Contacts of the strand formed by residues 106 - 112 (chain E) in PDB entry 5IJ7
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 ARG 106 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A CYS* 3.3 35.2 - - - +
84A SER 4.5 4.4 + - - -
85A VAL* 5.7 1.4 - - - +
98A LEU* 4.1 17.4 - - - +
76E GLU* 4.9 6.2 + - - +
77E ASP* 2.8 39.1 + - - +
78E HIS* 3.8 34.1 - - + +
101E THR 4.4 0.7 - - - -
102E VAL* 3.5 4.0 - - - -
103E GLY 2.9 32.8 + - - +
104E SER* 3.2 0.8 + - - -
105E ASN* 1.3 85.5 - - - +
107E VAL* 1.3 65.8 + - - +
108E THR* 4.3 12.5 + - - +
123E SER* 3.6 12.9 + - - -
124E TYR 3.2 14.6 - - - +
125E VAL* 4.0 11.0 - - + -
133E PHE* 3.6 4.6 - - - -
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Residues in contact with VAL 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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101A LEU* 4.8 0.9 - - + -
100E ALA* 5.1 0.4 - - + -
101E THR 3.4 8.7 - - - +
102E VAL* 4.1 3.4 - - + -
106E ARG* 1.3 77.2 - - - +
108E THR* 1.3 62.6 + - - +
109E LEU* 4.2 9.0 - - + -
123E SER* 3.2 2.9 + - - -
124E TYR* 2.8 50.5 + - + -
133E PHE* 4.0 13.9 - - + -
149E LEU* 3.6 31.2 - - + -
151E VAL* 3.6 35.2 - - + -
161E ILE* 4.2 11.9 - - + -
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Residues in contact with THR 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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85A VAL* 5.1 1.8 - - + -
76E GLU* 3.6 26.9 + - - +
99E PHE 4.0 0.3 - - - +
100E ALA* 3.3 3.3 - - - -
101E THR* 2.7 40.4 + - - +
106E ARG* 4.5 10.0 + - - +
107E VAL* 1.3 76.7 + - - +
109E LEU* 1.3 64.2 + - - +
110E TYR* 3.5 24.6 - - + +
120E LEU* 3.5 21.1 - - + -
122E GLN 3.4 10.8 - - - +
123E SER* 3.3 15.3 + - - +
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Residues in contact with LEU 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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68A VAL* 3.8 16.6 - - + -
98E VAL* 5.1 2.9 - - + -
99E PHE 3.5 3.1 - - - +
100E ALA* 4.4 0.4 - - + -
107E VAL* 4.2 9.2 - - + -
108E THR* 1.3 78.4 - - - +
110E TYR* 1.3 67.5 - - - +
120E LEU* 4.0 2.3 - - - +
121E LEU* 3.0 27.1 + - + -
122E GLN* 2.8 30.0 + - + +
124E TYR* 4.4 15.7 - - + -
138E TRP* 3.8 24.9 - - + -
149E LEU* 4.1 23.3 - - + -
161E ILE* 6.3 0.2 - - + -
163E PRO* 3.7 30.3 - - + -
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Residues in contact with TYR 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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85A VAL* 3.4 20.4 - - + +
74E LEU* 3.6 17.3 - - + -
76E GLU* 2.6 30.2 + - - -
98E VAL* 3.1 11.9 - - - +
99E PHE* 2.9 68.4 + + + +
101E THR* 4.0 6.7 - - - -
108E THR* 3.5 21.6 - - + +
109E LEU* 1.3 77.4 - - - +
111E GLU* 1.3 59.6 - - - +
118E ILE* 3.7 17.7 - - + -
119E ARG 3.4 3.6 - - - -
120E LEU* 3.9 27.4 - - + -
121E LEU* 4.4 3.1 - - - +
420E ILE* 3.4 19.0 - - + +
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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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67A PRO* 5.7 0.9 - - - +
68A VAL 3.6 20.8 - - - +
69A HIS* 5.3 1.6 + - - -
96E PRO* 3.2 41.1 - - + +
97E LEU 3.6 2.2 - - - +
98E VAL* 3.8 10.8 - - + +
110E TYR* 1.3 73.1 - - - +
112E CYS* 1.3 63.2 + - - +
113E HIS* 3.1 25.1 + - + -
117E GLU 3.8 0.3 - - - +
118E ILE* 3.5 4.6 - - - -
119E ARG* 2.8 58.1 + - + +
121E LEU* 3.8 22.0 - - + +
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Residues in contact with CYS 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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87E PHE* 3.9 15.0 - - - -
96E PRO* 4.1 11.4 - - - +
97E LEU* 2.8 26.9 + - + +
99E PHE* 3.6 33.0 - - - -
111E GLU* 1.3 71.6 - - - +
113E HIS* 1.3 71.9 + - - +
117E GLU 3.8 3.4 - - - -
118E ILE* 4.8 2.2 - - - +
410E ILE* 3.7 28.0 - - + -
422E ARG* 4.0 14.8 - - - -
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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