Contacts of the strand formed by residues 76 - 83 (chain E) in PDB entry 3ALQ
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 LEU 76 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E PHE* 3.4 60.1 - - + -
74E VAL* 4.2 9.6 - - + -
75E LEU* 1.3 83.8 - - - +
77E THR* 1.3 62.6 + - - +
96E ALA 3.8 0.3 - - - +
97E ILE* 3.2 3.2 - - - -
98E ARG* 2.8 45.9 + - + +
100E PRO* 3.7 28.7 - - + -
114E TRP* 4.0 5.6 - - + -
116E GLU* 4.3 6.7 - - + -
118E ILE* 3.8 4.2 - - - +
137E ASN* 3.4 2.2 - - - -
138E ARG* 3.8 22.0 - - + -
141E TYR* 4.3 6.5 - - + -
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Residues in contact with THR 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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64E PHE* 4.4 1.5 - - - -
76E LEU* 1.3 76.3 - - - +
78E HIS* 1.3 60.4 + - - +
79E THR* 4.3 8.1 - - - -
95E SER* 5.8 0.7 - - - +
96E ALA 3.3 4.5 - - - -
97E ILE* 3.5 35.4 - - + -
118E ILE* 4.9 0.4 - - - -
136E ILE* 3.2 27.3 - - - +
137E ASN* 2.9 29.5 + - - +
106U LEU* 4.1 18.8 - - + +
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Residues in contact with HIS 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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26E LEU* 5.8 0.2 - - + -
28E TRP* 5.5 0.7 - + - -
60E SER* 3.2 35.3 + - - -
61E GLN 4.2 0.2 - - - -
62E VAL* 3.4 31.8 - - + +
64E PHE* 5.2 0.2 - - + -
77E THR* 1.3 73.4 - - - +
79E THR* 1.3 71.6 + - - +
95E SER* 3.3 2.3 - - - -
96E ALA 2.8 31.8 + - - -
118E ILE* 3.7 41.3 - - + +
120E LEU* 3.3 28.3 - - + +
134E ALA* 4.4 15.7 - - + -
135E GLU 3.5 9.0 + - - -
136E ILE* 3.6 7.6 - - + +
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Residues in contact with THR 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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146D GLU* 5.1 1.7 + - - -
77E THR* 4.9 6.5 - - - -
78E HIS* 1.3 83.7 + - - +
80E ILE* 1.3 70.5 + - - +
81E SER* 3.7 5.0 + - - +
92E ASN* 3.5 37.9 + - - +
94E LEU 3.3 10.1 - - - +
95E SER* 3.2 13.1 + - - -
120E LEU* 4.1 0.2 - - - -
133E SER 3.4 2.3 - - - +
134E ALA* 3.4 1.5 - - - -
135E GLU* 2.9 43.4 + - - +
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Residues in contact with ILE 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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58E ILE* 3.9 22.9 - - + -
59E TYR 3.9 4.5 - - - -
60E SER* 3.6 25.1 - - - +
78E HIS* 5.2 0.4 - - + -
79E THR* 1.3 74.7 - - - +
81E SER* 1.3 65.8 + - - +
92E ASN 3.8 0.2 - - - -
93E LEU* 2.8 34.7 + - + +
94E LEU* 2.8 39.5 + - + +
120E LEU* 4.1 11.6 - - + +
132E LEU* 5.0 3.6 - - + -
133E SER 3.1 9.0 - - - +
134E ALA* 4.0 15.7 - - + -
152E PHE* 3.8 19.3 - - + -
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Residues in contact with SER 81 (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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79E THR* 3.7 5.7 + - - -
80E ILE* 1.3 74.9 - - - +
82E ARG* 1.3 60.9 + - - +
83E ILE* 4.2 1.6 - - - +
90E PRO* 4.3 13.8 - - - +
91E VAL 3.4 15.3 - - - -
92E ASN* 3.8 19.7 - - - +
93E LEU* 4.6 0.9 - - - -
131E ARG 4.1 0.5 - - - +
132E LEU* 3.7 7.8 - - - +
133E SER* 2.7 53.5 + - - +
135E GLU* 4.6 4.7 + - - -
109U GLN* 5.1 1.6 - - - -
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Residues in contact with ARG 82 (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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34D ASN* 2.7 42.3 + - - +
81E SER* 1.3 73.8 - - - +
83E ILE* 1.3 63.8 + - - +
84E ALA* 3.4 28.7 + - - +
86E SER* 4.3 9.1 + - - -
89E THR 3.3 4.9 - - - +
91E VAL* 2.8 34.2 + - - +
93E LEU* 3.6 24.0 - - + +
124E PHE* 6.3 0.2 - - - -
125E GLN* 3.8 18.1 + - - +
126E LEU* 3.5 15.3 - - + +
127E GLU* 4.2 9.7 - - - +
130E ASP* 2.6 32.6 + - + +
131E ARG 3.8 3.1 - - - +
132E LEU* 3.8 13.2 - - + -
69U PRO* 6.4 0.2 - - - +
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Residues in contact with ILE 83 (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 GLN* 4.7 15.3 - - - +
81E SER* 4.2 2.9 - - - +
82E ARG* 1.3 73.4 - - - +
84E ALA* 1.3 66.2 + - - +
88E GLN* 4.5 6.5 - - + -
89E THR* 4.2 14.6 - - - +
90E PRO* 4.0 31.4 - - + -
129E GLY 4.4 1.0 - - - +
130E ASP* 3.5 2.1 - - - -
131E ARG* 2.9 84.0 + - + +
133E SER* 5.6 4.5 - - - +
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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