Contacts of the strand formed by residues 102 - 112 (chain E) in PDB entry 1OQE
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 ASN 102 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D ILE 3.5 1.8 - - - -
93D GLN* 3.4 9.5 + - - +
94D ASN* 2.6 52.0 + - - +
59E LEU* 3.9 2.2 - - - +
60E TYR* 2.6 44.0 + - - +
93E GLN* 3.9 23.1 + - + +
94E ASN 3.0 26.7 + - - -
95E MET* 3.5 17.5 - - - -
96E PRO* 3.9 2.4 - - - +
101E ASN* 1.3 73.1 - - - +
103E SER* 1.3 56.4 + - - +
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Residues in contact with SER 103 (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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90D ARG 5.2 0.2 - - - -
91D CYS* 3.1 14.2 - - - +
92D ILE 2.9 33.2 + - - -
93D GLN* 3.4 15.6 - - - +
104D CYS* 4.2 5.8 - - - -
57E GLN* 4.1 19.3 + - - -
58E VAL 3.0 12.8 - - - -
59E LEU* 3.9 15.0 - - - +
93E GLN* 4.2 3.6 + - - -
102E ASN* 1.3 75.4 - - - +
104E CYS* 1.3 60.4 + - - +
105E TYR 4.3 0.2 - - - -
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Residues in contact with CYS 104 (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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57E GLN* 3.3 12.5 - - - -
58E VAL 3.0 7.6 + - - -
60E TYR* 4.6 8.2 - - + -
68E GLY* 5.7 0.4 - - - -
69E HIS* 3.1 23.4 - - + -
91E CYS* 2.1 52.0 - - - -
92E ILE 4.6 2.0 - - - +
93E GLN* 3.6 24.2 - - + -
103E SER* 1.3 74.0 - - - +
105E TYR* 1.3 67.6 + - - +
57F GLN* 5.5 0.2 - - - -
103F SER* 4.3 9.9 - - - -
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Residues in contact with TYR 105 (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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53D PHE* 4.6 1.7 - - - -
105D TYR* 3.5 36.8 + + - +
107D ALA* 3.3 43.0 + - + +
53E PHE* 4.0 10.4 - - - -
55E TYR* 3.5 26.5 - + + +
56E GLY 3.4 12.8 - - - -
57E GLN* 3.7 22.2 + - + +
103E SER 4.3 0.2 - - - -
104E CYS* 1.3 80.6 - - - +
106E SER* 1.3 62.9 + - - +
107E ALA* 3.6 20.1 - - + +
137E PHE* 4.3 4.5 - + - -
57F GLN* 4.3 0.3 - - - +
105F TYR* 3.5 51.1 + + - +
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Residues in contact with SER 106 (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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55E TYR* 3.5 1.2 - - - +
56E GLY 3.0 31.8 + - - +
69E HIS* 5.1 3.8 - - - -
71E ILE* 4.0 8.2 - - - +
89E PHE* 4.0 13.5 - - - +
90E ARG 4.6 2.8 + - - -
91E CYS* 4.0 18.1 - - - -
105E TYR* 1.3 81.5 - - - +
107E ALA* 1.3 63.3 + - - +
57F GLN* 2.7 30.0 + - - -
105F TYR* 4.4 2.2 - - - -
137F PHE* 3.9 7.3 - - - -
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Residues in contact with ALA 107 (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 PHE* 3.6 15.5 - - + -
54E ILE 3.0 16.4 - - - +
55E TYR* 3.5 15.0 - - + -
89E PHE* 4.5 8.0 - - - +
105E TYR* 3.6 16.8 - - + +
106E SER* 1.3 79.6 + - - +
108E GLY* 1.3 58.3 + - - +
55F TYR* 4.4 1.0 - - - -
105F TYR* 3.3 18.4 + - - +
137F PHE* 3.3 22.5 - - - -
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Residues in contact with GLY 108 (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 PHE 3.8 0.2 - - - +
53E PHE* 3.5 8.1 - - - -
54E ILE* 2.8 30.6 + - - +
89E PHE* 3.3 26.4 - - - -
107E ALA* 1.3 76.0 - - - +
109E ILE* 1.3 63.9 + - - -
7F GLN* 3.8 6.7 - - - -
55F TYR* 4.5 7.2 - - - -
137F PHE* 4.8 0.2 - - - -
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Residues in contact with ILE 109 (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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51E TYR* 4.3 8.7 - - + -
52E PHE 3.2 12.1 - - - +
53E PHE* 4.2 13.9 - - + -
89E PHE* 3.8 4.4 - - - -
108E GLY* 1.3 77.1 - - - +
110E ALA* 1.3 69.4 + - - +
143E LEU* 3.9 18.6 - - + -
5F CYS* 4.2 15.5 - - + -
6F LEU 6.4 0.2 - - - -
7F GLN* 2.9 29.5 - - - +
31F PHE* 3.5 26.7 - - + -
53F PHE* 6.2 0.2 - - + -
55F TYR* 3.7 24.9 - - + +
140F ALA 5.3 0.2 - - - +
141F LEU* 3.8 29.2 - - + -
79J PHE* 3.9 5.0 - - - -
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Residues in contact with ALA 110 (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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51E TYR* 3.6 5.6 - - - -
52E PHE* 2.9 32.0 + - - +
54E ILE* 4.2 11.2 - - + +
73E ARG* 6.1 0.2 - - - -
88E LEU* 4.1 31.9 - - + -
89E PHE* 4.6 1.6 - - + -
109E ILE* 1.3 78.1 - - - +
111E LYS* 1.3 66.3 + - - +
112E LEU* 3.7 6.7 + - + +
79J PHE* 3.6 17.5 - - + -
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Residues in contact with LYS 111 (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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49E THR* 5.1 8.7 - - - -
50E GLY* 3.4 13.5 - - - +
51E TYR* 3.7 41.1 + - + +
73E ARG* 3.6 18.0 + - - +
110E ALA* 1.3 75.7 - - - +
112E LEU* 1.3 78.1 + - - +
113E GLU* 5.2 10.3 - - + -
79J PHE* 3.8 21.6 - - + -
111J LYS* 4.6 18.4 - - - +
113J GLU* 4.1 21.1 + - - +
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Residues in contact with LEU 112 (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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46E VAL* 3.7 26.5 - - + -
49E THR* 3.1 3.4 - - - -
50E GLY 2.9 31.2 + - - -
52E PHE* 3.7 32.8 - - + -
54E ILE* 4.0 7.0 - - + -
73E ARG* 3.7 30.7 - - + +
88E LEU* 4.8 0.4 - - + -
110E ALA* 4.1 15.0 - - + +
111E LYS* 1.3 88.3 - - - +
113E GLU* 1.3 64.7 + - - +
116E ASP* 3.4 7.6 - - + +
118E LEU* 3.8 30.5 - - + -
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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