Contacts of the helix formed by residues 124 - 134 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B ASP 4.3 4.0 + - - +
121B LEU* 3.2 27.4 + - + +
122B ARG 3.3 0.2 - - - -
123B ASN* 1.3 76.0 - - - +
125B GLU* 1.3 65.7 + - - +
126B HIS* 3.4 15.5 + - - +
127B THR* 2.7 36.5 + - - +
128B ARG* 3.0 30.4 + - - +
125E GLU* 4.8 6.8 - - - +
126E HIS 5.4 0.3 + - - -
129E ARG* 4.0 22.9 + - - -
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ASN 3.8 12.8 - - - +
124B ASP* 1.3 76.1 - - - +
126B HIS* 1.3 63.6 + - - +
128B ARG* 3.3 7.5 + - - +
129B ARG* 3.1 49.4 + - - +
124E ASP* 4.8 7.1 - - - +
125E GLU* 3.9 18.0 - - - +
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Residues in contact with HIS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 3.3 12.6 + - - +
125B GLU* 1.3 78.6 + - - +
127B THR* 1.3 65.6 + - - +
129B ARG* 3.3 20.1 + - + +
130B GLU* 3.1 59.4 + - + +
124E ASP* 4.9 3.2 + - - +
126E HIS* 3.5 62.1 - + + +
129E ARG* 4.8 4.0 + - - -
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Residues in contact with THR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ASP* 3.7 27.4 - - + +
121B LEU* 3.5 32.1 + - - +
124B ASP* 2.7 37.6 + - - +
126B HIS* 1.3 77.9 + - - +
128B ARG* 1.3 62.6 + - - +
130B GLU* 3.3 6.5 + - - +
131B LEU* 3.0 37.5 + - + +
138B PRO* 4.5 3.6 - - + -
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ARG* 3.2 32.6 + - - +
123B ASN* 5.0 9.5 + - - +
124B ASP 3.0 21.5 + - - +
125B GLU* 3.8 7.6 - - - +
126B HIS 3.3 0.2 - - - -
127B THR* 1.3 76.1 - - - +
129B ARG* 1.3 59.5 + - + +
131B LEU* 3.9 2.2 - - - +
132B ALA* 3.0 27.5 + - - +
136B GLN 4.5 1.4 - - - +
137B GLU* 5.0 11.2 + - - +
138B PRO* 3.6 38.0 + - + +
140B LYS* 6.0 4.9 - - - +
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLU* 3.1 34.0 + - - +
126B HIS* 3.9 21.0 - - + +
127B THR 3.2 0.4 - - - -
128B ARG* 1.3 76.6 - - + +
130B GLU* 1.3 68.1 + - - +
132B ALA* 3.4 8.4 + - + +
133B LYS* 3.2 29.9 + - - +
124E ASP* 3.7 23.0 + - - -
162E LYS* 5.5 14.3 - - - +
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B HIS* 3.1 48.3 + - + +
127B THR* 3.6 6.3 - - - +
129B ARG* 1.3 79.3 - - - +
131B LEU* 1.3 63.5 + - + +
133B LYS* 2.9 50.1 + - - +
134B MET* 3.7 10.2 + - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ASP 3.5 28.3 - - - +
88B SER* 5.1 0.4 - - - -
89B PRO* 4.2 4.0 - - + -
127B THR* 3.0 23.6 + - + +
128B ARG 4.0 3.6 - - - +
130B GLU* 1.3 76.5 - - + +
132B ALA* 1.3 56.1 - - - +
134B MET* 2.9 18.5 + - + +
136B GLN* 2.7 59.4 + - + +
137B GLU* 3.7 5.6 - - - +
138B PRO* 3.5 40.2 - - + -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ARG 3.0 19.9 + - - +
129B ARG* 3.6 10.1 - - - +
131B LEU* 1.3 77.0 - - - +
133B LYS* 1.3 57.8 + - + +
135B LYS* 3.0 19.8 + - - +
136B GLN 3.5 10.8 - - - +
170D THR* 6.1 0.2 - - - +
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG* 3.2 19.2 + - - +
130B GLU* 2.9 47.1 + - - +
131B LEU 3.2 0.2 - - - -
132B ALA* 1.3 78.0 - - - +
134B MET* 1.3 66.4 + - + +
135B LYS* 3.2 8.0 + - - -
170D THR* 3.4 24.2 + - - +
174D ARG* 4.9 17.0 - - - +
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Residues in contact with MET 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU 4.1 9.9 - - - +
131B LEU* 2.9 12.2 + - + +
133B LYS* 1.3 81.9 - - + +
135B LYS* 1.3 82.6 + - - +
136B GLN* 3.1 27.7 + - - +
169D THR* 6.0 4.9 - - + -
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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