Contacts of the strand formed by residues 34 - 40 (chain N) in PDB entry 1T6V
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 THR 34 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31N LEU* 4.0 15.3 - - + -
32N GLY 3.8 9.6 - - - +
33N SER* 1.4 82.2 - - - +
35N CYS* 1.3 67.2 + - - +
51N LYS* 2.8 33.3 + - - +
57N GLU* 2.6 29.7 + - - -
59N VAL* 4.3 6.6 - - + +
66N PHE* 3.6 38.1 - - + -
84N GLY 3.5 3.4 - - - +
85N LEU* 5.1 0.4 - - + -
86N GLY 4.2 0.2 - - - +
90N GLY* 6.0 0.5 - - - -
92N CYS* 3.9 4.5 - - - -
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Residues in contact with CYS 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N THR* 1.3 73.7 - - - +
36N TRP* 1.3 68.3 + - - +
37N TYR* 3.2 26.2 - - + +
51N LYS* 4.9 1.3 - - - +
66N PHE* 4.8 0.3 - - - -
83N CYS* 3.3 5.0 - - - +
84N GLY 2.8 35.2 + - - +
85N LEU 4.1 0.4 - - - -
86N GLY* 3.4 30.7 - - - -
92N CYS* 2.0 50.3 - - + -
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Residues in contact with TRP 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N GLN* 5.0 0.4 - - - -
20N ILE* 3.7 34.8 - - + -
22N CYS* 3.9 4.7 - - - -
35N CYS* 1.3 80.2 + - - +
37N TYR* 1.3 60.6 + - - +
48N SER* 3.5 5.9 - - - -
49N ILE* 2.8 53.9 + - + +
51N LYS* 4.2 15.2 - - + +
57N GLU* 2.9 29.5 + - - +
66N PHE* 3.6 29.2 - + - -
67N SER 3.6 2.5 - - - -
68N LEU* 3.6 56.3 - - + +
81N TYR* 5.7 1.6 - - + -
82N ARG 3.4 10.8 - - - -
83N CYS* 3.5 33.0 - - + -
92N CYS* 5.0 0.7 - - - +
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Residues in contact with TYR 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N CYS* 3.2 34.3 - - + +
36N TRP* 1.3 79.1 - - - +
38N ARG* 1.3 61.4 + - - +
46N GLU* 3.5 21.3 - - + +
47N GLU 3.2 9.0 - - - +
48N SER* 3.7 21.8 - - - -
49N ILE* 3.9 5.5 - - - +
81N TYR* 3.2 7.1 - - - +
82N ARG* 2.8 44.6 + - + +
84N GLY* 4.6 2.5 - - - -
85N LEU 4.8 1.7 + - - -
92N CYS* 3.7 4.0 - - + -
93N ASP 3.1 33.7 + - - -
94N TYR* 3.3 35.2 - + + -
96N LEU* 4.2 5.9 - - - +
97N CYS* 4.0 19.1 - - - -
104N CYS* 4.6 4.8 - - - -
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Residues in contact with ARG 38 (chain N).
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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37N TYR* 1.3 76.0 - - - +
39N LYS* 1.3 69.8 + - - +
40N LYS* 3.6 38.7 + - + +
45N ASN 3.9 1.4 - - - +
46N GLU* 3.4 4.1 - - - -
47N GLU* 2.9 60.0 + - + +
49N ILE* 3.9 11.1 - - + +
54N ARG* 5.0 1.2 - - - +
55N TYR* 3.7 19.4 + - - -
76N GLU 4.4 4.8 + - - -
77N ASP* 4.2 14.3 + - - +
79N GLY* 5.7 0.2 - - - -
80N THR 3.3 6.5 - - - +
81N TYR* 3.6 39.9 - - + -
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Residues in contact with LYS 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ARG* 1.3 74.4 - - - +
40N LYS* 1.3 68.5 - - - +
44N GLY* 3.7 40.2 - - - +
45N ASN 3.7 14.8 - - - +
46N GLU* 4.0 27.9 + - + +
79N GLY* 3.2 0.9 - - - -
80N THR* 2.8 51.0 + - - +
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Residues in contact with LYS 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N ARG* 3.6 44.4 + - - +
39N LYS* 1.3 81.2 - - - +
41N SER* 1.3 70.6 + - - +
42N GLY 3.3 0.2 + - - -
43N GLU* 3.0 54.3 + - + +
44N GLY 4.1 0.2 + - - -
45N ASN 4.6 1.8 + - - -
47N GLU* 5.9 1.3 - - - +
76N GLU* 3.0 48.1 + - - +
78N GLY 3.7 6.7 - - - +
79N GLY* 4.2 0.2 - - - -
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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