Contacts of the helix formed by residues 92 - 105 (chain E) in PDB entry 5IC4
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 THR 92 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90E ASP 5.2 1.6 - - - +
91E LEU* 1.3 75.3 - - - +
93E ARG* 1.3 65.7 + - - +
94E GLU* 3.3 11.1 + - - +
95E GLU* 2.8 42.1 + - - +
96E ILE* 3.0 21.8 + - - +
129E GLY* 4.1 1.1 - - - -
130E THR* 3.4 15.9 - - - +
131E ASN* 3.3 23.6 - - + +
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Residues in contact with ARG 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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92E THR* 1.3 71.2 - - - +
94E GLU* 1.3 84.0 + - + +
96E ILE* 3.6 1.2 + - - +
97E VAL* 3.3 28.5 + - - +
129E GLY* 3.9 5.1 - - - -
131E ASN* 2.6 35.1 + - - +
132E GLY* 3.8 16.3 - - - +
133E PRO* 3.4 39.2 + - - +
134E VAL* 3.5 26.4 - - + +
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Residues in contact with GLU 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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92E THR* 3.3 8.7 + - - +
93E ARG* 1.3 91.1 + - + +
95E GLU* 1.3 62.6 + - + +
97E VAL* 3.5 6.3 + - - +
98E GLU* 3.0 31.1 + - - +
131E ASN* 2.9 25.0 + - - -
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Residues in contact with GLU 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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90E ASP 4.1 2.8 - - - +
91E LEU* 3.4 27.9 - - + +
92E THR* 2.8 46.8 + - - +
94E GLU* 1.3 75.7 - - + +
96E ILE* 1.3 61.6 + - - +
98E GLU* 3.8 12.4 - - - +
99E LEU* 2.9 31.8 + - - +
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Residues in contact with ILE 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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50E ILE* 3.9 27.8 - - + -
52E ASN* 4.0 12.6 - - - +
91E LEU* 3.7 19.5 - - + +
92E THR 3.0 17.1 + - - +
93E ARG* 3.8 5.8 - - - +
94E GLU 3.3 0.2 - - - -
95E GLU* 1.3 76.1 - - - +
97E VAL* 1.3 63.7 + - - +
99E LEU* 3.3 2.3 + - - +
100E MET* 3.0 32.3 + - + +
118E LEU* 5.3 2.2 - - + -
127E ILE* 5.0 7.4 - - + -
128E PHE 4.5 2.5 - - - +
129E GLY* 3.8 26.5 - - - +
134E VAL* 4.7 7.0 - - + -
139E ILE* 3.8 29.2 - - + -
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Residues in contact with VAL 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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93E ARG 3.3 17.6 + - - +
94E GLU* 3.8 5.8 - - - +
96E ILE* 1.3 75.8 - - - +
98E GLU* 1.3 58.7 + - - +
100E MET* 3.5 1.7 + - - -
101E ARG* 3.0 55.4 + - - +
134E VAL* 3.8 25.4 - - + -
138E LYS* 4.0 26.7 - - + +
139E ILE* 5.2 2.7 - - + -
142E PHE* 3.7 18.0 - - + -
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Residues in contact with GLU 98 (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 GLU 3.0 19.0 + - - +
95E GLU* 3.8 14.0 - - - +
97E VAL* 1.3 75.2 - - - +
99E LEU* 1.3 64.8 + - - +
101E ARG* 3.9 16.7 - - - +
102E ASP* 3.1 48.0 + - - +
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Residues in contact with LEU 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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48E ILE* 4.1 19.7 - - + -
50E ILE* 4.3 9.9 - - + -
86E ARG* 5.9 1.8 - - - +
88E LYS* 3.8 44.6 - - + +
91E LEU* 3.9 15.5 - - + -
95E GLU 2.9 19.6 + - - +
96E ILE 3.7 2.9 - - - +
98E GLU* 1.3 75.1 + - - +
100E MET* 1.3 57.6 + - - +
102E ASP* 3.1 8.6 + - + +
103E VAL* 2.7 55.6 + - + +
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Residues in contact with MET 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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48E ILE* 4.3 12.8 - - + -
50E ILE* 4.3 13.0 - - + -
96E ILE* 3.0 24.2 + - + +
97E VAL* 3.9 3.4 - - - +
99E LEU* 1.3 78.7 - - - +
101E ARG* 1.3 58.5 + - - +
103E VAL* 4.3 4.5 - - - -
104E SER* 2.9 30.5 + - - -
114E PHE* 3.9 10.5 - - + -
116E CYS* 3.5 32.5 - - + -
139E ILE* 3.5 24.2 - - + -
142E PHE* 4.0 17.4 - - + +
143E PHE* 3.5 34.1 - - + -
158E PHE* 4.2 1.1 - - + -
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Residues in contact with ARG 101 (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 VAL* 3.0 43.2 + - - +
98E GLU* 3.9 18.7 - - - +
100E MET* 1.3 73.7 - - - +
102E ASP* 1.3 67.7 + - - +
104E SER* 2.6 22.8 + - - +
105E LYS* 3.1 39.8 + - + +
138E LYS* 4.7 8.5 - - - +
142E PHE* 3.3 32.0 - - + -
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Residues in contact with ASP 102 (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 GLU* 3.1 36.9 + - - +
99E LEU* 3.6 7.3 - - + +
101E ARG* 1.3 80.3 - - - +
103E VAL* 1.3 63.0 + - + +
105E LYS* 3.4 26.8 + - - +
106E GLU* 3.5 16.0 + - - +
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Residues in contact with VAL 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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46E LEU* 3.9 16.6 - - + -
48E ILE* 4.3 14.1 - - + -
86E ARG* 4.3 9.2 - - - +
99E LEU* 2.7 45.0 + - + +
100E MET* 3.9 7.9 - - - +
102E ASP* 1.3 73.7 - - + +
104E SER* 1.3 60.9 + - - +
106E GLU* 3.1 24.0 + - - +
108E HIS* 2.9 24.3 + - + -
114E PHE* 3.6 33.4 - - + -
143E PHE* 4.2 2.5 - - + -
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Residues in contact with SER 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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100E MET 2.9 16.4 + - - -
101E ARG* 2.6 25.1 + - - +
103E VAL* 1.3 77.5 - - - +
105E LYS* 1.3 63.1 + - - +
106E GLU 3.3 4.0 + - - +
108E HIS* 4.4 0.9 - - - -
142E PHE* 3.5 34.1 + - - +
143E PHE* 3.6 21.3 - - - -
147E ARG 4.9 2.1 - - - +
148E CYS* 3.2 27.1 - - - +
150E SER* 5.0 0.2 + - - -
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Residues in contact with LYS 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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101E ARG* 3.1 45.4 + - + +
102E ASP* 3.4 15.9 + - - +
103E VAL 3.2 0.4 - - - -
104E SER* 1.3 79.9 - - - +
106E GLU* 1.3 64.3 + - - +
147E ARG 5.6 5.4 - - - +
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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