Contacts of the strand formed by residues 57 - 61 (chain E) in PDB entry 5ANC
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 MET 57 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 4.3 8.5 - - + +
2E SER* 3.2 37.7 - - - +
3E LYS* 5.0 3.2 - - - +
39E VAL* 3.5 6.2 - - - +
40E LYS* 3.1 42.6 + - + +
56E ASP* 1.3 76.9 - - - +
58E VAL* 1.3 59.1 + - - +
75E THR* 3.6 29.6 - - + -
76E GLY 3.4 20.4 - - - +
77E LEU* 3.9 3.2 - - - +
103E CYS* 4.7 0.2 - - - -
104E ASN 3.9 3.8 - - - +
105E PRO* 3.5 21.3 - - + +
107E GLY* 4.3 6.1 - - - -
125E TRP* 3.5 26.2 - - + -
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Residues in contact with VAL 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E MET* 5.0 12.6 - - + -
36E VAL* 4.6 11.9 - - + -
38E ALA 3.6 7.6 - - - +
39E VAL* 3.7 29.8 - - + +
40E LYS* 4.3 4.5 - - - -
52E ALA* 5.5 2.0 - - + -
53E GLY 4.8 5.8 - - - +
56E ASP 3.8 9.2 - - - +
57E MET* 1.3 82.0 - - - +
59E MET* 1.3 61.9 + - - +
60E ALA* 4.2 14.4 - - + -
74E CYS 3.3 1.6 - - - +
75E THR* 3.1 8.3 - - - -
76E GLY* 2.8 47.2 + - - +
77E LEU* 4.5 2.0 - - - +
78E VAL* 5.1 6.3 - - + +
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Residues in contact with MET 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 5.9 0.4 - - - -
36E VAL* 3.6 3.6 - - - +
37E ILE* 2.8 41.3 + - + -
38E ALA 2.8 27.2 + - - +
40E LYS* 3.7 26.3 - - + +
58E VAL* 1.3 69.8 - - - +
60E ALA* 1.3 53.9 + - - +
73E VAL* 3.8 27.1 - - + -
74E CYS 4.0 2.7 - - - +
75E THR* 4.5 7.2 - - + -
3263N A 3.1 50.3 - - - +
3264N C 3.0 31.4 - - - +
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Residues in contact with ALA 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E MET* 5.5 1.6 - - + -
34E LEU* 4.3 15.5 - - + -
35E TYR 3.3 15.5 - - - +
36E VAL* 4.6 2.2 - - + -
37E ILE* 3.0 15.6 - - - +
58E VAL* 4.2 16.4 - - + -
59E MET* 1.3 74.1 - - - +
61E THR* 1.3 62.8 + - - +
73E VAL* 3.3 0.9 - - - -
74E CYS* 2.8 44.2 + - - +
76E GLY* 4.9 2.9 - - - +
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Residues in contact with THR 61 (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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34E LEU* 3.5 6.0 - - - -
35E TYR* 2.8 58.7 + - + +
37E ILE* 4.6 3.1 - - - -
60E ALA* 1.3 77.6 - - - +
62E VAL* 1.3 62.6 + - - +
63E LYS* 3.4 9.8 + - + +
71E LYS* 4.1 4.7 + - - -
72E LYS 3.7 12.6 + - - -
73E VAL* 5.0 0.2 - - - -
74E CYS* 3.5 10.5 - - - -
2561N A 3.2 48.9 + - + +
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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
------------------------------------------------------------
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