Contacts of the helix formed by residues 3 - 20 (chain B) in PDB entry 2BBM
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 ARG 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLU* 4.3 17.9 - - - +
109A MET* 6.0 0.2 - - - +
124A MET* 4.8 2.5 - - - +
144A MET* 6.3 0.7 - - - -
1B LYS* 3.3 28.3 + - - +
2B ARG* 1.3 120.5 - - - +
4B TRP* 1.3 58.1 + - - +
5B LYS* 2.7 31.3 + - + +
6B LYS* 3.7 34.3 + - + +
7B ASN* 4.2 4.9 + - - +
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Residues in contact with TRP 4 (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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92A PHE* 4.1 18.5 - + + -
100A ILE* 3.5 31.6 - - + -
105A LEU* 3.4 43.7 - - + -
109A MET* 5.2 5.6 - - + -
124A MET* 4.0 26.9 + - + +
125A ILE* 4.2 27.8 - - + -
128A ALA* 4.7 2.5 - - + +
136A VAL* 5.0 6.5 - - + -
141A PHE* 5.4 2.2 - + - -
144A MET* 3.8 28.7 - - + +
145A MET* 3.7 26.7 - - + -
2B ARG* 3.1 17.1 + - - +
3B ARG* 1.3 70.9 - - - +
5B LYS* 1.3 53.8 + - + +
7B ASN* 3.5 8.8 + - - +
8B PHE* 2.6 38.8 + - + +
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Residues in contact with LYS 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 3.4 30.0 + - - +
144A MET* 5.2 15.0 + - - -
145A MET* 4.9 22.8 + - + +
147A SER* 5.5 7.7 - - - -
3B ARG* 2.7 23.5 - - + +
4B TRP* 1.3 76.8 - - + +
6B LYS* 1.3 63.5 + - + +
7B ASN 2.9 1.1 - - - -
8B PHE* 2.6 10.1 + - + -
9B ILE* 2.5 48.4 + - + +
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Residues in contact with LYS 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 5.3 13.0 - - + +
14A GLU* 3.0 43.0 + - + +
15A ALA* 4.8 9.8 - - - +
18A LEU* 4.6 13.8 - - + +
1B LYS 4.1 21.9 + - - +
3B ARG* 3.8 36.6 + - + +
5B LYS* 1.3 75.9 - - + +
7B ASN* 1.3 55.9 + - - +
9B ILE* 4.4 9.6 - - - +
10B ALA* 2.9 31.0 + - - +
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Residues in contact with ASN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 5.2 5.1 - - - +
92A PHE* 4.1 18.2 - - + -
108A VAL* 5.7 1.6 - - - +
109A MET* 2.9 40.5 - - + +
112A LEU* 3.6 32.7 - - - +
116A LEU* 5.9 0.4 - - - +
3B ARG 4.2 2.3 + - - +
4B TRP* 3.5 15.8 - - - +
5B LYS 2.7 1.0 + - - -
6B LYS* 1.3 79.8 - - - +
8B PHE* 1.3 64.6 + - - +
10B ALA* 3.7 2.8 - - - +
11B VAL* 3.2 29.6 + - - +
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Residues in contact with PHE 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 4.0 35.9 - - + -
88A ALA* 3.6 31.4 - - + -
92A PHE* 4.2 15.0 - + + -
141A PHE* 4.7 12.6 - + + -
145A MET* 4.6 20.4 - - + -
4B TRP* 2.6 25.1 + - + +
5B LYS* 2.6 8.0 + - + +
7B ASN* 1.3 69.5 - - - +
9B ILE* 1.3 80.4 + - + +
11B VAL* 3.0 5.7 + - - +
12B SER* 2.6 50.2 + - - -
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Residues in contact with ILE 9 (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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11A GLU* 5.1 17.3 - - + +
12A PHE* 4.7 20.6 - - + -
15A ALA* 3.9 23.3 - - + -
68A PHE* 4.7 9.0 - - + -
72A MET* 4.7 21.0 - - + +
5B LYS* 2.5 35.7 + - + +
6B LYS* 4.2 2.7 - - - +
8B PHE* 1.3 88.0 - - + +
10B ALA* 1.3 59.2 + - - +
12B SER* 2.6 34.5 + - - -
13B ALA* 2.8 6.9 + - - +
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Residues in contact with ALA 10 (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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15A ALA* 4.8 11.2 - - + +
18A LEU* 4.9 12.3 - - + -
19A PHE* 3.3 30.4 - - + -
112A LEU* 5.7 3.8 - - + -
6B LYS 2.9 20.5 + - - +
7B ASN* 3.7 5.6 - - - +
9B ILE* 1.3 83.9 - - - +
11B VAL* 1.3 65.4 + - + +
13B ALA* 2.9 23.1 + - - +
14B ALA 3.3 0.3 + - - -
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Residues in contact with VAL 11 (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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19A PHE* 5.0 1.6 - - - -
39A LEU* 4.6 19.7 - - + -
88A ALA* 4.5 19.1 - - + -
91A VAL* 4.6 19.3 - - + -
92A PHE* 3.9 19.1 - - + -
112A LEU* 5.4 10.5 - - + -
7B ASN* 3.2 17.7 + - - +
8B PHE* 3.0 7.3 + - - +
10B ALA* 1.3 78.8 - - + +
12B SER* 1.3 53.9 + - - +
14B ALA* 3.4 5.7 + - + +
15B ASN* 2.7 46.3 + - + +
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Residues in contact with SER 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A MET* 4.9 13.2 - - - +
84A GLU* 5.0 10.4 + - - +
85A ILE 5.9 0.2 + - - -
88A ALA* 5.4 1.1 - - - -
8B PHE* 2.6 34.7 + - - -
9B ILE* 2.6 25.1 + - - -
11B VAL* 1.3 72.2 - - - +
13B ALA* 1.3 55.4 + - - +
15B ASN* 3.9 11.8 + - - +
16B ARG* 2.8 38.0 + - - +
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 6.3 0.2 - - + -
19A PHE* 4.5 3.8 - - + -
27A ILE* 4.4 22.7 - - + -
68A PHE* 4.6 24.9 - - + -
72A MET* 5.6 1.5 - - - +
9B ILE 2.8 8.9 + - - +
10B ALA* 2.9 11.4 + - - +
12B SER* 1.3 80.0 - - - +
14B ALA* 1.3 63.4 + - - +
16B ARG* 3.1 5.0 + - - +
17B PHE* 3.0 32.1 + - + -
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.6 27.8 - - + -
32A LEU* 4.3 14.4 - - + -
35A VAL* 5.2 6.5 - - + -
36A MET* 3.5 22.7 - - + +
39A LEU* 5.6 8.1 - - + -
10B ALA 3.3 3.6 + - - +
11B VAL* 3.9 6.5 - - - +
13B ALA* 1.3 79.8 - - - +
15B ASN* 1.3 67.0 + - - +
17B PHE* 2.8 14.7 + - - +
18B LYS 3.1 8.5 + - - -
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Residues in contact with ASN 15 (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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36A MET* 5.6 0.2 - - - -
39A LEU* 6.1 1.9 - - + +
84A GLU* 3.2 43.4 + - - +
87A GLU* 3.9 26.7 - - + +
88A ALA* 4.2 7.3 - - - +
91A VAL* 5.9 2.7 - - + -
11B VAL* 2.7 33.5 + - + +
12B SER* 3.9 8.2 + - - +
14B ALA* 1.3 72.6 - - - +
16B ARG* 1.3 63.9 + - - +
18B LYS* 3.1 19.2 + - - +
19B LYS* 3.2 16.5 + - - +
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Residues in contact with ARG 16 (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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71A MET* 4.4 34.5 + - + +
72A MET* 4.9 18.9 - - - +
84A GLU* 2.8 43.4 + - - -
12B SER* 2.8 27.8 + - - +
13B ALA* 3.4 7.0 - - - +
15B ASN* 1.3 81.0 - - - +
17B PHE* 1.3 60.2 + - + +
18B LYS 3.0 0.2 - - - -
19B LYS* 3.7 5.6 - - + +
20B ILE* 2.8 45.2 + - + +
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Residues in contact with PHE 17 (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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27A ILE* 4.0 17.0 - - + -
32A LEU* 3.7 23.3 - - + -
36A MET* 4.4 2.2 - - + -
51A MET* 2.7 41.5 - - + +
52A ILE* 4.6 17.7 - - + -
55A VAL* 4.0 20.2 - - + -
63A ILE* 3.1 34.3 - - + -
68A PHE* 6.5 1.1 - + - -
71A MET* 5.3 11.0 - - + -
13B ALA* 3.0 29.5 + - + -
14B ALA 2.8 9.0 + - - +
16B ARG* 1.3 80.4 - - + +
18B LYS* 1.3 58.2 + - - +
20B ILE* 3.6 26.6 + - + +
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Residues in contact with LYS 18 (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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36A MET* 3.9 24.2 - - + +
40A GLY* 4.9 14.3 + - - -
51A MET* 4.2 4.6 - - + +
87A GLU* 6.1 3.8 - - + +
14B ALA 3.1 8.6 + - - +
15B ASN* 3.4 14.6 - - - +
16B ARG 3.0 0.8 - - - -
17B PHE* 1.3 81.5 - - - +
19B LYS* 1.3 60.6 + - + +
21B SER* 3.1 21.8 + - - -
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Residues in contact with LYS 19 (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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81A SER* 5.2 1.8 + - - -
83A GLU* 2.5 47.0 + - - +
84A GLU* 4.6 21.1 - - + -
87A GLU* 3.3 27.1 - - - +
15B ASN* 3.2 16.1 + - - +
16B ARG* 4.0 6.3 - - + +
18B LYS* 1.3 79.2 - - + +
20B ILE* 1.3 64.2 + - - +
21B SER* 2.7 18.9 + - - +
22B SER* 4.7 0.9 - - - -
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Residues in contact with ILE 20 (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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51A MET* 4.1 27.8 - - + +
54A GLU* 4.6 12.0 - - + +
55A VAL* 4.1 13.7 - - + -
71A MET* 3.8 30.3 - - + -
16B ARG* 2.8 27.3 + - + +
17B PHE* 3.6 37.5 - - + +
18B LYS 3.4 0.2 - - - -
19B LYS* 1.3 76.8 - - - +
21B SER* 1.3 52.6 + - - +
22B SER* 2.5 24.4 + - - -
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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
------------------------------------------------------------
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