Contacts of the strand formed by residues 69 - 76 (chain C) in PDB entry 1D1T
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 ALA 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C ILE* 4.1 8.3 - - + -
42C ALA 3.0 17.3 - - - +
43C THR* 3.5 14.4 - - - +
67C HIS 3.7 4.8 + - - -
68C GLU* 1.3 77.1 - - - +
70C THR* 1.3 64.7 + - - +
90C ILE* 3.2 14.9 - - - +
91C PRO* 3.2 21.4 - - + +
145C THR* 3.6 20.0 - - + -
170C CYS* 3.7 10.9 + - - -
173C GLY* 4.9 1.4 - - - -
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Residues in contact with THR 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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40C ILE* 3.9 4.6 - - - +
41C LEU* 2.9 22.3 + - - +
42C ALA 3.0 9.4 + - - +
69C ALA* 1.3 74.1 + - - +
71C GLY* 1.3 61.7 + - - +
88C LYS* 4.1 12.1 - - + -
89C VAL 3.5 13.5 - - - +
90C ILE* 4.2 1.9 - - + +
91C PRO* 4.6 2.9 - - - -
160C ILE* 3.9 22.2 - - + -
166C PRO* 2.8 39.0 + - + -
169C VAL* 3.6 9.0 - - + +
170C CYS* 3.1 19.2 + - - -
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Residues in contact with GLY 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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38C ILE* 3.9 13.1 - - - +
39C LYS 3.1 14.1 - - - -
40C ILE* 4.3 0.4 - - - -
41C LEU* 3.9 8.7 - - - -
70C THR* 1.3 77.0 - - - +
72C ILE* 1.3 62.4 + - - -
88C LYS* 3.4 6.6 - - - +
89C VAL* 2.7 40.3 + - - -
91C PRO* 4.9 0.8 - - - +
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Residues in contact with ILE 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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38C ILE* 3.5 3.7 - - - -
39C LYS* 2.9 43.6 + - + +
41C LEU* 3.6 31.2 - - + -
71C GLY* 1.3 75.0 - - - +
73C VAL* 1.3 70.1 + - - +
74C GLU* 3.2 0.7 + - - -
86C GLY* 3.3 33.2 - - - +
87C ASP 3.3 2.0 - - - +
88C LYS* 3.7 32.3 - - + -
89C VAL* 4.7 0.2 - - - -
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Residues in contact with VAL 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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36C VAL* 3.7 30.7 - - + -
37C ARG 3.9 3.6 - - - -
38C ILE* 4.6 1.8 - - - +
72C ILE* 1.3 71.2 - - - +
74C GLU* 1.3 62.5 + - - +
75C SER 3.8 8.3 - - - +
76C ILE* 3.8 20.2 - - + -
83C VAL* 4.1 7.0 - - + -
84C LYS 3.5 23.1 - - - +
85C PRO* 3.3 4.0 - - + +
86C GLY* 2.7 27.0 + - - -
87C ASP* 2.8 16.8 + - + +
89C VAL* 3.5 31.6 - - + -
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Residues in contact with GLU 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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2C THR* 3.2 30.2 + - - +
3C ALA* 3.4 17.0 + - - +
7C ILE* 3.6 4.9 - - - -
37C ARG* 2.8 39.6 + - - +
39C LYS* 4.6 4.3 - - + +
72C ILE* 3.2 6.6 + - - +
73C VAL* 1.3 73.9 - - - +
75C SER* 1.3 85.1 + - - +
85C PRO* 4.3 8.7 - - - +
149C TYR* 3.7 30.7 - - + +
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Residues in contact with SER 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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3C ALA* 4.1 19.5 - - - -
4C GLY 5.1 0.8 + - - -
31C PRO* 3.7 18.7 - - - +
36C VAL* 3.9 0.3 - - - -
37C ARG* 3.1 29.8 + - - +
73C VAL* 3.4 7.4 - - - +
74C GLU* 1.3 109.7 + - - +
76C ILE* 1.3 67.3 + - - +
85C PRO* 4.3 9.0 - - - -
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Residues in contact with ILE 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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31C PRO* 3.9 7.0 - - - +
35C GLU 4.0 3.4 - - - -
36C VAL* 4.7 0.9 - - + +
73C VAL* 3.8 19.1 - - + -
75C SER* 1.3 79.0 - - - +
77C GLY* 1.3 66.5 + - - +
80C VAL* 3.8 35.4 - - + +
83C VAL* 3.3 28.9 - - + +
84C LYS* 3.8 10.3 - - + -
85C PRO* 4.1 15.2 - - + +
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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