Contacts of the strand formed by residues 61 - 69 (chain E) in PDB entry 1A81
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 61 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184C ILE* 5.5 8.8 - - + +
26E GLU* 4.3 14.4 - - + +
29E LEU* 4.3 15.3 - - + -
34E MET* 3.8 17.4 - - + +
55E VAL 3.8 3.4 - - - -
60E LYS* 1.3 79.2 - - - +
62E HIS* 1.3 68.0 + - - +
63E HIS* 4.3 21.6 - - - +
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Residues in contact with HIS 62 (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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53E LEU 3.6 1.2 - - - +
54E SER* 3.1 6.4 - - - -
55E VAL* 2.8 58.3 + - + +
57E HIS* 2.5 46.5 + + + +
60E LYS* 3.8 17.8 + - + +
61E ALA* 1.3 79.2 + - - +
63E HIS* 1.3 61.0 + - - +
64E TYR* 4.2 15.1 - - + -
100E VAL* 3.8 27.0 - - + +
182F SER* 3.8 8.1 + - - +
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Residues in contact with HIS 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ARG* 3.4 40.7 - - + +
25E ALA* 5.2 0.4 - - + -
26E GLU* 3.0 44.0 + - + +
29E LEU* 5.3 0.2 - - + -
42E ARG* 3.3 26.2 + - - +
53E LEU 3.5 0.4 - - - -
54E SER* 3.4 23.4 - - - -
61E ALA* 4.3 13.9 - - + +
62E HIS* 1.3 73.4 - - - +
64E TYR* 1.3 62.9 + - - +
180F LEU 4.5 1.3 - - - +
181F PTR 3.7 13.9 - - + +
182F SER* 2.7 43.5 + - - +
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Residues in contact with TYR 64 (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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52E ALA* 2.9 6.3 - - - +
53E LEU* 2.3 66.0 + - + +
55E VAL* 5.0 5.2 - - + -
62E HIS* 4.2 17.3 - - + -
63E HIS* 1.3 76.1 - - - +
65E THR* 1.3 62.0 + - - +
76E ILE* 4.5 22.7 - - + -
98E GLY 4.5 3.6 + - - -
99E LEU* 3.6 32.0 - - + +
100E VAL* 3.9 27.0 + - + +
181F PTR 5.1 1.8 - - - -
182F SER* 2.9 42.0 - - - -
183F GLY 3.0 31.9 + - - -
184F LEU* 4.8 3.4 - - + -
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Residues in contact with THR 65 (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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44E SER* 4.3 7.5 + - - -
46E ASN* 6.2 0.7 - - - +
47E TYR* 3.7 33.4 - - + -
51E PHE 3.2 9.6 + - - -
52E ALA* 4.2 2.5 - - - +
63E HIS 4.3 0.4 + - - -
64E TYR* 1.3 74.2 - - - +
66E ILE* 1.3 66.0 + - - +
67E GLU* 3.5 12.8 + - - +
76E ILE* 3.5 25.0 - - + +
77E ALA* 4.3 1.5 + - + -
181F PTR 4.4 28.0 - - + -
182F SER 5.4 3.6 - - - +
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Residues in contact with ILE 66 (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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41E LEU* 3.5 34.5 - - + -
50E GLY* 3.2 2.3 - - - -
51E PHE* 2.5 53.7 + - + +
52E ALA 4.1 5.8 - - - +
53E LEU* 4.1 10.3 - - + +
64E TYR 4.5 3.4 - - - +
65E THR* 1.3 72.3 - - - +
67E GLU* 1.3 56.8 + - - +
74E TYR* 3.6 33.4 - - + -
75E ALA 4.2 4.0 - - - +
76E ILE* 3.8 24.5 - - + +
85E PRO* 4.9 9.9 - - + -
88E LEU* 4.8 14.6 - - + -
89E CYS* 6.3 1.3 - - - -
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Residues in contact with GLU 67 (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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47E TYR* 4.1 34.8 - - + -
50E GLY* 4.2 5.6 - - - -
65E THR* 3.5 14.4 + - - +
66E ILE* 1.3 75.3 - - - +
68E ARG* 1.3 63.8 + - - +
69E GLU* 3.6 10.6 + - - +
74E TYR* 3.7 1.6 - - - -
75E ALA 3.3 37.9 + - - +
77E ALA* 3.0 30.1 - - - +
225E LYS* 5.9 0.2 + - - -
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Residues in contact with ARG 68 (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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48E LEU 4.6 11.5 + - - +
49E GLY* 4.4 12.1 - - - +
50E GLY* 4.2 4.0 - - - +
66E ILE 3.9 1.0 + - - -
67E GLU* 1.3 73.1 - - - +
69E GLU* 1.3 86.7 + - - +
70E LEU* 3.6 5.1 + - - +
72E GLY* 2.9 32.1 + - - +
74E TYR* 3.0 49.5 + - + -
152E PRO* 4.7 23.3 + - - +
155E GLU* 5.4 12.8 + - - +
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Residues in contact with GLU 69 (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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67E GLU* 3.6 16.0 + - - +
68E ARG* 1.3 83.6 - - - +
70E LEU* 1.3 77.3 + - - +
71E ASN* 3.4 12.6 - - - +
72E GLY 2.6 27.7 + - - -
73E THR* 2.5 37.3 + - - +
75E ALA* 4.5 21.3 - - + +
81E THR* 4.7 7.4 - - + -
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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