Contacts of the strand formed by residues 100 - 105 (chain C) in PDB entry 1MBU
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 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C LEU* 3.8 4.1 - - - +
33C VAL* 2.9 52.8 + - + +
35C ASP* 4.7 0.4 + - - +
89C ASN* 3.9 11.2 - - - +
98C PRO 3.0 8.9 + - - +
99C LEU* 1.3 76.3 - - - +
101C CYS* 1.3 74.4 + - - +
102C THR* 3.9 21.1 - - + -
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Residues in contact with CYS 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 3.7 25.1 - - - -
31C ILE 3.2 11.7 - - - -
32C LEU* 4.0 8.3 - - + -
51C PHE* 4.9 0.7 - - - -
85C VAL* 3.6 22.0 - - - +
88C VAL* 3.6 33.2 - - + -
89C ASN* 3.0 35.8 + - - +
99C LEU 4.0 0.2 + - - -
100C LEU* 1.3 79.2 - - - +
102C THR* 1.3 66.9 + - - +
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Residues in contact with THR 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 3.5 4.0 - - - +
31C ILE* 2.7 55.3 + - - +
33C VAL* 4.3 9.4 - - + +
85C VAL* 3.7 11.5 - - - +
100C LEU* 3.9 25.1 - - + -
101C CYS* 1.3 80.0 - - - +
103C LEU* 1.3 64.6 + - - +
104C GLU* 5.5 0.7 + - - -
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GOL 3.9 37.0 - - - +
28C TYR* 4.0 16.2 - - + -
29C LYS 3.1 12.6 - - - +
31C ILE* 5.1 0.7 - - - -
81C ALA* 3.8 12.6 - - + +
82C GLU* 3.6 36.3 - - - +
85C VAL* 3.9 13.5 - - + -
102C THR* 1.3 80.7 + - - +
104C GLU* 1.3 65.6 + - - +
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C TYR* 3.3 7.8 - - - -
29C LYS* 2.3 64.4 + - - +
31C ILE* 3.6 24.2 - - + +
70C LYS* 5.8 3.6 - - - +
102C THR* 5.5 1.3 + - - +
103C LEU* 1.3 78.3 - - - +
105C LYS* 1.3 65.2 + - - +
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Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A GLU* 4.4 5.1 - - - -
26C SER* 3.3 27.4 - - - +
27C MET 3.7 3.8 - - - -
28C TYR* 3.5 32.5 + - + +
29C LYS* 3.6 11.3 + - - -
104C GLU* 1.3 76.3 - - - +
106C ALA* 1.3 67.4 + - - +
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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
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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