Contacts of the strand formed by residues 66 - 71 (chain Z) in PDB entry 5OOM
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 66 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Z HIS* 3.1 11.9 - - - +
65Z LYS* 1.3 93.5 - - + +
67Z HIS* 1.3 56.6 + - - +
99Z VAL* 4.1 12.3 - - + -
100Z HIS 3.2 14.4 - - - +
101Z LYS* 4.5 3.1 - - + -
122Z LEU* 2.7 65.5 + - + +
124Z LEU* 5.1 6.3 - - + -
77j VAL* 3.7 16.6 - - + +
80j LEU* 3.8 27.1 - - + +
81j SER* 3.5 24.7 - - - +
84j MET* 5.1 1.8 - - + -
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Residues in contact with HIS 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64Z HIS* 3.2 27.3 + + - -
66Z LEU* 1.3 76.9 - - - +
68Z ILE* 1.3 63.1 + - - +
69Z VAL* 4.0 16.4 - - + -
99Z VAL* 3.2 8.8 - - - +
100Z HIS* 2.9 34.2 + - + +
101Z LYS 3.7 18.4 - - - -
102Z ASN* 3.0 22.9 + - - -
107Z ASN* 3.0 21.6 + - - -
110Z LEU* 3.9 11.2 - - + +
119Z ILE* 3.3 23.7 - - + +
120Z LYS 3.6 2.4 + - - -
48o TRP 3.3 21.3 - - - -
49o LEU* 4.8 1.3 - - + -
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Residues in contact with ILE 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67Z HIS* 1.3 75.7 - - - +
69Z VAL* 1.3 62.1 + - - +
70Z THR* 4.4 6.2 + - - +
97Z PRO* 3.6 28.7 - - + -
98Z GLN 3.3 4.5 - - - +
99Z VAL* 4.7 7.4 - - + -
118Z ARG 3.3 5.4 - - - +
119Z ILE* 3.3 1.7 - - - -
120Z LYS* 2.8 41.0 + - + +
121Z PRO 4.3 2.0 - - - +
122Z LEU* 3.7 38.4 - - + -
139Z LEU* 3.7 18.6 - - + -
143Z GLY* 3.7 21.8 - - - +
73j PHE* 5.7 0.2 - - + -
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Residues in contact with VAL 69 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67Z HIS* 4.0 11.2 - - + -
68Z ILE* 1.3 76.8 - - - +
70Z THR* 1.3 68.5 + - - +
89Z LEU* 5.2 0.2 - - + -
91Z LEU* 3.7 32.3 - - + +
97Z PRO* 3.5 1.4 - - - +
98Z GLN 2.9 30.9 + - - +
100Z HIS* 3.8 25.1 - - + -
110Z LEU* 3.9 27.4 - - + -
117Z ILE* 3.7 26.2 - - + -
118Z ARG 3.2 2.9 - - - +
119Z ILE* 4.3 4.3 - - + -
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Residues in contact with THR 70 (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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68Z ILE* 4.4 5.2 - - - +
69Z VAL* 1.3 80.4 + - - +
71Z ARG* 1.3 63.0 + - - +
72Z ILE* 3.4 16.8 + - + +
95Z HIS* 3.7 33.4 - - - +
96Z THR 4.0 4.0 - - - +
97Z PRO* 3.6 17.4 - - + +
117Z ILE* 3.1 7.2 - - - -
118Z ARG* 2.9 45.4 + - + +
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Residues in contact with ARG 71 (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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2140A G 3.4 29.9 + - - -
70Z THR* 1.3 71.5 - - - +
72Z ILE* 1.3 59.9 + - - +
73Z LYS 3.2 28.9 - - - +
74Z SER* 5.0 0.4 + - - -
75Z THR* 3.5 31.4 + - + +
86Z ILE* 4.0 22.4 - - + +
91Z LEU* 3.5 35.3 + - + +
92Z GLU* 2.4 31.8 + - - +
93Z LYS* 3.8 5.8 + - - +
94Z ALA* 3.2 28.8 - - - +
95Z HIS 3.0 26.9 + - - +
96Z THR 4.6 1.6 + - - -
116Z LEU* 3.7 6.3 - - + +
117Z ILE* 4.4 3.6 - - - +
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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