Contacts of the strand formed by residues 68 - 77 (chain C) in PDB entry 1EQR
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 CYS 68 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C CYS 6.1 0.7 - - - -
22C GLY* 3.3 11.9 - - - -
23C TRP* 3.7 31.4 - - - +
66C GLU 3.4 2.6 + - - +
67C PHE* 1.3 69.6 - - - +
69C ILE* 1.3 66.4 + - - +
101C ILE 3.7 0.9 - - - -
102C ILE* 3.1 30.1 + - - -
103C ASN* 2.9 47.6 + - + +
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Residues in contact with ILE 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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21C CYS* 3.5 2.4 - - - -
22C GLY 2.7 40.0 + - - +
24C VAL* 4.2 16.2 - - + +
36C ILE* 5.0 7.6 - - + -
38C MET* 3.3 21.6 - - + +
63C LEU* 4.0 21.1 - - + -
67C PHE* 3.7 22.9 - - + +
68C CYS* 1.3 81.4 - - - +
70C GLN* 1.3 62.2 + - - +
71C VAL* 3.5 23.3 - - + -
99C LEU* 4.3 9.0 - - + -
100C THR 3.4 13.2 - - - +
101C ILE* 4.3 6.3 - - + -
102C ILE* 4.1 9.5 - - - +
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Residues in contact with GLN 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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1C MET* 3.3 31.7 - - - +
19C THR* 3.7 24.5 - - + +
20C LEU 3.2 14.1 - - - +
21C CYS* 4.1 4.0 - - - -
69C ILE* 1.3 75.6 - - - +
71C VAL* 1.3 64.3 + - - +
72C THR* 4.0 15.6 - - - +
99C LEU* 3.2 2.6 - - - -
100C THR* 2.8 54.5 + - - +
102C ILE* 4.2 13.6 - - + +
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Residues in contact with VAL 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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18C VAL 4.2 0.2 - - - +
20C LEU* 2.8 37.7 + - + +
38C MET* 3.9 18.1 - - - +
47C VAL* 4.1 21.8 - - + -
49C PHE* 3.6 24.0 - - + -
69C ILE* 3.5 28.9 - - + -
70C GLN* 1.3 79.7 - - - +
72C THR* 1.3 63.9 + - - +
94C VAL* 5.0 4.0 - - + -
96C ALA* 4.8 1.8 - - + -
98C SER 3.4 11.7 - - - +
99C LEU* 3.7 6.5 - - + -
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Residues in contact with THR 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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17C GLN* 3.9 17.2 + - - +
18C VAL 3.0 13.6 + - - -
19C THR* 3.5 15.2 + - - +
70C GLN* 4.0 20.9 - - - +
71C VAL* 1.3 78.3 - - - +
73C GLY* 1.3 59.7 + - - +
96C ALA* 4.0 2.2 - - - -
97C SER* 3.1 24.7 + - - -
98C SER* 3.2 35.6 + - - +
99C LEU 4.9 0.2 - - - +
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Residues in contact with GLY 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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17C GLN* 3.0 10.3 - - - +
18C VAL* 2.7 39.6 + - - +
71C VAL 4.3 0.2 - - - -
72C THR* 1.3 77.3 + - - +
74C THR* 1.3 62.8 + - - -
94C VAL* 3.9 10.0 - - - +
95C LEU 3.2 13.5 - - - -
97C SER* 4.1 9.2 - - - -
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Residues in contact with THR 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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15C GLY* 3.7 15.3 + - - +
16C GLN 3.2 10.4 + - - +
17C GLN* 4.3 7.3 - - - +
73C GLY* 1.3 77.4 + - - -
75C VAL* 1.3 79.4 + - - +
76C ARG* 3.7 5.4 + - + +
94C VAL* 3.3 4.5 - - - +
95C LEU* 2.6 49.8 + - + +
97C SER* 6.1 0.3 - - - -
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Residues in contact with VAL 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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9C LEU* 4.5 8.1 - - + -
10C ARG 4.1 1.1 - - - +
13C HIS* 3.3 28.3 - - + +
14C VAL* 3.4 23.1 - - - +
15C GLY* 2.7 26.6 + - - -
16C GLN 2.9 8.9 + - - +
18C VAL* 3.8 28.5 - - + -
74C THR* 1.3 78.9 - - - +
76C ARG* 1.3 61.0 + - - +
92C ILE* 3.8 24.7 - - + -
93C GLU 3.5 6.1 - - - +
94C VAL* 4.2 13.7 - - + +
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Residues in contact with ARG 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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14C VAL* 4.2 9.2 - - + -
48C PHE* 3.5 27.5 - - - -
74C THR* 4.6 7.0 - - + +
75C VAL* 1.3 77.7 - - - +
77C ALA* 1.3 69.3 + - - +
92C ILE* 3.2 6.9 - - - -
93C GLU* 2.8 62.8 + - + +
95C LEU* 4.1 33.6 - - - +
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Residues in contact with ALA 77 (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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11C LEU* 4.1 21.3 - - + -
14C VAL* 3.9 8.6 - - + +
76C ARG* 1.3 88.2 + - - +
78C ARG* 1.3 68.4 + - - +
79C ASP* 3.9 2.4 + - - +
83C ILE* 5.9 0.4 - - + -
91C GLU 3.6 8.5 - - - +
92C ILE* 4.0 3.1 - - - -
93C GLU* 4.8 1.1 - - - +
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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