Contacts of the strand formed by residues 90 - 100 (chain E) in PDB entry 3IT8
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 SER 90 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E THR* 4.3 9.6 - - - +
9E VAL 3.1 15.5 - - - -
10E THR* 3.6 19.7 - - - +
77E LEU* 4.1 7.4 - - - +
88E THR* 3.1 22.3 - - - +
89E THR* 1.3 82.4 - - - +
91E LEU* 1.3 63.1 + - - +
92E SER* 5.1 1.9 + - - -
112E THR* 3.8 3.3 + - - -
113E ALA* 3.5 21.6 + - - +
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Residues in contact with LEU 91 (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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8E THR* 3.3 4.7 - - - +
9E VAL* 3.0 40.3 + - + -
73E MET* 3.3 18.2 - - + +
76E THR* 3.5 37.0 - - + -
77E LEU* 4.1 12.3 - - + +
80E ILE* 4.1 13.5 - - + -
90E SER* 1.3 75.8 - - - +
92E SER* 1.3 64.3 + - - +
110E VAL* 3.5 20.0 - - + -
111E GLU 3.5 17.0 - - - +
112E THR* 3.7 16.2 - - - +
117E LEU* 4.5 1.1 - - + -
140E MET* 3.9 13.2 - - + -
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Residues in contact with SER 92 (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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6E ASN* 4.1 7.2 + - - -
7E TYR 3.1 8.1 - - - -
8E THR* 3.0 27.3 + - - +
73E MET* 3.9 3.6 - - - -
90E SER* 5.1 1.9 + - - -
91E LEU* 1.3 73.7 - - - +
93E LEU* 1.3 60.3 + - - +
94E ILE* 3.9 6.1 - - - -
110E VAL* 3.2 10.0 - - - +
111E GLU* 2.9 54.3 + - - -
325E NAG 4.5 6.0 - - - -
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Residues in contact with LEU 93 (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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5E TYR 3.4 5.5 - - - +
6E ASN* 3.6 0.7 - - - -
7E TYR* 2.8 56.4 + - + -
69E TRP* 3.7 48.5 - - + -
73E MET* 3.7 10.0 - - + +
92E SER* 1.3 72.3 - - - +
94E ILE* 1.3 63.1 + - - +
95E THR* 3.9 3.5 + - + -
109E TYR 3.7 13.2 - - - +
110E VAL* 3.8 18.8 - - + -
140E MET* 5.0 3.6 - - + -
155E LEU* 4.3 30.1 - - + -
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Residues in contact with ILE 94 (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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4E LYS* 4.7 3.6 - - + -
5E TYR 3.6 4.0 - - - +
6E ASN* 3.4 33.4 - - + +
92E SER* 4.2 6.5 - - - -
93E LEU* 1.3 72.5 - - - +
95E THR* 1.3 63.8 + - - +
107E TYR* 3.8 5.6 - - + -
108E GLY* 3.2 2.3 + - - -
109E TYR* 2.8 70.9 + - + +
111E GLU* 4.1 11.4 - - + -
248E PRO* 3.4 33.2 - - + -
325E NAG 3.5 27.1 - - + +
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Residues in contact with THR 95 (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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4E LYS 3.7 0.2 - - - -
5E TYR* 2.7 54.5 + - + +
7E TYR* 4.7 10.3 - - + -
93E LEU* 5.0 5.4 - - + +
94E ILE* 1.3 77.1 - - - +
96E GLY* 1.3 52.6 + - - +
107E TYR* 2.7 27.1 + - - -
108E GLY* 3.9 4.0 - - - -
155E LEU* 3.7 23.3 - - + +
158E PHE* 3.8 23.3 - - + -
159E GLU* 4.7 4.3 - - - +
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Residues in contact with GLY 96 (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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3E LEU 3.1 13.9 - - - -
5E TYR 4.6 0.2 - - - -
95E THR* 1.3 78.6 + - - +
97E CYS* 1.3 61.2 + - - +
106E SER* 3.3 4.3 - - - -
107E TYR* 2.8 41.5 + - - +
158E PHE* 4.3 2.7 - - - -
159E GLU* 5.7 0.7 - - - -
163E CYS* 3.6 15.7 - - - +
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Residues in contact with CYS 97 (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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2E THR* 3.9 2.1 + - - -
3E LEU* 2.9 30.1 + - - +
96E GLY* 1.3 75.3 - - - +
98E TYR* 1.3 70.3 + - - +
105E GLY 3.2 15.3 - - - +
106E SER* 3.9 9.4 - - - +
107E TYR* 3.8 6.6 + - - -
163E CYS* 3.2 34.1 - - + -
164E SER* 3.9 9.2 - - - +
167E ILE* 3.7 33.4 - - - -
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Residues in contact with TYR 98 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E ILE 3.5 11.4 - - - +
2E THR* 3.9 9.4 - - - +
97E CYS* 1.3 86.5 - - - +
99E GLU* 1.3 63.1 + - - +
100E THR* 3.6 22.0 - - - +
103E LEU* 4.0 10.5 - - + +
104E PHE* 3.2 33.2 + - - +
105E GLY* 2.9 45.2 + - - +
106E SER 4.1 2.0 - - - -
107E TYR* 4.5 6.5 - + + -
167E ILE* 4.5 3.1 - - - -
211E ASP* 5.7 0.4 - - + -
213E ILE* 4.3 11.2 - - + +
245E PRO 4.1 9.4 + - - -
246E GLY* 3.7 35.4 - - - +
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Residues in contact with GLU 99 (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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31B ARG* 3.2 42.1 + - - +
32B ARG* 2.9 37.1 + - - -
1E ILE* 2.9 53.2 + - + +
98E TYR* 1.3 76.4 - - - +
100E THR* 1.3 59.8 + - - +
101E GLY 3.5 2.9 + - - +
103E LEU 3.5 4.9 - - - -
104E PHE* 4.1 9.0 - - + -
164E SER 5.3 1.2 - - - +
167E ILE* 4.9 7.8 - - + +
168E LEU* 4.0 8.2 - - - +
286E ASP* 3.0 7.6 - - - +
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Residues in contact with THR 100 (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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98E TYR* 3.6 21.8 - - - +
99E GLU* 1.3 69.1 - - - +
101E GLY* 1.3 66.1 + - - +
102E LEU 3.2 0.5 + - - -
103E LEU* 3.0 25.0 + - - +
211E ASP* 3.0 45.3 + - - +
212E VAL 4.1 0.2 - - - +
213E ILE* 3.9 25.0 - - + +
284E PHE* 3.2 29.5 - - - +
285E HIS* 4.3 1.8 - - - -
286E ASP* 4.0 1.1 - - - -
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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