Contacts of the strand formed by residues 92 - 103 (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 ILE 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C LEU* 3.7 31.4 - - + +
10C ARG* 3.8 21.1 - - - +
11C LEU* 3.7 16.2 - - + +
14C VAL* 3.4 33.2 - - + -
45C VAL* 4.2 8.3 - - + -
46C GLN* 4.8 2.6 + - - +
75C VAL* 3.8 11.4 - - + -
76C ARG 3.2 12.1 - - - +
77C ALA* 4.0 1.6 - - - -
78C ARG* 3.2 15.4 + - - -
89C THR* 2.9 30.7 - - - +
91C GLU* 1.3 80.9 - - + +
93C GLU* 1.3 64.6 + - - +
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Residues in contact with GLU 93 (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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35C PHE* 4.8 3.6 - - - -
45C VAL* 5.0 0.2 - - - -
46C GLN* 2.8 55.0 + - + +
47C VAL* 5.2 0.2 - - - -
48C PHE* 4.1 17.3 - - - +
74C THR 3.7 0.3 - - - +
75C VAL* 3.5 4.2 - - - -
76C ARG* 2.8 74.3 + - + +
77C ALA 4.8 2.9 - - - +
78C ARG* 3.9 14.0 - - + +
92C ILE* 1.3 77.3 - - - +
94C VAL* 1.3 66.1 + - - +
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Residues in contact with VAL 94 (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* 4.1 25.8 - - + -
18C VAL* 4.3 6.1 - - + -
20C LEU* 4.2 14.1 - - + -
45C VAL* 4.3 6.7 - - + -
46C GLN 2.8 13.1 + - - +
47C VAL* 3.4 12.9 - - + -
48C PHE* 2.8 29.2 + - - -
71C VAL* 5.0 3.8 - - + -
73C GLY* 3.9 12.3 - - - +
74C THR 3.3 20.0 - - - +
75C VAL* 4.2 12.8 - - + -
92C ILE* 5.6 0.2 - - + -
93C GLU* 1.3 80.6 - - - +
95C LEU* 1.3 67.5 + - - +
96C ALA* 3.1 7.2 + - - +
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Residues in contact with LEU 95 (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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48C PHE* 3.8 27.1 - - + +
50C ASP* 3.1 38.6 - - - +
53C ARG* 4.6 6.1 - - - +
73C GLY* 3.2 2.1 - - - -
74C THR* 2.6 43.6 + - + +
76C ARG* 4.1 33.0 - - - +
93C GLU 4.1 0.6 + - - -
94C VAL* 1.3 70.3 - - - +
96C ALA* 1.3 67.1 + - - +
97C SER* 4.4 1.7 - - - -
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Residues in contact with ALA 96 (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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47C VAL* 3.7 13.5 - - + -
48C PHE 2.9 15.6 + - - +
49C PHE* 3.4 41.1 - - + -
50C ASP* 2.3 33.3 + - - +
53C ARG* 3.8 0.9 + - - -
56C ALA* 5.0 2.4 - - + +
71C VAL* 4.8 2.7 - - + -
72C THR 4.0 5.8 - - - -
73C GLY* 4.4 1.3 - - - -
94C VAL* 3.1 6.0 + - - -
95C LEU* 1.3 72.4 - - - +
97C SER* 1.3 59.2 + - - +
98C SER 4.5 5.2 - - - +
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Residues in contact with SER 97 (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* 4.9 5.5 + - - -
53C ARG* 3.6 53.2 + - - +
55C ASP* 3.7 5.9 - - - +
56C ALA* 5.1 1.8 - - - -
72C THR* 3.1 18.1 + - - -
73C GLY* 4.1 4.9 - - - -
74C THR* 6.1 0.4 - - - -
95C LEU* 3.4 4.7 + - - -
96C ALA* 1.3 74.6 - - - +
98C SER* 1.3 67.5 + - - +
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Residues in contact with SER 98 (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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49C PHE* 5.2 1.3 - - - -
55C ASP* 4.3 17.4 + - - +
56C ALA* 5.0 3.1 - - - +
71C VAL* 3.4 5.4 - - - +
72C THR* 3.2 43.8 + - - +
96C ALA* 3.6 2.5 - - - +
97C SER* 1.3 90.5 + - - +
99C LEU* 1.3 70.0 + - - +
100C THR* 5.1 2.1 + - - -
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Residues in contact with LEU 99 (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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49C PHE* 3.5 36.6 - - + -
55C ASP* 4.6 7.0 - - - +
56C ALA* 5.2 2.9 - - - +
59C LEU* 3.3 51.7 - - + +
60C ALA* 4.3 4.9 - - + +
63C LEU* 3.9 25.4 - - + -
69C ILE* 4.3 5.6 - - + -
70C GLN 3.2 11.0 - - - +
71C VAL* 3.7 10.1 - - + -
72C THR* 5.3 0.7 - - - -
98C SER* 1.3 83.5 + - - +
100C THR* 1.3 79.9 + - - +
101C ILE* 4.3 5.6 - - + -
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Residues in contact with THR 100 (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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59C LEU* 5.3 0.7 - - - -
69C ILE* 3.4 4.2 - - - +
70C GLN* 2.8 53.3 + - - -
98C SER* 5.1 2.1 + - - -
99C LEU* 1.3 81.2 + - - +
101C ILE* 1.3 64.3 + - - +
102C ILE* 3.2 15.6 + - + +
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Residues in contact with ILE 101 (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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59C LEU* 4.1 19.7 - - + +
62C GLU* 5.5 0.2 - - - +
63C LEU* 3.9 28.7 - - + +
67C PHE* 4.0 16.8 - - + -
68C CYS 3.7 4.9 - - - +
69C ILE* 4.3 3.4 - - + -
99C LEU* 4.3 9.8 - - + +
100C THR* 1.3 73.8 - - - +
102C ILE* 1.3 65.0 + - - +
103C ASN* 3.0 9.4 + - - +
104C ARG* 3.8 46.4 - - + +
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Residues in contact with ILE 102 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET* 3.4 33.9 - - + -
21C CYS* 4.7 6.7 - - + -
68C CYS* 3.1 27.6 + - - +
69C ILE 4.1 24.0 - - - +
70C GLN* 4.2 13.7 - - + +
100C THR* 3.2 11.5 + - + +
101C ILE* 1.3 72.9 - - - +
103C ASN* 1.3 66.7 + - + +
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Residues in contact with ASN 103 (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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67C PHE* 3.8 0.9 - - - -
68C CYS* 2.9 44.3 + - + +
101C ILE* 3.0 7.7 + - - +
102C ILE* 1.3 86.0 + - + +
104C ARG* 1.3 77.8 + - - +
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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