Contacts of the helix formed by residues 132 - 139 (chain B) in PDB entry 4EOH
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 LEU 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B THR* 3.1 32.3 - - - +
86B ARG 4.2 2.9 - - - +
87B ASP 4.1 2.5 - - - +
88B LYS* 3.7 26.7 - - - +
91B LEU* 4.1 16.2 - - + -
128B VAL* 3.6 22.9 - - + -
129B PRO* 3.2 25.1 + - + +
130B GLU 3.0 1.4 - - - -
131B ASP* 1.3 94.3 - - - +
133B LEU* 1.3 60.1 + - - +
134B PRO 3.4 0.2 - - - -
135B VAL* 3.0 9.3 + - - +
136B TYR* 2.8 44.8 + - + -
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Residues in contact with LEU 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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116B LEU* 3.9 30.3 - - + +
126B MET* 4.7 8.9 - - + +
129B PRO 4.5 0.6 + - - -
130B GLU* 3.2 9.5 + - - +
132B LEU* 1.3 79.6 - - - +
134B PRO* 1.3 72.1 - - + +
136B TYR* 3.1 4.8 + - - +
137B LYS* 2.9 55.1 + - - +
156B LEU* 4.1 23.8 - - + +
157B LEU* 4.0 11.9 - - + -
406B MPD 4.1 22.9 - - + -
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Residues in contact with PRO 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 3.4 10.5 - - - +
131B ASP* 3.8 11.0 - - - +
132B LEU 3.7 2.2 - - - -
133B LEU* 1.3 97.0 - - + +
135B VAL* 1.3 58.4 + - + +
137B LYS* 4.4 8.7 - - + -
138B GLU* 2.9 51.7 + - - +
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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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88B LYS* 3.9 28.5 - - + -
91B LEU* 3.7 28.7 - - + -
92B ALA* 4.8 10.5 - - + +
95B VAL* 4.8 4.0 - - + -
131B ASP 3.6 17.5 - - - +
132B LEU* 3.0 8.6 + - - +
134B PRO* 1.3 77.2 - - + +
136B TYR* 1.3 60.4 + - - +
139B LYS* 2.8 48.1 + - + +
140B VAL* 3.0 9.6 + - + -
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Residues in contact with TYR 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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82B THR* 5.7 0.9 + - - -
83B GLY 3.5 20.4 + - - -
85B THR* 3.8 12.8 + - - -
91B LEU* 3.8 19.7 - - + +
112B CYS* 4.0 6.7 - - - -
113B ASP 4.2 0.9 + - - -
114B PRO* 3.9 28.5 - - + -
115B VAL 3.9 14.2 + - - -
116B LEU* 3.5 31.4 - - + -
132B LEU* 2.8 27.6 + - + -
133B LEU* 3.1 8.3 + - + +
135B VAL* 1.3 79.3 - - - +
137B LYS* 1.3 61.2 + - - +
140B VAL* 3.4 34.1 + - + -
141B VAL* 2.9 34.7 + - + +
157B LEU* 4.0 14.1 - - + -
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Residues in contact with LYS 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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133B LEU* 2.9 45.7 + - + +
134B PRO* 3.8 7.6 - - + +
136B TYR* 1.3 77.0 - - - +
138B GLU* 1.3 64.0 + - + +
142B PRO* 3.2 22.0 - - - +
156B LEU 3.0 28.1 + - - -
157B LEU* 3.7 21.5 - - + +
158B SER 5.6 0.2 - - - -
159B GLY* 5.1 7.2 - - - +
178B MET* 3.7 21.8 - - + +
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Residues in contact with GLU 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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134B PRO* 2.9 33.2 + - - +
137B LYS* 1.3 80.5 - - + +
139B LYS* 1.3 72.4 + - + +
142B PRO* 3.7 13.1 - - - +
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Residues in contact with LYS 139 (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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92B ALA* 5.8 2.7 - - - +
95B VAL* 3.5 37.4 - - + +
96B ASP* 4.6 8.5 + - - -
99B GLN* 3.9 13.3 + - - +
135B VAL* 2.8 32.6 + - + +
137B LYS 3.6 0.4 - - - -
138B GLU* 1.3 86.8 - - + +
140B VAL* 1.3 65.0 + - - +
142B PRO* 3.8 5.0 - - - +
143B LEU* 3.7 26.2 + - - +
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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