Contacts of the strand formed by residues 72 - 76 (chain C) in PDB entry 5A0Q
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 MET 72 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C LEU* 3.6 5.8 + - + -
69C ASN* 3.0 57.7 + - - +
70C GLU 3.6 0.6 - - - -
71C ASP* 1.4 115.1 - - + +
73C ALA* 1.4 61.6 + - - +
104C PRO* 4.9 10.3 - - + +
105C ILE* 3.0 27.6 - - - +
106C PRO* 4.6 0.2 - - + -
107C CYS* 3.6 32.1 - - + +
110C LEU* 4.6 5.6 - - + -
137C ILE 3.6 7.4 - - - -
138C GLY* 3.9 0.7 - - - -
140C ASP* 4.1 22.9 - - - +
141C LYS* 5.3 2.2 - - + +
216C LEU* 4.9 0.9 - - - -
225C ILE* 3.3 5.9 - - - +
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Residues in contact with ALA 73 (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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65C ILE* 3.5 14.1 - - + -
66C TYR 3.1 19.5 - - - +
68C LEU* 4.0 9.9 - - - +
72C MET* 1.4 75.0 - - - +
74C CYS* 1.4 59.7 + - - +
107C CYS* 5.5 0.2 - - - -
136C TYR* 3.5 5.0 - - - +
137C ILE* 2.9 47.5 + - + +
225C ILE* 3.9 19.1 - - + -
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Residues in contact with CYS 74 (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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45C LEU* 4.5 0.7 - - - -
64C LYS 4.1 0.5 - - - +
65C ILE* 3.0 20.8 - - - +
66C TYR* 3.2 26.8 + - - -
68C LEU* 3.4 37.9 - - + -
73C ALA* 1.4 73.2 - - - +
75C SER* 1.4 62.8 + - - +
76C VAL* 4.1 6.2 + - + -
87C THR* 4.2 9.6 - - - -
90C LEU* 4.2 11.0 - - + -
134C LEU* 5.0 3.8 - - + -
135C LEU 3.2 13.5 - - - +
136C TYR* 4.3 5.8 - - + -
137C ILE* 5.7 0.2 - - - -
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Residues in contact with SER 75 (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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34C CYS* 3.1 25.9 - - - -
45C LEU* 3.4 35.5 - - - +
47C ALA* 4.5 6.4 - - - +
64C LYS* 4.9 1.9 - - - +
65C ILE* 4.6 5.9 + - - +
74C CYS* 1.4 72.4 - - - +
76C VAL* 1.3 64.8 + - - +
77C ALA* 4.0 1.5 + - - +
133C SER 3.9 0.2 - - - +
134C LEU* 3.2 9.7 - - - +
135C LEU* 3.0 35.5 + - - +
137C ILE 5.7 0.2 - - - +
164C ILE* 5.8 1.0 - - - +
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Residues in contact with VAL 76 (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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34C CYS* 6.4 0.2 - - - -
64C LYS* 3.7 45.0 + - + +
66C TYR* 3.9 22.0 - - + -
74C CYS* 4.4 7.0 - - - -
75C SER* 1.3 76.3 + - - +
77C ALA* 1.3 59.4 + - - +
79C ILE 4.1 2.1 - - - +
83C ALA* 2.8 37.2 - - + +
87C THR* 4.1 8.7 - - - +
132C VAL* 3.2 14.4 - - + -
134C LEU* 3.1 26.2 - - + -
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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