Contacts of the strand formed by residues 29 - 35 (chain B) in PDB entry 1BMZ
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 ALA 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ASN 3.7 3.2 + - - -
28B VAL* 1.3 77.2 - - - +
30B VAL* 1.3 62.3 + - - +
31B HIS* 4.4 17.9 - - + -
47B GLY 3.5 7.4 - - - +
48B LYS* 4.0 19.2 - - + +
72B GLU 3.9 0.2 - - - +
74B ASP* 2.8 47.5 + - + +
77B SER* 6.3 1.1 - - - -
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Residues in contact with VAL 30 (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* 4.5 13.5 - - + -
16B VAL* 5.0 0.4 - - + -
28B VAL* 3.9 11.0 - - + +
29B ALA* 1.3 81.1 - - - +
31B HIS* 1.3 68.2 + - - +
32B VAL* 4.3 8.1 - - + -
46B SER* 3.2 6.8 - - - -
47B GLY 2.8 30.6 + - - +
49B THR* 4.3 11.9 - - + -
55B LEU* 3.6 28.7 - - + -
58B LEU* 5.1 0.4 - - + -
71B VAL* 3.6 31.0 - - + -
72B GLU 3.3 5.8 - - - +
73B ILE* 4.5 13.2 - - + -
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Residues in contact with HIS 31 (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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29B ALA* 4.4 19.5 - - + +
30B VAL* 1.3 80.0 + - - +
32B VAL* 1.3 62.4 + - - +
33B PHE* 3.6 29.0 - + + -
45B ALA 3.7 2.5 - - - -
46B SER* 3.7 20.1 + - - -
47B GLY 5.8 0.2 - - - -
70B LYS 3.6 1.9 - - - +
71B VAL* 3.7 0.2 - - - -
72B GLU* 2.8 49.2 + - - +
74B ASP* 5.9 2.4 + - + +
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Residues in contact with VAL 32 (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* 4.3 12.8 - - + -
30B VAL* 4.4 10.5 - - + -
31B HIS* 1.3 78.2 - - - +
33B PHE* 1.3 66.7 + - - +
43B PRO* 3.7 1.7 - - - +
44B PHE* 2.8 51.4 + - + -
45B ALA* 2.7 28.7 + - + +
58B LEU* 4.0 26.9 - - + -
69B TYR* 4.2 10.3 - - + -
70B LYS 3.3 7.4 - - - +
71B VAL* 4.4 15.7 - - + -
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Residues in contact with PHE 33 (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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31B HIS* 3.6 41.5 - + + -
32B VAL* 1.3 73.1 - - - +
34B ARG* 1.3 61.3 + - - +
41B TRP* 3.7 36.1 - - + -
42B GLU 3.1 9.9 - - - +
43B PRO* 3.7 32.8 - - + -
44B PHE* 4.1 2.7 - - - -
69B TYR* 3.2 10.0 - - - +
70B LYS* 2.8 53.5 + - + +
72B GLU* 4.0 23.1 - - + -
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Residues in contact with ARG 34 (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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33B PHE* 1.3 75.4 - - - +
35B LYS* 1.3 80.8 + - - +
36B ALA* 3.2 2.5 + - - +
37B ALA 5.8 0.4 - - - +
41B TRP* 3.5 3.2 - - - -
42B GLU* 2.7 43.6 + - + +
44B PHE* 4.0 21.3 - - + +
65B VAL* 3.7 15.9 - - - +
66B GLU 2.6 26.5 + - - -
67B GLY* 3.5 9.3 - - - -
68B ILE 3.5 7.9 - - - +
69B TYR* 3.2 40.5 + - + -
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Residues in contact with LYS 35 (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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34B ARG* 1.3 92.6 + - - +
36B ALA* 1.3 68.5 + - - +
37B ALA 4.2 0.2 + - - -
39B ASP* 3.4 44.1 + - - +
40B THR 3.6 5.4 - - - +
41B TRP* 3.6 44.1 - - + +
42B GLU* 5.0 0.2 - - - -
68B ILE* 2.9 48.9 + - + +
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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