Contacts of the strand formed by residues 103 - 112 (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 LEU 103 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98E TYR* 4.0 11.0 - - + +
99E GLU* 3.5 3.1 - - - +
100E THR 3.0 29.7 + - - +
101E GLY 3.8 1.0 - - - +
102E LEU* 1.3 79.9 - - + +
104E PHE* 1.3 64.9 + - - +
213E ILE* 3.5 42.0 - - + -
215E LYS* 4.2 21.1 - - - +
228E TYR* 5.1 3.1 - - + +
284E PHE* 3.5 43.3 - - + -
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Residues in contact with PHE 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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30B ASN* 3.8 21.5 - - - -
31B ARG* 3.2 43.5 - - + +
32B ARG* 4.8 5.4 - - - -
98E TYR* 3.2 25.3 + - - +
99E GLU* 4.1 15.7 - - + -
102E LEU 3.4 11.7 - - - -
103E LEU* 1.3 76.8 - - - +
105E GLY* 1.3 60.4 + - - +
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Residues in contact with GLY 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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97E CYS* 3.2 5.2 - - - +
98E TYR* 2.9 50.4 + - - +
104E PHE* 1.3 78.7 - - - +
106E SER* 1.3 58.9 + - - -
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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
----------------------------------------------------------
96E GLY 3.3 12.3 - - - -
97E CYS* 3.9 9.2 - - - +
98E TYR* 4.1 2.3 - - - -
105E GLY* 1.3 75.7 - - - -
107E TYR* 1.3 67.9 + - - +
159E GLU* 2.7 43.3 + - - +
163E CYS* 5.2 3.1 - - - -
164E SER* 5.9 3.4 - - - -
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Residues in contact with TYR 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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2E THR* 5.5 1.7 - - - +
3E LEU 3.5 17.3 + - - -
4E LYS* 3.6 18.2 - - - +
94E ILE* 3.8 12.3 - - + -
95E THR* 2.7 35.7 + - - -
96E GLY 2.8 45.2 + - - +
97E CYS* 3.8 10.3 + - - -
98E TYR* 4.5 4.5 - + + -
106E SER* 1.3 80.7 - - - +
108E GLY* 1.3 53.2 + - - +
109E TYR* 4.1 6.3 - + + -
159E GLU* 3.5 15.0 - - - +
246E GLY 3.5 26.7 - - - -
247E GLU* 4.0 27.4 - - + +
248E PRO* 3.3 21.9 - - + +
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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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94E ILE 3.2 8.1 - - - -
95E THR* 3.7 8.7 - - - -
107E TYR* 1.3 78.5 - - - +
109E TYR* 1.3 60.8 + - - +
119E ARG* 3.9 3.2 - - - +
120E TYR* 2.8 34.7 + - - +
155E LEU* 4.1 9.9 - - - -
159E GLU* 3.4 15.0 + - - +
247E GLU* 5.4 0.2 + - - -
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Residues in contact with TYR 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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93E LEU* 3.7 4.7 - - - +
94E ILE* 2.8 62.1 + - + +
107E TYR* 4.1 9.4 - + - -
108E GLY* 1.3 77.2 - - - +
110E VAL* 1.3 70.1 + - - +
111E GLU* 3.3 25.6 + - + -
118E ALA 3.2 13.2 - - - +
119E ARG* 3.8 8.7 - - + -
120E TYR 4.5 0.2 - - - +
127E PHE* 4.9 1.6 - - - -
130E MET* 3.6 24.0 - - + -
243E TYR* 3.7 12.5 - + - -
247E GLU* 3.7 36.6 - - + -
248E PRO* 3.4 11.0 - - + +
249E GLY* 3.2 26.3 + - - -
325E NAG 4.6 2.3 - - - +
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Residues in contact with VAL 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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91E LEU* 3.5 32.8 - - + -
92E SER 3.2 7.6 - - - +
93E LEU* 3.8 20.0 - - + -
109E TYR* 1.3 76.1 - - - +
111E GLU* 1.3 61.2 + - - +
117E LEU* 2.9 37.2 + - + +
118E ALA 2.7 16.5 + - - +
127E PHE* 4.0 15.5 - - + -
130E MET* 3.2 2.8 - - - +
140E MET* 4.0 20.9 - - + -
141E LEU* 4.3 13.9 - - + -
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Residues in contact with GLU 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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91E LEU* 3.5 7.1 - - - +
92E SER* 2.9 46.3 + - - -
94E ILE* 4.1 11.5 - - + +
109E TYR* 3.3 23.8 + - + -
110E VAL* 1.3 75.1 - - - +
112E THR* 1.3 64.9 - - - +
115E GLY* 3.9 4.5 - - - +
116E PRO* 3.9 17.3 - - + -
117E LEU* 3.9 1.6 - - - +
243E TYR* 3.1 20.1 + - - -
249E GLY* 5.4 0.9 - - - -
325E NAG 3.7 25.7 + - - +
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Residues in contact with THR 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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77E LEU* 6.1 0.2 - - - +
80E ILE* 4.7 5.0 - - - +
86E THR* 5.9 1.8 - - + +
88E THR* 3.2 15.1 + - + +
90E SER* 3.8 7.9 + - - -
91E LEU* 3.7 18.1 - - - +
111E GLU* 1.3 77.7 - - - +
113E ALA* 1.3 62.8 + - - +
114E ASN* 2.8 40.8 - - + +
115E GLY* 2.8 30.9 + - - +
117E LEU* 4.1 17.6 - - - +
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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