Contacts of the strand formed by residues 79 - 85 (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 GLY 79 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38N ARG* 5.7 0.2 - - - -
39N LYS 3.2 11.9 - - - -
41N SER* 3.2 16.5 + - - -
77N ASP 3.5 1.6 + - - -
78N GLY* 1.3 74.8 - - - -
80N THR* 1.3 65.0 + - - -
81N TYR* 4.1 6.3 - - - -
109N ALA* 3.7 1.2 - - - +
110N VAL* 2.8 37.3 + - - +
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Residues in contact with THR 80 (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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37N TYR 4.6 0.2 - - - -
38N ARG* 3.3 3.6 - - - +
39N LYS* 2.8 49.5 + - - +
46N GLU* 4.7 3.7 - - - +
79N GLY* 1.3 77.1 + - - -
81N TYR* 1.3 68.7 + - - +
82N ARG* 4.3 20.4 - - - +
107N GLY* 4.8 2.0 - - - -
108N THR 3.3 16.8 - - - +
109N ALA* 4.3 9.8 - - + +
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Residues in contact with TYR 81 (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* 3.1 4.7 + - - -
20N ILE* 3.7 22.9 - - + -
36N TRP* 5.7 2.7 - - + -
37N TYR 3.2 4.3 - - - +
38N ARG* 3.6 33.6 - - + -
46N GLU* 5.2 0.2 - - - -
49N ILE* 3.8 22.9 - - + -
55N TYR* 5.1 4.1 + + - -
68N LEU* 5.5 1.3 - - + -
70N ILE* 3.5 29.3 - - + +
73N LEU* 6.0 0.4 - - + -
77N ASP* 2.6 44.8 + - - +
79N GLY 3.9 8.7 - - - -
80N THR* 1.3 78.6 - - - +
82N ARG* 1.3 59.8 + - - +
107N GLY* 3.2 4.2 - - - -
108N THR 2.8 32.0 + - - +
110N VAL* 3.6 32.3 - - + -
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Residues in contact with ARG 82 (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* 3.6 4.3 - - - +
36N TRP* 3.4 7.2 - - - -
37N TYR* 2.8 37.3 + - + -
46N GLU* 4.1 13.6 + - - +
80N THR* 4.3 18.0 - - - +
81N TYR* 1.3 76.2 - - - +
83N CYS* 1.3 67.4 + - - +
94N TYR* 2.8 39.2 + - + -
97N CYS* 3.9 6.3 - - - -
104N CYS* 3.8 15.7 - - + -
105N GLY 3.2 18.6 + - - +
106N ASP* 3.1 38.2 + - - +
107N GLY* 3.2 5.6 - - - +
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Residues in contact with CYS 83 (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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3N VAL* 3.7 15.5 - - - -
5N GLN* 3.3 12.3 + - - +
22N CYS* 2.0 49.8 - - - -
35N CYS 3.3 6.7 - - - +
36N TRP* 3.5 22.4 - - + -
37N TYR* 4.9 1.3 - - - -
66N PHE* 3.7 8.5 - - + -
82N ARG* 1.3 74.6 - - - +
84N GLY* 1.3 58.9 + - - +
104N CYS* 3.2 8.2 - - - +
105N GLY 2.8 26.8 + - - -
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Residues in contact with GLY 84 (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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3N VAL* 5.3 0.4 - - - -
34N THR* 3.5 4.3 - - - -
35N CYS* 2.8 38.0 + - - +
37N TYR* 4.6 1.5 - - - -
66N PHE* 3.8 13.0 - - - -
83N CYS* 1.3 78.0 - - - +
85N LEU* 1.3 64.0 + - - -
103N GLU 3.4 11.4 - - - -
104N CYS* 3.9 9.4 - - - -
105N GLY 4.8 0.2 - - - -
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Residues in contact with LEU 85 (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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102L GLY* 4.2 20.6 - - - +
103L ASN* 4.4 2.5 - - + -
3N VAL* 4.3 7.0 - - + -
24N LEU* 4.4 8.3 - - + -
29N TYR* 3.7 26.2 - - + +
31N LEU* 3.7 29.2 - - + -
32N GLY 5.6 1.3 - - - +
33N SER 3.7 6.5 - - - +
35N CYS* 4.1 2.9 - - - +
37N TYR* 4.8 1.2 + - - -
66N PHE* 4.2 15.7 - - + -
84N GLY* 1.3 74.3 - - - +
86N GLY* 1.3 67.0 + - - +
96N LEU* 4.1 8.3 - - - +
102N ALA* 3.3 21.7 - - + +
103N GLU* 2.9 42.3 + - + +
104N CYS* 5.4 1.4 - - - -
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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