Contacts of the strand formed by residues 69 - 78 (chain B) in PDB entry 1MUI
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 HIS 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A PHE* 3.5 42.2 + + - -
1B PRO* 5.0 5.8 - - + +
64B ILE 3.8 0.2 - - - +
65B GLU* 3.2 1.6 - - - -
66B ILE* 2.8 42.3 + - - +
67B CYS* 2.7 22.0 + - + -
68B GLY* 1.3 69.0 - - - -
70B LYS* 1.3 63.6 + - - +
71B ALA* 5.0 1.0 - - - +
93B ILE* 4.3 27.1 - - + +
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Residues in contact with LYS 70 (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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63B LEU* 4.2 24.2 - - + +
64B ILE 3.7 3.6 - - - -
65B GLU* 3.7 33.2 - - + +
68B GLY 3.9 2.7 - - - +
69B HIS* 1.3 74.1 - - - +
71B ALA* 1.3 61.7 + - - +
93B ILE* 5.6 0.2 - - - +
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Residues in contact with ALA 71 (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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63B LEU* 3.3 5.0 - - - +
64B ILE* 2.7 39.8 + - - +
66B ILE* 5.3 2.9 - - + -
69B HIS 5.0 0.4 - - - +
70B LYS* 1.3 76.5 - - - +
72B ILE* 1.3 61.1 + - - +
89B LEU* 4.4 13.2 - - + -
92B GLN* 3.8 29.8 - - + +
93B ILE* 4.5 15.5 - - + -
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Residues in contact with ILE 72 (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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61B GLN* 3.6 49.1 - - - +
62B ILE 3.4 3.8 - - - +
63B LEU* 3.3 41.1 - - + +
71B ALA* 1.3 73.6 - - - +
73B GLY* 1.3 61.6 + - - +
89B LEU* 4.4 1.3 - - - -
92B GLN* 2.8 29.5 + - - +
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Residues in contact with GLY 73 (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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59B TYR 3.8 0.2 - - - +
61B GLN* 3.5 8.7 + - - -
62B ILE* 3.1 31.9 + - - +
72B ILE* 1.3 78.1 - - - +
74B THR* 1.3 63.1 + - - -
75B VAL* 3.6 5.1 + - - +
88B ASN* 4.6 2.2 - - - -
89B LEU* 4.2 10.7 - - - +
92B GLN* 4.3 6.5 - - - -
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Residues in contact with THR 74 (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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30B ASP* 5.7 1.0 - - - +
31B THR* 4.0 10.2 + - - +
45B LYS* 6.2 0.7 - - - +
58B GLN* 3.6 32.7 + - + +
59B TYR 3.0 15.5 - - - +
60B ASP* 3.8 18.3 + - - +
73B GLY* 1.3 70.5 - - - -
75B VAL* 1.3 61.6 + - - +
76B LEU* 4.2 9.3 + - + +
88B ASN* 3.0 26.9 + - - +
89B LEU* 6.0 0.2 - - - -
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Residues in contact with VAL 75 (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 ILE* 4.4 4.3 - - + -
31B THR* 3.9 8.1 - - + +
33B LEU* 3.4 35.7 - - + -
38B LEU* 5.1 2.7 - - + -
57B ARG 3.6 1.6 - - - +
59B TYR* 2.7 38.5 + - + +
62B ILE* 4.0 24.0 - - + +
64B ILE* 3.2 34.3 - - + -
73B GLY* 3.6 4.2 + - - +
74B THR* 1.3 76.8 - - - +
76B LEU* 1.3 68.9 + - - +
77B VAL* 4.0 7.7 + - + -
89B LEU* 4.8 2.0 - - + -
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Residues in contact with LEU 76 (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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30B ASP* 4.1 20.6 - - + -
31B THR 2.7 23.8 + - - +
32B VAL* 3.0 11.5 - - + +
33B LEU* 2.5 35.0 + - - +
45B LYS* 4.4 14.6 - - + +
47B ILE* 3.7 34.8 - - + -
56B VAL* 4.0 17.3 - - + -
57B ARG 3.4 2.2 - - - +
58B GLN* 3.7 37.5 - - + -
74B THR* 4.5 7.4 - - + +
75B VAL* 1.3 75.0 - - - +
77B VAL* 1.3 58.5 + - - +
100B AB1 5.6 0.2 - - + -
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Residues in contact with VAL 77 (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 LEU* 3.4 4.3 - - + +
34B GLU 3.8 5.4 - - - +
35B GLU* 3.7 37.3 - - - +
36B MET* 3.7 22.2 - - + +
38B LEU* 4.6 8.1 - - + -
55B LYS 4.5 0.3 - - - +
56B VAL* 3.1 5.8 - - - -
57B ARG* 2.8 49.4 + - - +
59B TYR* 3.9 25.6 - - + -
75B VAL* 4.5 11.0 - - + +
76B LEU* 1.3 78.0 - - - +
78B GLY* 1.3 61.0 + - - +
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Residues in contact with GLY 78 (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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32B VAL* 4.5 1.8 - - - +
33B LEU 3.0 11.4 + - - +
34B GLU* 3.6 1.9 - - - -
35B GLU* 3.4 29.7 + - - -
55B LYS 4.4 0.4 - - - -
56B VAL* 3.8 12.5 - - - +
76B LEU 4.1 0.4 + - - -
77B VAL* 1.3 78.5 - - - +
79B PRO* 1.3 69.2 - - - +
80B THR* 2.9 13.0 + - - -
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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
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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