Contacts of the strand formed by residues 12 - 18 (chain B) in PDB entry 1BM7
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 LEU 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B CYS* 3.3 15.3 - - - +
11B PRO* 1.3 81.0 - - - +
13B MET* 1.3 62.6 + - - +
14B VAL* 5.1 2.2 - - + -
32B VAL* 4.2 26.9 - - + -
44B PHE* 5.1 1.6 - - + -
55B LEU 4.3 1.9 - - - +
58B LEU* 4.3 34.3 + - + +
59B THR* 3.9 18.0 + - - +
64B PHE* 4.2 21.5 - - + -
69B TYR* 5.6 0.4 - - + -
71B VAL* 4.9 5.6 - - + -
95B PHE* 4.0 15.0 - - + -
105B TYR* 3.4 23.3 - - + +
107B ILE* 4.0 22.2 - - + -
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Residues in contact with MET 13 (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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10B CYS* 4.9 6.5 - - - +
12B LEU* 1.3 75.0 - - - +
14B VAL* 1.3 97.3 + - - +
15B LYS* 3.4 12.6 - - + -
54B GLU* 3.4 37.9 - - + +
55B LEU 3.4 9.0 - - - +
56B HIS* 3.4 26.9 - - + -
105B TYR 2.8 10.1 + - - +
106B THR* 3.3 21.9 - - + +
107B ILE* 2.8 27.2 + - - +
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Residues in contact with VAL 14 (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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12B LEU* 5.1 2.5 - - + -
13B MET* 1.3 86.6 - - - +
15B LYS* 1.3 62.8 + - - +
16B VAL* 3.9 21.3 - - + -
30B VAL* 4.2 18.4 - - + -
49B THR* 5.2 0.8 - - + +
53B GLY 4.5 0.2 - - - -
54B GLU* 3.4 0.2 - - - -
55B LEU* 2.9 42.5 + - + -
58B LEU* 4.2 19.1 - - + -
71B VAL* 4.1 23.1 - - + -
73B ILE* 4.4 12.8 - - + -
107B ILE* 3.3 19.1 - - + +
108B ALA 6.1 0.2 - - - -
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Residues in contact with LYS 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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13B MET* 3.4 12.5 - - + +
14B VAL* 1.3 73.4 - - - +
16B VAL* 1.3 66.9 + - - +
17B LEU* 3.9 24.4 - - + +
52B SER 4.2 7.2 + - - -
53B GLY 3.2 10.3 - - - +
54B GLU* 3.2 29.7 + - + +
106B THR* 4.9 1.8 - - + -
107B ILE 3.0 9.2 + - - +
108B ALA* 3.2 10.1 - - + +
109B ALA 2.9 24.1 + - - +
502B FLF 2.9 46.9 + - + +
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Residues in contact with VAL 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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14B VAL* 3.9 16.2 - - + -
15B LYS* 1.3 81.7 - - - +
17B LEU* 1.3 66.5 + - - +
24B PRO* 3.7 1.9 - - - +
25B ALA* 2.8 30.0 + - + -
28B VAL* 4.5 3.6 - - + -
30B VAL* 4.9 1.1 - - + -
49B THR* 3.8 22.4 - - + -
53B GLY* 2.7 21.8 + - - +
73B ILE* 4.4 24.2 - - + -
109B ALA* 3.4 6.3 - - + +
111B LEU* 3.6 37.9 - - + -
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Residues in contact with LEU 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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15B LYS* 3.9 27.8 - - + -
16B VAL* 1.3 80.0 - - - +
18B ASP* 1.3 57.5 + - - +
19B ALA 4.0 0.4 - - - -
23B SER 3.6 5.6 - - - +
24B PRO* 4.1 17.7 - - + -
25B ALA* 3.9 4.7 - - - +
108B ALA* 6.0 1.6 - - + -
109B ALA 2.8 11.5 + - - +
110B LEU* 3.9 21.5 - - + -
111B LEU* 2.8 35.9 + - - +
502B FLF 4.1 36.8 - - + +
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Residues in contact with ASP 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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17B LEU* 1.3 71.2 - - - +
19B ALA* 1.3 56.9 + - - +
20B VAL* 2.8 35.5 + - - +
21B ARG* 2.6 37.3 + - - +
22B GLY* 3.0 21.1 + - - -
23B SER* 2.7 23.1 + - - +
24B PRO 4.4 2.0 - - - +
25B ALA* 4.1 1.1 - - - +
78B TYR* 2.4 36.7 + - + +
79B TRP* 3.5 9.7 - - - -
82B LEU* 3.9 1.6 - - - +
110B LEU* 4.4 2.9 - - - +
111B LEU* 3.8 4.9 - - - -
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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