Contacts of the strand formed by residues 43 - 49 (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 GLY 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C GLY* 3.6 10.2 + - - -
38C MET 3.6 0.9 - - - +
39C ARG* 3.5 4.6 - - - -
40C ASP* 3.0 32.8 + - - +
41C ARG 3.5 1.2 - - - -
42C GLU* 1.3 82.0 - - - +
44C ILE* 1.3 63.1 + - - -
132C PRO* 5.2 12.3 - - - -
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Residues in contact with ILE 44 (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 4.6 1.8 - - - -
7C GLY* 4.3 0.2 - - - -
25C ASN* 3.2 33.9 - - - +
37C ASP* 3.5 32.5 - - + +
38C MET 3.1 4.3 - - - +
39C ARG* 3.7 22.7 - - + -
43C GLY* 1.3 73.4 - - - -
45C VAL* 1.3 56.4 + - - +
87C MET* 3.1 25.0 - - + +
88C ALA 5.6 0.5 + - - -
89C THR* 2.7 29.5 + - - +
132C PRO* 4.4 15.7 - - + -
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Residues in contact with VAL 45 (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* 3.2 42.8 - - + +
9C LEU* 3.6 22.0 - - + -
20C LEU* 3.7 15.3 - - + -
36C ILE 3.6 0.2 - - - +
38C MET* 2.6 46.0 + - + +
43C GLY 4.2 0.2 + - - -
44C ILE* 1.3 75.2 - - - +
46C GLN* 1.3 71.4 + - - +
47C VAL* 4.9 1.3 - - + -
89C THR* 3.7 6.3 - - - -
92C ILE* 4.2 20.0 - - + -
94C VAL* 4.3 6.1 - - + -
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Residues in contact with GLN 46 (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* 4.2 17.0 + - - -
35C PHE* 4.3 20.8 - - + +
36C ILE 3.4 8.1 - - - +
37C ASP* 4.0 10.1 + - - +
45C VAL* 1.3 76.1 - - - +
47C VAL* 1.3 67.6 + - - +
48C PHE 4.7 0.7 - - - +
78C ARG* 3.9 40.2 + - - +
82C ASN* 6.0 1.8 - - - +
87C MET* 4.8 3.7 - - + +
89C THR* 4.7 2.0 + - - -
92C ILE 5.0 1.2 + - - -
93C GLU* 2.8 40.1 + - + +
94C VAL* 2.8 24.3 + - - +
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Residues in contact with VAL 47 (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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20C LEU* 5.7 0.4 - - + -
34C ILE 3.8 1.2 - - - +
35C PHE* 3.8 1.4 - - - -
36C ILE* 2.8 57.8 + - + +
38C MET* 3.8 22.4 - - + -
45C VAL* 4.1 2.7 - - + +
46C GLN* 1.3 77.7 - - - +
48C PHE* 1.3 61.9 + - - +
49C PHE* 3.5 25.0 - - + -
71C VAL* 4.1 11.9 - - + -
94C VAL* 3.4 20.2 - - + +
96C ALA* 3.7 16.4 - - + +
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Residues in contact with PHE 48 (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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33C LEU* 3.4 44.6 - - + -
34C ILE 3.7 5.6 - - - -
35C PHE* 3.5 33.0 - + + -
46C GLN* 4.2 1.2 + - - +
47C VAL* 1.3 70.8 - - - +
49C PHE* 1.3 83.4 + - - +
50C ASP* 3.6 3.5 - - - +
51C PRO* 5.0 6.3 - - + -
76C ARG* 3.5 29.2 - - - -
93C GLU* 4.1 13.2 - - - +
94C VAL 2.8 13.2 + - - +
95C LEU* 3.8 14.6 - - + -
96C ALA 2.9 26.3 + - - -
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Residues in contact with PHE 49 (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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33C LEU* 4.5 0.9 - - - -
34C ILE* 2.9 32.1 + - + +
36C ILE* 4.2 10.3 - - + -
47C VAL* 3.5 24.2 - - + -
48C PHE* 1.3 88.5 - - - +
50C ASP* 1.3 67.3 + - - +
51C PRO* 4.3 0.2 - - - +
56C ALA* 4.0 13.0 - - + -
57C LEU* 3.5 24.0 - - + +
60C ALA* 3.6 21.5 - - + -
63C LEU* 4.0 14.1 - - + -
69C ILE* 5.0 0.2 - - + -
71C VAL* 3.6 16.4 - - + -
96C ALA* 3.4 18.8 - - + -
98C SER 4.7 0.2 - - - -
99C LEU* 3.5 43.1 - - + -
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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