Contacts of the helix formed by residues 124 - 134 (chain E) in PDB entry 4XH9
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 ASP 124 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B GLU* 4.8 9.7 - - - +
126B HIS* 4.9 2.6 + - - +
129B ARG* 3.7 23.1 + - - -
120E ASP 4.3 4.0 + - - +
121E LEU* 3.1 26.4 + - + +
122E ARG 3.3 0.2 - - - -
123E ASN* 1.3 77.6 - - - +
125E GLU* 1.3 62.4 + - - +
126E HIS* 3.4 13.6 + - - +
127E THR* 2.8 37.2 + - - +
128E ARG* 2.9 29.8 + - - +
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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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124B ASP* 4.8 6.9 - - - +
125B GLU* 3.9 19.1 - - - +
123E ASN 3.7 15.2 - - - +
124E ASP* 1.3 72.9 + - - +
126E HIS* 1.3 60.2 + - - +
128E ARG* 3.1 10.8 + - + +
129E ARG* 2.8 55.6 + - + +
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Residues in contact with HIS 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 5.4 0.4 + - - -
126B HIS* 3.5 61.1 + + + -
124E ASP* 3.4 10.7 + - - +
125E GLU* 1.3 77.1 - - - +
127E THR* 1.3 67.1 + - - +
129E ARG* 3.7 21.3 - - - +
130E GLU* 3.0 59.5 + - + +
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Residues in contact with THR 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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87E ASP* 3.6 31.9 - - + +
121E LEU* 3.6 31.0 - - + +
124E ASP* 2.8 32.7 + - - +
126E HIS* 1.3 80.2 + - - +
128E ARG* 1.3 57.6 + - - +
130E GLU* 3.9 4.0 - - - +
131E LEU* 3.0 44.5 + - + +
138E PRO* 4.5 3.8 - - + -
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Residues in contact with ARG 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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122E ARG* 2.8 39.5 + - - +
123E ASN* 4.1 14.5 + - - +
124E ASP 2.9 21.7 + - - +
125E GLU* 3.1 10.3 + - + +
127E THR* 1.3 75.1 - - - +
129E ARG* 1.3 58.4 + - + +
131E LEU* 3.9 1.6 - - - +
132E ALA* 3.0 28.2 + - - +
136E GLN 4.6 1.4 - - - +
137E GLU* 3.9 21.7 + - - +
138E PRO* 3.5 39.4 + - + +
140E LYS* 5.9 3.0 - - - +
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Residues in contact with ARG 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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124B ASP* 4.0 21.0 + - - -
126B HIS* 4.8 3.6 + - - -
162B LYS* 5.4 15.3 - - - +
125E GLU* 2.8 47.0 + - + +
126E HIS* 3.7 34.0 - - - +
128E ARG* 1.3 74.0 - - + +
130E GLU* 1.3 71.1 + - - +
132E ALA* 3.2 16.4 + - - +
133E LYS* 3.2 20.9 + - - +
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Residues in contact with GLU 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 HIS* 3.0 51.4 + - + +
127E THR* 3.9 4.9 - - - +
129E ARG* 1.3 79.7 + - - +
131E LEU* 1.3 63.3 + - + +
133E LYS* 2.6 55.0 + - - +
134E MET* 3.8 8.5 + - - +
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Residues in contact with LEU 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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87E ASP 3.4 29.2 - - - +
88E SER* 5.2 0.7 - - - -
89E PRO* 4.3 4.5 - - + -
127E THR* 3.0 25.3 + - + +
128E ARG* 4.0 2.9 - - - +
130E GLU* 1.3 75.0 - - + +
132E ALA* 1.3 58.1 + - - +
133E LYS 3.1 2.2 - - - -
134E MET* 2.9 17.6 + - + +
136E GLN* 2.8 55.9 + - - +
137E GLU* 3.7 6.3 - - - +
138E PRO* 3.6 37.2 - - + -
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Residues in contact with ALA 132 (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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170A THR* 4.9 4.0 - - - +
128E ARG 3.0 19.8 + - - +
129E ARG* 3.2 9.8 + - - +
131E LEU* 1.3 75.8 - - - +
133E LYS* 1.3 62.8 + - + +
135E LYS* 3.1 14.5 + - - +
136E GLN 3.3 10.7 + - - +
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Residues in contact with LYS 133 (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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169A THR* 6.0 0.2 - - - -
170A THR* 3.0 32.3 + - - +
174A ARG* 4.8 14.4 - - - +
129E ARG* 3.2 15.6 + - - +
130E GLU* 2.6 52.0 + - - +
131E LEU 3.1 0.4 - - - -
132E ALA* 1.3 78.5 - - - +
134E MET* 1.3 65.9 + - + +
135E LYS* 3.4 2.9 + - - +
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Residues in contact with MET 134 (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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169A THR* 5.7 11.4 - - + -
171A ARG* 6.5 0.4 - - - -
130E GLU 4.2 9.2 - - - +
131E LEU* 2.9 12.6 + - + +
133E LYS* 1.3 84.3 - - + +
135E LYS* 1.3 71.0 + - - +
136E GLN* 3.1 29.9 + - - +
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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