Contacts of the strand formed by residues 34 - 40 (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 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C ARG* 3.7 22.0 - - - +
28C ARG 4.2 1.6 - - - -
29C ASP* 3.6 12.8 - - - +
32C SER 3.7 8.3 + - - +
33C LEU* 1.3 79.6 - - - +
35C PHE* 1.3 61.8 + - - +
36C ILE* 3.4 27.1 - - + -
48C PHE* 3.7 1.4 - - - -
49C PHE* 2.9 50.3 + - + -
57C LEU* 3.9 19.1 - - + +
60C ALA 3.8 8.7 - - - +
61C SER* 3.4 40.8 - - - +
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Residues in contact with PHE 35 (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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26C ARG* 4.5 12.8 + - - +
27C ARG* 3.4 1.2 - - - -
28C ARG* 3.0 48.3 + - + +
29C ASP 3.7 9.2 - - - -
30C LEU* 4.1 20.2 - - + -
33C LEU* 3.6 31.6 - - + -
34C ILE* 1.3 72.5 - - - +
36C ILE* 1.3 68.1 + - - +
46C GLN* 4.3 21.5 - - + +
47C VAL 3.8 1.6 - - - -
48C PHE* 3.5 47.3 - + + -
93C GLU* 4.8 6.3 - - - -
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Residues in contact with ILE 36 (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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24C VAL* 3.8 26.2 - - + -
26C ARG* 3.6 3.8 - - - -
27C ARG* 3.5 16.6 - - + -
34C ILE* 3.4 26.2 - - + -
35C PHE* 1.3 86.8 - - - +
37C ASP* 1.3 74.5 + - - +
38C MET* 3.6 7.9 - - + +
46C GLN* 3.4 3.1 - - - +
47C VAL* 2.8 59.3 + - + +
49C PHE* 4.2 7.2 - - + -
63C LEU* 3.8 20.2 - - + -
69C ILE* 5.0 7.0 - - + -
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Residues in contact with ASP 37 (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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25C ASN* 3.0 31.2 + - + +
26C ARG* 2.8 63.1 + - + +
36C ILE* 1.3 75.4 - - - +
38C MET* 1.3 59.3 + - - +
44C ILE* 3.5 26.7 - - + +
45C VAL 3.6 2.2 - - - -
46C GLN* 4.0 14.6 + - - +
87C MET* 4.6 10.7 - - - +
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Residues in contact with MET 38 (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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6C CYS* 3.4 9.9 - - - +
20C LEU* 3.6 36.6 - - + +
21C CYS 3.6 2.2 - - - -
22C GLY* 3.0 33.7 - - - +
23C TRP 3.6 8.7 - - - +
36C ILE* 3.5 4.8 + - + -
37C ASP* 1.3 73.2 - - - +
39C ARG* 1.3 63.0 + - - +
43C GLY 3.6 1.4 - - - +
44C ILE* 3.1 4.8 - - - -
45C VAL* 2.6 52.6 + - + +
47C VAL* 3.8 12.6 - - + -
69C ILE* 3.3 29.2 - - + +
71C VAL* 3.9 22.7 - - - +
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Residues in contact with ARG 39 (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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6C CYS* 4.5 1.1 - - - -
22C GLY* 3.2 2.7 - - - -
23C TRP* 2.9 73.5 + - - +
25C ASN* 2.7 42.5 + - + +
37C ASP 3.9 0.2 + - - -
38C MET* 1.3 79.0 - - - +
40C ASP* 1.3 75.3 + - - +
43C GLY 3.5 7.9 - - - +
44C ILE* 3.7 14.4 - - + -
66C GLU* 3.0 38.4 + - - -
130C ARG* 3.2 44.0 + - - +
132C PRO* 3.9 15.0 - - + -
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Residues in contact with ASP 40 (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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2C ARG* 4.2 7.8 + - - +
4C GLU 4.6 0.2 - - - +
5C TYR* 3.0 26.4 - - + +
6C CYS* 2.3 36.1 + - - +
7C GLY 3.3 15.1 + - - -
20C LEU* 5.2 0.2 - - - +
21C CYS 3.7 19.2 + - - +
23C TRP* 4.3 9.6 - - + -
39C ARG* 1.3 85.8 - - - +
41C ARG* 1.3 59.4 + - - +
42C GLU* 2.7 18.4 + - - +
43C GLY* 3.0 10.6 + - - +
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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