Contacts of the strand formed by residues 6 - 13 (chain E) in PDB entry 6AHU
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 HIS 6 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A A 3.7 21.7 + - - +
275A A 4.6 7.0 + - - +
4E PHE* 3.6 25.3 + - + +
5E LYS* 1.3 77.0 + - - +
7E ARG* 1.3 70.8 + - - +
8E TYR* 3.8 25.1 - + + -
52E GLY 5.2 3.6 + - - -
68E ARG* 3.3 33.0 + - + +
69E CYS 3.6 13.2 + - - +
70E ARG* 3.3 34.6 + - - -
104E GLY 3.9 1.0 - - - -
105E GLY* 3.3 20.9 + - - -
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Residues in contact with ARG 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A G 5.2 7.1 + - - -
25A U 5.7 3.8 - - - -
275A A 4.4 0.4 + - - -
276A U 3.0 29.4 + - - -
5E LYS 6.2 0.2 - - - -
6E HIS* 1.3 81.2 + - - +
8E TYR* 1.3 64.7 + - - +
67E LEU 3.7 2.8 - - - +
68E ARG* 4.0 0.7 - - - -
69E CYS* 2.9 48.8 + - - +
70E ARG 3.3 20.6 - - - +
71E LYS* 3.1 31.9 - - - +
74E TYR* 4.1 20.0 + - + -
102E HIS* 4.0 21.4 + - - +
104E GLY* 3.4 26.8 - - - -
105E GLY 3.7 3.1 - - - +
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Residues in contact with TYR 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A C 3.4 21.0 + - - -
274A A 3.5 14.6 + - - -
6E HIS* 3.8 25.0 - - + +
7E ARG* 1.3 73.2 - - - +
9E LEU* 1.3 60.9 + - - +
10E LEU 4.2 0.3 + - - -
56E ARG* 4.7 8.3 - - + -
66E LEU* 3.8 21.5 - - + -
67E LEU 3.6 13.7 - - - -
68E ARG* 3.6 35.4 + - + -
102E HIS* 4.7 1.1 - - - -
103E VAL* 2.9 42.6 + - - +
105E GLY* 3.5 33.2 - - - +
106E THR 4.8 0.2 - - - -
107E ILE* 3.6 31.0 - - + -
110E CYS* 4.7 5.6 - - - -
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Residues in contact with LEU 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E TYR* 1.3 74.3 - - - +
10E LEU* 1.3 62.0 + - - +
11E CYS* 3.8 25.6 - - - -
65E VAL 3.5 3.6 - - - +
66E LEU* 3.7 2.5 - - - +
67E LEU* 3.4 46.7 + - + +
69E CYS* 4.0 21.8 - - + -
74E TYR 4.9 0.2 - - - +
77E VAL* 3.8 24.9 - - + -
78E TRP* 4.4 22.7 - - + +
81E LEU* 3.9 12.1 - - + -
99E ASN* 6.4 0.7 - - + -
102E HIS* 3.6 24.2 - - + +
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Residues in contact with LEU 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LEU* 1.3 76.5 - - - +
11E CYS* 1.3 70.7 + - - +
57E TYR* 5.7 0.9 - - + -
64E ILE* 4.1 23.3 - - + -
65E VAL 3.4 3.1 - - - +
66E LEU* 3.8 26.0 - - + -
99E ASN* 3.4 22.4 - - - +
100E THR* 3.3 27.0 + - + +
101E LEU 4.1 15.7 + - - +
103E VAL* 5.0 2.0 - - + -
110E CYS* 3.9 33.4 - - - +
111E GLN* 5.6 1.3 - - - +
113E PHE* 4.3 15.3 - - + -
114E LEU* 4.9 13.0 - - + -
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Residues in contact with CYS 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LEU* 3.8 15.0 - - - -
10E LEU* 1.3 82.2 - - - +
12E GLU* 1.3 63.0 + - - +
64E ILE* 3.5 11.4 - - - +
65E VAL* 2.9 43.5 + - + -
67E LEU* 5.0 1.6 - - - -
81E LEU* 3.7 35.2 - - - -
97E PHE* 3.6 25.6 - - + -
98E PHE 3.4 9.0 - - - +
99E ASN* 5.1 0.9 - - - -
100E THR* 5.3 2.4 - - - +
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Residues in contact with GLU 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E CYS* 1.3 78.4 - - - +
13E LEU* 1.3 66.8 + - - +
14E VAL* 3.5 15.2 + - + +
62E THR 5.8 1.1 - - - +
63E GLY 3.4 12.6 - - - +
64E ILE* 4.5 7.4 - - + -
65E VAL* 5.8 0.2 - - - -
97E PHE* 3.6 3.9 - - - -
98E PHE* 2.8 43.6 + - + +
100E THR* 4.1 11.1 - - + +
117E TYR* 2.6 43.6 + - - -
121E GLN* 5.1 5.2 + - - +
27I HIS* 3.2 20.9 + - - -
28I LEU* 6.0 0.9 - - - +
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Residues in contact with LEU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E GLU* 1.3 73.8 - - - +
14E VAL* 1.3 62.4 + - - +
15E SER* 3.9 6.0 + - - +
20E CYS* 5.7 3.4 - - - +
21E ARG* 4.9 24.4 + - + -
24E LEU* 3.9 38.1 - - + -
62E THR 5.6 0.7 - - - +
63E GLY* 3.6 16.0 + - - +
65E VAL* 5.2 6.5 - - + +
87E LEU* 6.0 0.2 - - + -
95E PRO* 3.8 32.1 - - + -
96E CYS 3.9 13.2 - - - +
97E PHE* 3.7 42.2 - - + -
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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