Contacts of the strand formed by residues 66 - 74 (chain C) in PDB entry 1OQE
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 ALA 66 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ASN* 4.8 3.1 - - + -
64C THR 2.6 12.7 + - - +
65C TYR* 1.3 105.6 - - + +
67C MET* 1.3 64.6 + - - +
92C ILE* 4.1 17.3 - - + -
93C GLN 3.4 6.5 - - - +
94C ASN* 4.4 4.7 - - - +
95C MET* 4.3 0.4 - - - +
124C ARG* 2.4 37.5 + - - +
13M LEU* 4.7 0.2 - - + -
14M VAL* 4.9 2.7 - - + -
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Residues in contact with MET 67 (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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60C TYR* 3.5 37.9 - - + -
62C ASP* 3.6 35.0 - - + +
64C THR* 3.8 17.9 - - - -
66C ALA* 1.3 81.9 - - - +
68C GLY* 1.3 58.0 + - - +
92C ILE* 3.2 4.5 - - - +
93C GLN* 2.8 32.4 + - - +
95C MET* 3.6 24.7 - - + -
122C ILE* 4.4 0.9 - - + -
124C ARG* 3.6 30.7 - - + +
127C ALA* 3.9 15.3 - - + -
129C ILE* 4.3 0.2 - - + -
13M LEU* 3.3 8.7 - - - -
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Residues in contact with GLY 68 (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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60C TYR* 2.9 25.4 + - - -
67C MET* 1.3 79.7 - - - +
69C HIS* 1.3 58.4 + - - -
91C CYS* 3.0 17.0 - - - -
92C ILE* 4.3 0.2 - - - -
104C CYS* 5.7 0.7 - - - -
122C ILE* 3.4 19.1 - - - +
123C PRO* 3.4 7.6 - - - +
124C ARG* 5.2 0.5 - - - +
13M LEU* 3.4 11.3 - - - +
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Residues in contact with HIS 69 (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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56C GLY* 3.7 20.4 + - - -
58C VAL* 3.6 14.6 - - + +
60C TYR* 2.6 26.1 + + - +
68C GLY* 1.3 71.9 - - - +
70C LEU* 1.3 66.4 + - - +
71C ILE* 4.7 8.0 - - + +
89C PHE 5.9 0.2 - - - -
90C ARG* 3.2 5.6 - - - +
91C CYS* 3.1 44.3 + - - +
104C CYS* 3.1 28.3 - - + -
106C SER* 5.0 3.5 + - - -
120C LEU* 3.4 39.5 - - + -
121C ALA 3.1 12.6 - - - +
122C ILE* 4.0 3.1 - - + -
123C PRO* 4.4 1.3 - - - -
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Residues in contact with LEU 70 (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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22C TYR* 4.4 14.8 - - + +
69C HIS* 1.3 78.5 - - - +
71C ILE* 1.3 62.6 + - - +
72C GLN* 3.6 33.8 + - + +
87C THR* 4.4 12.6 - - + +
89C PHE 3.5 5.4 - - - +
90C ARG* 3.3 37.5 - - + -
119C GLN 3.5 1.4 - - - +
120C LEU* 3.3 5.7 - - - +
121C ALA* 2.7 41.4 + - + +
123C PRO* 3.9 25.8 - - + -
12M LEU 5.2 5.4 - - - +
13M LEU* 4.3 5.4 - - + -
15M ARG* 5.5 3.1 - - - +
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Residues in contact with ILE 71 (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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54C ILE* 3.6 26.2 - - + -
55C TYR* 3.9 11.4 - - - +
56C GLY* 3.8 28.0 - - - +
69C HIS* 4.7 5.4 - - + -
70C LEU* 1.3 75.0 - - - +
72C GLN* 1.3 62.7 + - - +
87C THR* 3.7 1.6 - - - -
88C LEU* 2.9 32.1 + - + +
89C PHE* 2.8 40.9 + - + +
106C SER* 4.0 12.8 - - - +
118C LEU* 5.1 1.8 - - + -
119C GLN 3.5 4.5 - - - +
120C LEU* 4.0 17.0 - - + -
138C PHE* 4.1 11.0 - - + -
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Residues in contact with GLN 72 (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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22C TYR* 5.4 5.4 + - - -
24C PHE* 5.6 0.3 - - - -
70C LEU* 3.6 35.2 - - + +
71C ILE* 1.3 79.7 - - - +
73C ARG* 1.3 60.1 + - - +
85C LEU* 3.2 31.0 - - + +
86C VAL 3.3 7.4 - - - +
87C THR* 3.7 19.2 - - - +
88C LEU* 4.7 1.1 - - - -
117C GLU 3.7 0.5 - - - +
118C LEU* 3.2 12.8 - - - +
119C GLN* 2.8 62.4 + - + +
121C ALA* 3.9 13.2 - - + +
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Residues in contact with ARG 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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72C GLN* 1.3 75.9 - - - +
74C LYS* 1.3 68.5 + - - +
75C LYS* 3.6 37.7 + - - +
84C SER 3.3 4.5 - - - +
85C LEU* 3.4 3.1 - - - -
86C VAL* 2.7 45.6 + - + +
88C LEU* 3.9 24.2 - - + +
110C ALA* 6.1 0.4 - - - -
111C LYS* 3.6 17.8 + - - +
112C LEU* 3.7 20.9 - - + +
113C GLU* 3.9 18.4 - - - +
116C ASP* 2.8 32.2 + - - +
117C GLU 3.5 6.1 - - - +
118C LEU* 4.2 2.7 - - + -
79G PHE* 5.7 5.9 - - - +
82G GLU* 4.1 8.7 + - - -
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Residues in contact with LYS 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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43C LYS* 3.2 25.4 - - + +
72C GLN 4.3 0.2 - - - -
73C ARG* 1.3 71.6 - - - +
75C LYS* 1.3 66.8 + - - +
84C SER 3.4 5.8 - - - +
85C LEU* 3.6 18.6 - - + -
115C GLY 4.4 1.6 - - - +
116C ASP* 3.3 7.2 - - - -
117C GLU* 2.8 55.5 + - + +
119C GLN* 3.5 31.3 - - + +
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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