Contacts of the strand formed by residues 100 - 104 (chain Z) 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 100 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3Z THR* 2.8 29.8 - - - +
4Z LEU 4.0 1.3 - - - +
5Z ALA* 3.5 24.2 - - + -
14Z VAL* 4.5 3.1 - - + -
42Z LEU 3.2 13.2 - - - +
43Z GLY* 3.4 15.8 - - - -
44Z THR* 3.3 25.5 + - + +
98Z GLY 4.1 1.6 - - - +
99Z THR* 1.3 80.7 + - - +
101Z ILE* 1.3 65.1 + - - +
102Z CYS* 4.2 7.9 - - - -
111Z LEU* 4.6 4.3 - - + -
112Z TYR 3.7 8.7 - - - +
113Z TYR* 3.9 15.3 - - + -
114Z VAL* 4.4 0.9 - - - +
126Z PHE* 3.8 22.4 - - - -
128Z VAL* 3.4 21.1 - - + -
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Residues in contact with ILE 101 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Z ILE* 5.0 4.5 - - + -
41Z LEU* 4.7 6.7 - - + -
42Z LEU 3.7 7.6 - - - +
43Z GLY* 4.6 5.6 - - - -
56Z GLU* 5.5 0.2 - - - +
59Z LEU* 4.0 16.4 - - + -
76Z VAL* 3.7 35.7 - - + +
79Z ALA* 4.1 10.1 - - + -
80Z SER* 3.8 31.2 - - - +
83Z LEU* 3.7 23.3 - - + -
99Z THR* 4.5 2.9 - - - +
100Z MET* 1.3 81.7 - - - +
102Z CYS* 1.3 65.3 + - - +
110Z GLY 4.2 0.2 - - - +
111Z LEU* 3.5 4.5 - - - +
112Z TYR 2.9 35.4 + - - +
114Z VAL* 4.4 1.8 - - + -
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Residues in contact with CYS 102 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Z ALA* 4.4 1.6 - - - -
12Z VAL* 4.1 13.2 - - + -
14Z VAL* 3.5 40.8 - - + -
41Z LEU* 3.3 8.8 - - - +
42Z LEU* 3.2 34.4 + - + +
43Z GLY 4.9 0.7 - - - -
44Z THR* 4.8 0.7 - - - -
76Z VAL* 4.1 5.1 - - - +
100Z MET* 4.2 11.7 - - - -
101Z ILE* 1.3 79.5 - - - +
103Z GLY* 1.3 59.3 + - - +
110Z GLY 3.4 7.4 - - - -
111Z LEU* 4.0 14.1 - - + -
179Z VAL* 4.5 6.1 - - + -
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Residues in contact with GLY 103 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z VAL* 4.7 5.5 - - - +
40Z TYR 3.5 15.5 - - - -
41Z LEU* 3.7 4.0 - - - -
76Z VAL* 3.6 0.5 - - - +
102Z CYS* 1.3 78.0 - - - +
104Z TRP* 1.4 60.9 + - - -
105Z ASP* 3.1 10.9 - - - +
109Z PRO* 4.6 0.7 - - - -
110Z GLY* 2.9 29.2 + - - +
179Z VAL* 3.8 12.9 - - - +
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Residues in contact with TRP 104 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Z PHE 4.4 0.4 - - - -
9Z ARG* 3.5 20.4 - - - -
10Z HIS* 4.3 2.2 - - - -
11Z GLY* 3.7 25.8 - - - -
40Z TYR* 3.9 10.7 + - + +
41Z LEU* 4.0 5.5 - - - +
73Z ARG* 3.9 8.0 + - - -
103Z GLY* 1.4 71.4 - - - -
105Z ASP* 1.3 87.5 + - - +
108Z GLY* 3.7 14.5 - - - +
109Z PRO* 3.8 41.7 - - + -
179Z VAL* 3.8 13.9 - - + +
180Z ARG 3.4 29.2 - - - +
181Z GLU* 3.0 57.1 + - + +
183Z GLY* 6.0 0.2 - - - -
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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