Contacts of the helix formed by residues 126 - 138 (chain B) in PDB entry 4OUH
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 ASN 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B ASP* 2.7 29.4 + - - +
111B TYR* 3.8 10.2 - - + -
125B LYS* 1.3 78.7 - - - +
127B SER* 1.3 59.3 + - - +
128B GLU 3.2 3.6 - - - -
129B GLU* 3.1 19.4 + - + +
130B LEU* 2.9 24.4 + - - +
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Residues in contact with SER 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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25B PHE* 4.0 19.9 - - - -
124B TYR* 4.5 16.9 + - - -
125B LYS 3.1 4.8 - - - -
126B ASN* 1.3 76.9 - - - +
128B GLU* 1.3 60.4 + - - +
130B LEU* 3.5 9.1 - - - +
131B ARG* 2.9 38.6 + - - +
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Residues in contact with GLU 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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126B ASN 3.2 1.0 - - - -
127B SER* 1.3 84.5 + - - +
129B GLU* 1.3 63.0 + - - +
131B ARG* 3.5 38.8 + - - +
132B SER* 3.2 22.2 + - - -
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Residues in contact with GLU 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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110B ASP* 5.8 0.5 - - - +
111B TYR* 2.7 29.8 + - + +
126B ASN* 3.1 22.6 + - + +
128B GLU* 1.3 77.5 - - - +
130B LEU* 1.3 64.6 + - - +
132B SER* 2.8 21.9 + - - +
133B ARG* 3.0 23.0 + - + +
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Residues in contact with LEU 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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22B LEU* 4.2 11.0 - - + -
25B PHE* 3.5 43.1 - - + -
106B LEU* 3.7 33.0 - - + -
111B TYR* 3.6 43.5 - - + +
124B TYR* 4.7 7.6 - - + -
125B LYS 5.3 0.4 - - - +
126B ASN 2.9 8.0 + - - +
127B SER* 3.5 10.8 - - - +
129B GLU* 1.3 78.1 - - - +
131B ARG* 1.3 60.9 + - - +
133B ARG* 3.5 1.9 + - - +
134B ILE* 3.0 39.3 + - + +
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Residues in contact with ARG 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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72A LYS* 6.0 2.6 - - - +
-1B SER 3.5 23.0 + - - -
0B PRO* 4.1 3.2 - - - +
1B MET* 3.6 34.9 - - + +
25B PHE* 3.6 17.9 - - + -
29B GLU* 3.2 20.5 + - - +
127B SER* 2.9 27.2 + - - +
128B GLU* 3.5 37.1 + - - +
129B GLU 3.2 0.2 - - - -
130B LEU* 1.3 76.7 - - - +
132B SER* 1.3 57.0 + - - +
134B ILE* 3.4 1.6 + - - +
135B VAL* 2.9 36.6 + - + +
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Residues in contact with SER 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 GLU 3.2 8.8 + - - -
129B GLU* 2.8 27.0 + - - +
131B ARG* 1.3 78.8 - - - +
133B ARG* 1.3 60.7 + - - +
135B VAL* 3.8 5.6 - - - +
136B SER* 2.9 34.1 + - - -
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Residues in contact with ARG 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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104B LEU* 3.6 27.7 - - + +
105B THR 3.0 25.5 + - - +
106B LEU* 3.7 20.0 - - + +
107B ASN 5.4 0.8 - - - +
110B ASP* 5.4 3.2 + - - -
111B TYR* 3.0 33.8 + - - -
129B GLU* 3.0 28.3 + - + +
130B LEU* 4.0 3.6 - - - +
132B SER* 1.3 78.7 + - - +
134B ILE* 1.3 58.2 + - - +
136B SER* 3.5 6.4 + - - +
137B GLY* 2.8 29.8 + - - -
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Residues in contact with ILE 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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22B LEU* 5.2 1.8 - - + -
25B PHE* 4.0 20.9 - - + -
26B LEU* 4.0 31.9 - - + +
29B GLU* 3.9 28.0 - - + -
91B LEU* 4.8 1.3 - - + -
104B LEU* 3.9 17.5 - - + -
106B LEU* 4.5 6.5 - - + -
130B LEU* 3.0 41.4 + - + +
131B ARG 3.8 3.1 - - - +
133B ARG* 1.3 74.1 - - + +
135B VAL* 1.3 60.1 + - - +
138B ILE* 2.8 34.1 + - + +
139B ILE* 3.1 14.0 + - + -
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Residues in contact with VAL 135 (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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29B GLU* 4.1 8.5 - - - +
33B HIS* 3.9 31.6 - - + +
131B ARG* 2.9 24.9 + - + +
132B SER* 3.8 6.1 - - - +
134B ILE* 1.3 76.2 - - - +
136B SER* 1.3 59.4 + - - +
139B ILE* 3.2 14.9 + - + -
140B THR* 2.6 46.3 + - - +
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Residues in contact with SER 136 (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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132B SER 2.9 25.7 + - - -
133B ARG* 3.5 7.8 + - - -
135B VAL* 1.3 76.4 - - - +
137B GLY* 1.3 59.8 + - - +
140B THR* 4.1 10.5 - - - +
141B PRO* 3.3 18.1 - - - +
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Residues in contact with GLY 137 (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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102B ALA* 3.4 19.2 - - - +
103B ASP 3.8 16.0 + - - +
104B LEU* 4.8 7.4 - - - -
133B ARG 2.8 17.9 + - - -
136B SER* 1.3 80.7 + - - +
138B ILE* 1.3 63.7 + - - +
141B PRO* 3.4 6.2 - - - +
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Residues in contact with ILE 138 (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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26B LEU* 5.0 9.6 - - + -
30B VAL* 5.4 4.3 - - + -
91B LEU* 4.3 17.9 - - + +
93B VAL* 3.5 36.8 - - + -
102B ALA* 4.2 16.7 - - - +
103B ASP 4.3 0.7 - - - -
104B LEU* 4.0 29.6 - - + -
134B ILE* 2.8 22.7 + - + +
137B GLY* 1.3 85.5 - - - +
139B ILE* 1.3 79.7 + - + +
140B THR 3.6 0.4 - - - -
141B PRO* 3.3 9.1 - - - +
142B ILE* 3.1 24.3 + - + +
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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