Contacts of the helix formed by residues 122 - 131 (chain E) in PDB entry 1P84
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 122 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103E LEU* 4.4 19.3 - - + -
104E GLY* 4.2 22.0 - - - -
121E ARG* 1.3 74.6 - - - +
123E PRO* 1.3 75.2 - - - +
124E HIS* 3.7 8.5 + - - +
125E GLU* 3.0 42.8 + - - +
126E ILE* 3.1 16.5 + - - +
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Residues in contact with PRO 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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103E LEU* 5.6 7.4 - - + -
121E ARG 4.6 1.6 - - - +
122E THR* 1.3 87.0 - - - +
124E HIS* 1.3 64.9 + - + +
126E ILE* 3.4 15.1 + - + +
127E GLN 3.3 15.1 + - - -
49K TYR* 5.6 0.7 - - - +
54K LEU* 3.8 34.1 - - + +
55K HIS 3.8 17.0 - - - +
56K ALA* 3.5 15.2 + - - +
57K GLY 5.1 0.4 - - - +
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Residues in contact with HIS 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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122E THR* 3.2 8.4 + - - +
123E PRO* 1.3 80.0 - - + +
125E GLU* 1.3 67.6 + - + +
127E GLN* 3.2 9.4 + - - +
128E GLU* 3.0 22.8 + - - +
56K ALA* 4.0 11.9 - - + +
57K GLY* 3.7 32.2 + - - -
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Residues in contact with GLU 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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119E ARG* 3.1 41.2 + - - -
121E ARG* 3.4 13.9 - - + +
122E THR* 3.0 39.4 + - - +
124E HIS* 1.3 76.8 - - + +
126E ILE* 1.3 62.3 + - - +
128E GLU* 3.1 13.2 + - - +
129E ALA* 3.0 21.9 + - - +
187E ILE* 3.6 30.3 - - + +
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Residues in contact with ILE 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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121E ARG* 4.1 18.4 - - + +
122E THR 3.1 15.2 + - - +
123E PRO* 3.6 14.6 - - + +
124E HIS 3.3 0.2 - - - -
125E GLU* 1.3 77.3 - - - +
127E GLN* 1.3 52.6 + - - +
129E ALA* 3.7 6.3 + - - +
130E ASN* 2.7 47.4 + - - +
150E PRO* 3.2 50.5 - - + +
151E GLN* 4.1 8.7 - - + +
100J GLU* 5.4 0.9 - - - +
102J TYR* 3.9 5.8 + - + +
49K TYR* 4.0 22.7 - - + +
53K ARG* 6.5 0.2 - - - -
54K LEU 6.0 0.2 - - - +
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Residues in contact with GLN 127 (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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123E PRO 3.3 9.6 + - - +
124E HIS* 3.2 13.7 + - - +
125E GLU 3.2 0.4 - - - -
126E ILE* 1.3 77.0 - - - +
128E GLU* 1.3 65.1 + - - +
130E ASN* 3.0 14.5 - - - +
131E SER* 2.7 27.6 + - - +
100J GLU* 5.6 0.4 - - - -
110J ASP* 5.2 1.5 + - - +
111J TYR* 3.4 38.0 + - + +
55K HIS* 3.5 31.3 + - + +
56K ALA* 4.0 16.1 + - + +
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Residues in contact with GLU 128 (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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124E HIS 3.0 13.7 + - - +
125E GLU* 3.1 15.9 + - - +
127E GLN* 1.3 76.5 - - - +
129E ALA* 1.3 61.4 + - - +
131E SER* 3.5 7.1 + - - -
132E VAL* 3.2 24.9 - - + +
173E PHE 4.0 19.4 - - - +
174E GLY* 4.8 5.0 - - - -
186E ASP* 5.9 0.5 - - - +
187E ILE* 4.2 16.1 - - + +
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Residues in contact with ALA 129 (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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121E ARG* 3.6 27.1 - - - +
125E GLU 3.0 13.1 + - - +
126E ILE 3.8 3.8 - - - +
128E GLU* 1.3 78.3 - - - +
130E ASN* 1.3 55.1 + - - +
131E SER 3.4 3.3 + - - -
132E VAL* 3.9 3.9 + - - +
143E ASP* 3.6 16.2 - - + +
187E ILE* 3.8 13.2 - - + +
188E SER* 4.2 4.9 - - - -
190E ARG* 2.8 37.5 + - - +
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Residues in contact with ASN 130 (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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126E ILE* 2.7 29.0 + - - +
127E GLN* 3.0 21.1 - - - +
129E ALA* 1.3 75.7 - - - +
131E SER* 1.3 61.0 + - - +
132E VAL 3.5 2.0 - - - -
143E ASP* 4.4 2.2 - - + -
190E ARG* 4.8 0.9 - - - +
27J TYR* 3.7 6.3 - - - -
33J TYR* 3.3 30.8 - - + +
98J ARG* 3.1 27.2 + - - -
100J GLU* 2.8 28.9 + - - +
102J TYR* 3.0 22.0 + - - +
110J ASP* 4.3 1.4 - - - +
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Residues in contact with SER 131 (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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127E GLN* 2.7 22.6 + - - +
128E GLU* 3.5 4.6 + - - +
129E ALA 3.3 1.4 - - - -
130E ASN* 1.3 81.9 + - - +
132E VAL* 1.3 63.0 + - - +
133E ASP 4.3 0.2 + - - -
1J GLU* 5.5 8.2 + - - -
2J VAL* 4.1 12.0 - - - +
26J GLY 4.3 9.9 - - - +
27J TYR* 4.1 11.9 - - - -
111J TYR* 3.0 30.7 + - - -
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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