PRO* 3.9 7.0 - - + -
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Residues in contact with TRP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A HIS* 4.2 20.0 - + - -
56A GLU* 2.8 26.6 + - - -
37B ARG* 3.2 20.8 - - - +
44B SER 3.0 20.3 + - - +
45B VAL* 3.8 6.5 - - - +
47B MET* 1.3 77.8 - - - +
49B GLY* 1.3 66.0 + - - +
51B ASN* 3.6 2.4 - - - +
52B HIS* 2.9 52.1 + + + +
77B ILE* 3.9 15.0 - - + -
79B VAL* 3.8 25.7 - - + +
89B LEU* 3.2 34.2 - - + +
93B PHE* 3.8 21.0 - + - -
95B PHE* 4.2 15.3 - - + -
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Residues in contact with GLY 49 (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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45B VAL 2.9 8.9 + - - -
46B LEU 2.8 8.9 + - - -
48B TRP* 1.3 86.0 - - - +
50B VAL* 1.3 52.3 + - - -
51B ASN 3.0 1.8 - - - -
52B HIS* 3.8 0.2 - - - +
53B THR* 2.7 41.6 + - - +
95B PHE* 3.3 27.8 - - - -
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Residues in contact with VAL 50 (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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46B LEU* 2.8 36.6 + - + +
47B MET 4.5 0.4 - - - +
49B GLY* 1.3 72.1 - - - -
51B ASN* 1.3 58.2 + - - +
53B THR* 3.4 7.4 - - - -
54B ILE* 3.1 31.0 + - + +
95B PHE* 3.8 0.4 - - + -
117B TYR* 3.8 27.8 - - + +
118B GLN* 4.2 8.8 + - - +
121B VAL* 3.8 32.1 - - + -
122B THR* 5.0 0.4 - - + -
187B TYR* 3.5 27.4 - - + +
200B VAL* 5.4 0.9 - - + -
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Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASN* 5.0 9.1 + - - -
37B ARG* 4.4 10.2 + - - +
47B MET 3.1 19.8 + - - +
48B TRP* 3.6 5.8 - - - +
49B GLY 3.0 0.4 - - - -
50B VAL* 1.3 77.8 - - - +
52B HIS* 1.3 60.7 + - - +
55B ASN* 3.0 37.4 + - - +
118B GLN* 3.0 39.8 + - - +
122B THR* 3.4 24.1 + - + +
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Residues in contact with HIS 52 (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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48A TRP* 4.3 12.3 - + - -
52A HIS* 3.6 36.1 + + - -
56A GLU* 5.2 0.4 + - - -
79A VAL* 6.0 0.2 - - - +
48B TRP* 2.9 38.9 + + + +
49B GLY* 3.8 2.2 - - - +
51B ASN* 1.3 79.1 + - - +
53B THR* 1.3 63.1 + - + +
55B ASN* 3.5 4.5 + - - +
56B GLU* 2.8 61.2 + - + +
77B ILE* 3.8 38.6 - - + +
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Residues in contact with THR 53 (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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84A PHE* 5.9 0.2 - - - -
49B GLY 2.7 29.1 + - - +
50B VAL* 3.4 10.7 + - - -
52B HIS* 1.3 71.2 - - + +
54B ILE* 1.3 64.7 + - - +
56B GLU* 3.5 7.2 - - - +
57B LEU* 2.8 33.4 + - - +
75B SER* 4.3 6.5 - - - +
77B ILE* 4.5 9.4 - - + -
95B PHE* 3.6 24.0 - - + -
97B GLU* 3.4 33.3 + - + +
187B TYR* 4.2 7.8 - - - -
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Residues in contact with ILE 54 (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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50B VAL* 3.1 24.9 + - + +
53B THR* 1.3 84.1 + - - +
55B ASN* 1.3 66.2 + - - +
57B LEU* 3.1 9.1 + - + +
58B SER* 3.0 19.9 + - - -
97B GLU* 5.5 1.1 - - - +
107B ARG* 3.8 13.5 - - - +
114B ASP* 3.7 35.7 - - + +
115B GLN* 5.2 0.4 - - - -
117B TYR* 3.4 35.7 - - + -
118B GLN* 3.1 41.1 - - + +
187B TYR* 4.5 3.1 - - - +
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Residues in contact with ASN 55 (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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51B ASN* 3.0 36.6 + - - +
52B HIS* 3.9 4.6 - - - +
54B ILE* 1.3 75.3 - - - +
56B GLU* 1.3 57.6 + - - +
58B SER* 2.7 39.3 + - - +
59B ASN* 3.7 7.5 + - - -
118B GLN* 2.9 26.0 + - - +
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Residues in contact with GLU 56 (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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37A ARG* 5.9 0.3 + - - -
48A TRP* 2.9 34.3 + - - -
52A HIS* 5.2 0.3 + - - -
84A PHE* 5.1 10.1 - - + -
85A ASN* 4.2 18.4 - - - +
89A LEU* 4.9 0.7 - - - +
52B HIS* 2.8 50.4 + - + +
53B THR* 3.5 9.2 - - - +
55B ASN* 1.3 76.6 - - - +
57B LEU* 1.3 62.0 + - + +
58B SER 3.3 0.3 + - - -
59B ASN* 3.4 18.5 + - - +
60B VAL* 3.3 14.1 + - - +
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Residues in contact with LEU 57 (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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84A PHE* 4.0 23.1 - - + -
53B THR 2.8 21.5 + - - +
54B ILE* 3.4 8.1 - - + +
55B ASN 3.1 0.4 - - - -
56B GLU* 1.3 73.2 - - - +
58B SER* 1.3 56.6 + - - +
59B ASN 3.0 11.0 + - - -
60B VAL* 3.0 39.7 + - + +
97B GLU* 4.3 10.8 - - - +
100B PRO* 4.1 11.7 - - + +
101B MET* 4.1 5.8 - - - -
104B ARG* 3.2 58.3 + - + +
107B ARG* 4.1 16.6 - - - +
114B ASP* 4.4 4.9 - - - +
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Residues in contact with SER 58 (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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34A LYS* 3.2 29.9 + - - +
54B ILE* 3.0 10.3 + - - -
55B ASN* 2.7 29.1 + - - +
57B LEU* 1.3 70.4 - - - +
59B ASN* 1.3 66.0 + - - +
104B ARG* 5.2 1.1 - - - +
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Residues in contact with ASN 59 (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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34A LYS* 3.1 29.9 + - - +
35A LEU* 3.0 44.0 + - - +
36A PHE* 4.2 5.5 - - - -
37A ARG* 4.2 12.1 - - - +
51A ASN* 4.8 8.9 + - - -
85A ASN* 6.1 0.2 - - - -
55B ASN 3.9 12.5 + - - -
56B GLU* 3.4 14.4 + - - +
57B LEU 3.0 0.4 - - - -
58B SER* 1.3 84.6 + - - +
60B VAL* 1.3 59.5 + - - +
61B PRO* 3.2 12.0 - - - +
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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
------------------------------------------------------------
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