Contacts of the strand formed by residues 74 - 80 (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 CYS 74 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E LEU* 4.2 6.3 - - - -
58E VAL 3.3 0.7 - - - +
59E MET* 4.7 2.5 - - - -
60E ALA* 2.8 65.0 + - - +
61E THR* 3.5 16.4 - - - -
62E VAL* 4.2 2.5 - - - -
72E LYS* 4.0 7.2 - - - +
73E VAL* 1.3 79.6 - - - +
75E THR* 1.3 64.7 + - - +
76E GLY* 6.3 0.2 - - - -
102E MET* 3.4 39.3 - - + -
103E CYS 5.4 1.1 - - - +
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Residues in contact with THR 75 (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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1E MET* 3.8 16.2 - - + -
40E LYS* 3.2 34.8 - - - +
57E MET* 3.6 16.8 - - + -
58E VAL 3.1 8.1 - - - -
59E MET* 4.5 7.2 - - + +
73E VAL* 5.6 0.2 - - - +
74E CYS* 1.3 75.0 - - - +
76E GLY* 1.3 57.8 + - - +
102E MET* 4.3 0.2 - - - -
103E CYS* 2.9 37.2 + - - +
104E ASN 3.5 14.6 + - - -
105E PRO* 3.7 5.5 - - + +
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Residues in contact with GLY 76 (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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23E MET* 6.0 0.2 - - - -
34E LEU* 5.7 1.8 - - - -
57E MET* 3.4 13.3 - - - +
58E VAL* 2.8 25.8 + - - -
60E ALA* 5.2 2.7 - - - -
74E CYS* 3.4 2.1 + - - -
75E THR* 1.3 73.5 - - - +
77E LEU* 1.3 74.5 + - - +
101E VAL 3.2 12.3 - - - -
102E MET* 4.3 2.7 - - - -
103E CYS* 3.3 11.7 - - - -
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Residues in contact with LEU 77 (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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23E MET* 5.2 3.1 - - - +
55E GLY 3.8 6.3 - - - +
56E ASP 4.2 1.8 - - - -
57E MET* 3.9 9.9 - - + +
58E VAL* 4.5 1.4 - - - +
76E GLY* 1.3 83.2 - - - +
78E VAL* 1.3 65.5 + - - +
79E VAL* 3.4 4.8 - - + +
100E GLY* 3.0 3.7 - - - -
101E VAL* 2.8 47.3 + - + -
103E CYS* 4.1 6.5 - - - -
107E GLY 3.4 20.2 - - - +
109E VAL* 4.2 3.6 - - + -
125E TRP* 3.3 51.1 - - + +
128E VAL* 3.4 32.3 - - + -
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Residues in contact with VAL 78 (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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23E MET* 5.1 5.8 - - + -
52E ALA* 5.3 4.9 - - + -
53E GLY* 3.2 33.0 - - - +
54E VAL 3.4 1.1 - - - -
55E GLY* 3.3 21.6 - - - +
56E ASP 3.2 34.4 + - - +
58E VAL* 5.1 7.3 - - + +
77E LEU* 1.3 75.1 - - - +
79E VAL* 1.3 63.7 + - - +
80E ARG 4.4 0.4 - - - +
81E GLN* 3.7 16.2 - - + +
98E ASN* 4.2 13.2 - - - +
99E ALA 3.9 11.2 - - - +
100E GLY* 4.0 2.7 - - - -
121E CYS* 3.8 5.2 - - - +
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Residues in contact with VAL 79 (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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26E ALA* 6.1 0.7 - - + -
77E LEU* 3.4 18.6 - - + +
78E VAL* 1.3 75.4 - - - +
80E ARG* 1.3 70.0 + - - +
81E GLN* 4.2 3.9 + - - -
99E ALA 2.8 15.7 + - - +
100E GLY* 3.7 13.9 - - - +
101E VAL* 4.2 13.2 - - + +
113E ILE* 4.7 9.2 - - + -
116E PRO 3.5 22.0 - - - +
117E VAL* 3.7 26.2 - - + -
118E ALA* 3.5 20.3 + - - +
121E CYS* 3.9 11.7 - - + -
128E VAL* 5.7 3.6 - - + -
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Residues in contact with ARG 80 (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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24E ASN* 5.4 3.8 + - - +
26E ALA* 4.1 11.7 - - - +
78E VAL* 4.9 0.2 - - - -
79E VAL* 1.3 90.9 - - - +
81E GLN* 1.3 63.7 + - - +
82E ARG 3.8 0.2 - - - -
95E PHE* 3.4 37.9 - - + -
96E GLU* 3.3 27.3 + - - -
97E ASP 4.3 0.7 - - - +
98E ASN* 3.1 9.0 - - - +
99E ALA* 2.8 58.2 + - + +
114E LEU* 3.4 25.9 + - - +
115E GLY* 4.5 2.2 - - - -
116E PRO* 2.7 48.2 + - - +
24G GLY* 5.8 1.2 - - - -
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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