Contacts of the strand formed by residues 118 - 126 (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 ILE 118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A PHE* 5.1 0.4 - - - -
94A GLN* 2.8 28.6 + - - -
72E ASN* 3.6 25.2 + - + +
74E LEU* 3.7 24.3 - - + +
99E PHE* 3.8 14.8 - - + -
110E TYR* 3.7 37.5 - - + -
111E GLU 3.5 6.3 - - - +
112E CYS* 5.0 1.1 - - - -
116E GLY 3.3 11.1 + - - +
117E GLU* 1.3 76.6 - - - +
119E ARG* 1.3 53.8 + - - +
120E LEU 4.0 0.2 - - - -
412E ILE* 4.6 7.9 - - + -
420E ILE* 4.8 5.8 - - + -
422E ARG* 3.7 37.7 - - + +
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Residues in contact with ARG 119 (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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69A HIS* 5.9 2.8 + - - +
70A ILE* 3.5 41.9 - - + +
94A GLN* 3.6 9.9 - - - +
110E TYR* 3.4 4.4 - - - -
111E GLU* 2.8 61.0 + - + +
113E HIS* 3.9 20.7 - - + +
117E GLU* 3.8 17.4 - - - +
118E ILE* 1.3 71.2 - - - +
120E LEU* 1.3 66.3 + - - +
121E LEU* 3.3 23.4 + - + +
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Residues in contact with LEU 120 (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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70A ILE* 3.8 10.4 - - - +
83A CYS* 4.2 9.2 - - - +
84A SER 4.5 0.4 - - - -
85A VAL* 3.9 22.0 - - + +
94A GLN* 2.9 56.2 + - + +
96A ILE* 3.6 47.9 - - + +
108E THR* 3.5 32.1 - - + -
109E LEU 4.2 0.7 - - - +
110E TYR* 3.9 19.5 - - + -
118E ILE 3.8 0.2 + - - -
119E ARG* 1.3 69.5 - - - +
121E LEU* 1.4 58.5 + - - +
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Residues in contact with LEU 121 (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 36.3 - - + +
69A HIS* 4.1 8.1 - - - +
70A ILE* 3.7 16.9 - - - +
71A MET* 3.1 26.3 + - - +
96A ILE* 3.7 7.9 - - - +
98E VAL* 4.2 9.9 - - + -
109E LEU* 3.0 16.0 + - + +
110E TYR 4.4 4.0 - - - +
111E GLU* 3.8 30.7 - - + +
119E ARG* 3.3 46.4 + - - +
120E LEU* 1.4 71.9 - - - +
122E GLN* 1.3 61.8 + - + +
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Residues in contact with GLN 122 (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* 3.3 15.9 - - + +
69A HIS 2.9 24.8 + - - +
71A MET* 3.8 23.3 - - + -
96A ILE* 3.6 6.3 - - - -
107E VAL 4.5 0.2 - - - -
108E THR* 3.4 4.5 - - - +
109E LEU* 2.8 38.3 + - + +
121E LEU* 1.3 85.7 - - + +
123E SER* 1.3 63.5 + - - +
124E TYR* 2.7 35.2 + - + -
163E PRO* 2.7 35.0 + - - +
166E MET* 3.8 7.6 - - - +
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Residues in contact with SER 123 (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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71A MET* 3.8 7.4 - - - +
83A CYS* 3.5 26.9 - - - -
96A ILE* 3.5 9.0 - - - +
97A PRO 3.8 1.8 - - - +
98A LEU* 3.5 15.6 - - - +
99A LYS 3.0 23.2 + - - -
106E ARG* 3.6 10.9 + - - -
107E VAL 3.2 6.0 + - - -
108E THR* 3.3 22.6 + - - -
122E GLN* 1.3 77.1 - - - +
124E TYR* 1.3 63.0 + - - +
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Residues in contact with TYR 124 (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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71A MET* 3.4 17.2 - - + +
98A LEU* 3.6 2.4 - - - +
99A LYS* 3.2 29.8 - - + +
101A LEU* 3.9 32.8 - - + -
105E ASN 4.6 0.2 - - - -
106E ARG* 3.2 11.3 - - - +
107E VAL* 2.8 48.0 + - + +
109E LEU* 4.4 9.2 - - + -
122E GLN* 2.7 38.7 + - + -
123E SER* 1.3 75.4 - - - +
125E VAL* 1.3 61.1 + - - +
161E ILE* 3.6 26.5 - - + +
163E PRO* 3.7 7.0 - - + +
166E MET* 3.3 28.5 - - - -
167E GLN* 4.5 0.9 - - - -
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Residues in contact with VAL 125 (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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81A ARG* 3.4 37.5 - - - +
98A LEU* 3.7 22.4 - - + -
99A LYS 2.9 12.7 + - - +
100A THR* 3.4 16.5 - - + +
101A LEU* 2.8 28.7 + - - +
105E ASN* 3.4 28.3 - - - +
106E ARG* 4.0 9.0 - - + -
124E TYR* 1.3 76.0 - - - +
126E ASP* 1.3 74.3 + - - +
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Residues in contact with ASP 126 (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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81A ARG* 5.3 1.2 + - - -
100A THR* 4.7 0.2 - - - -
101A LEU* 3.9 8.7 - - - +
103A ALA* 5.0 1.2 - - - -
105E ASN* 3.0 32.3 + - + +
125E VAL* 1.3 79.2 - - - +
127E ALA* 1.4 67.3 + - - +
128E ASP* 3.1 37.8 + - - +
131E GLU* 3.6 24.9 - - + +
133E PHE* 3.4 16.9 - - + -
155E ARG* 4.0 7.4 + - - -
159E ARG* 3.1 36.4 + - - -
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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