Contacts of the strand formed by residues 60 - 68 (chain C) in PDB entry 1EJH
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 LEU 60 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C TRP* 4.1 19.2 - - + -
47C PHE 3.7 4.0 - - - +
48C PHE* 3.7 31.9 - - + -
56C TRP* 3.7 35.4 + - + +
57C GLN* 3.2 17.8 + - + +
58C ALA 3.2 5.0 - - - +
59C ASN* 1.3 78.3 - - - +
61C ARG* 1.3 64.5 + - - +
92C SER* 5.7 2.7 - - - +
99C GLU* 5.7 1.8 - - + +
100C PRO* 3.5 36.6 - - + +
101C MET* 4.8 8.7 - - + -
173D ARG* 5.3 4.3 + - - +
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Residues in contact with ARG 61 (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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46C TRP* 3.2 5.6 - - - -
47C PHE* 2.7 59.7 + - + +
49C LYS* 5.5 12.6 - - - +
54C LYS* 5.5 6.9 - - - +
58C ALA 5.6 1.9 + - - +
59C ASN* 4.2 10.1 + - - +
60C LEU* 1.3 80.1 - - - +
62C LEU* 1.3 64.6 + - - +
63C ILE* 3.5 2.3 + - + +
214D ARG* 5.6 8.1 - - - +
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Residues in contact with LEU 62 (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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44C ALA* 3.5 31.6 - - + -
45C LEU 3.5 13.5 - - - +
46C TRP* 3.6 25.2 - - + -
61C ARG* 1.3 72.5 - - - +
63C ILE* 1.3 58.7 + - - +
64C SER 3.8 10.5 - - - +
65C LYS* 3.8 18.6 - - + -
173D ARG* 3.5 48.5 - - + +
174D ASP* 4.4 1.6 - - - +
177D THR* 3.7 19.3 - - - +
214D ARG 4.4 3.3 - - - +
215D PHE* 3.4 20.6 - - + -
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Residues in contact with ILE 63 (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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45C LEU* 2.7 39.4 + - + +
47C PHE* 3.3 38.4 - - + +
61C ARG* 3.8 2.7 - - + +
62C LEU* 1.3 75.5 - - - +
64C SER* 1.3 63.5 + - - +
79C ILE* 4.8 8.3 - - + -
91C TYR* 3.6 23.8 - - + -
214D ARG 4.7 8.1 - - - +
215D PHE* 3.5 13.6 - - - +
216D VAL* 3.5 33.2 + - + -
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Residues in contact with SER 64 (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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44C ALA* 3.3 3.8 - - - -
45C LEU* 2.8 29.4 + - - +
62C LEU* 3.8 3.7 - - - +
63C ILE* 1.3 83.6 - - - +
65C LYS* 1.3 79.5 + - - +
75C LEU* 3.9 31.5 - - - +
177D THR* 4.7 8.1 - - - -
181D ARG* 4.2 1.9 + - - -
215D PHE* 5.4 0.4 - - - -
216D VAL* 2.6 26.0 + - - -
217D VAL* 4.0 6.3 - - - +
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Residues in contact with LYS 65 (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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42C ARG* 4.4 13.0 - - - -
43C TRP 3.1 8.7 - - - +
44C ALA* 3.9 15.3 - - + -
62C LEU* 3.8 18.4 - - + -
64C SER* 1.3 82.2 + - - +
66C PHE* 1.3 64.6 + - - +
96C ASP* 2.7 38.0 + - - +
174D ASP* 3.0 36.9 + - - +
177D THR* 3.2 30.5 - - + +
181D ARG* 3.0 31.4 + - + +
217D VAL* 4.7 0.9 - - - +
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Residues in contact with PHE 66 (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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39C LEU* 3.8 24.5 - - + -
41C ASN 4.2 0.2 - - - +
42C ARG* 3.3 6.1 - - - +
43C TRP* 2.9 46.0 + - + -
45C LEU* 5.1 1.6 - - + -
64C SER 5.3 0.2 - - - -
65C LYS* 1.3 79.9 - - - +
67C ASP* 1.3 64.3 + - - +
68C THR 4.3 0.7 - - - -
71C ASP* 3.8 13.0 - - + -
72C PHE* 3.6 35.7 - + + +
75C LEU* 3.5 32.5 - - + -
93C LEU* 3.7 35.4 - - + -
138C ILE* 3.9 7.6 - - + -
181D ARG* 3.8 19.5 - - - +
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Residues in contact with ASP 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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38C PRO* 3.6 3.5 - - - +
39C LEU* 2.8 29.8 + - - +
41C ASN 4.0 9.6 - - - +
42C ARG* 2.8 50.2 + - + +
66C PHE* 1.3 77.1 - - - +
68C THR* 1.3 75.6 + - - +
71C ASP* 4.4 3.8 + - - +
181D ARG* 5.4 6.8 - - - +
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Residues in contact with THR 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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36C LYS* 3.7 29.3 - - + +
37C HIS 3.2 12.6 - - - +
38C PRO* 4.5 6.1 - - + -
39C LEU* 3.6 8.8 - - - +
66C PHE* 4.3 0.7 - - - -
67C ASP* 1.3 97.8 - - - +
69C VAL* 1.3 65.4 + - - +
70C GLU 3.6 1.6 + - - -
71C ASP* 2.6 38.5 + - - +
72C PHE* 3.1 20.4 + - - +
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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