Contacts of the helix formed by residues 145 - 152 (chain B) in PDB entry 1EE8
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 PRO 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ALA 4.6 0.4 - - - +
144B ARG* 1.3 91.5 - - + +
146B LEU* 1.3 66.3 - - - +
147B LYS* 3.3 1.1 - - + -
148B ALA* 3.3 18.3 + - + +
149B LEU* 3.1 21.0 + - - +
175B PRO 4.1 8.1 - - - +
176B PHE* 3.8 22.0 - - + +
177B ARG 3.7 7.6 - - - +
178B PRO* 4.6 0.2 - - + -
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 3.8 24.7 - - + -
144B ARG 3.4 0.8 + - - -
145B PRO* 1.3 72.2 - - - +
147B LYS* 1.3 62.2 + - - +
149B LEU* 3.5 2.1 + - - +
150B LEU* 3.2 29.5 + - + +
168B LEU* 3.5 29.8 - - + -
173B LEU* 4.2 8.3 - - + -
174B SER 3.7 12.3 - - - +
175B PRO 3.6 6.1 + - - +
177B ARG* 2.8 20.7 + - + +
179B ALA* 4.3 13.9 - - - +
182B LEU* 3.9 28.3 - - + -
190B LEU* 3.7 21.5 - - + -
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Residues in contact with LYS 147 (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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145B PRO* 5.3 1.1 - - + -
146B LEU* 1.3 76.1 - - - +
148B ALA* 1.3 65.6 + - - +
150B LEU* 3.0 17.0 + - - +
151B LEU* 3.1 26.4 + - + +
161B ASN* 3.3 26.6 + - - +
164B ALA* 3.6 28.0 - - + -
165B ASP* 2.9 24.4 + - - +
168B LEU* 4.0 13.5 - - + -
175B PRO* 2.9 29.7 + - + +
176B PHE* 5.8 2.2 - - + -
253B ARG* 4.5 4.4 - - + +
254B GLY 3.5 4.8 + - - -
255B THR* 2.7 34.5 + - + +
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Residues in contact with ALA 148 (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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144B ARG* 3.9 20.9 - - - +
145B PRO* 3.3 26.7 + - + +
147B LYS* 1.3 80.3 - - - +
149B LEU* 1.3 64.2 + - - +
151B LEU* 3.1 21.3 + - - +
152B ASP* 3.3 16.1 + - - +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLY 4.0 6.1 - - - +
139B LEU* 3.9 4.9 - - + -
142B SER* 3.7 25.8 - - - +
144B ARG* 3.9 22.8 - - + +
145B PRO 3.1 15.9 + - - +
146B LEU 3.7 5.6 - - - +
147B LYS 3.2 0.2 - - - -
148B ALA* 1.3 75.1 - - - +
150B LEU* 1.3 64.7 + - + +
152B ASP* 3.0 22.7 + - + +
153B GLN 3.9 1.6 + - - -
154B ARG* 4.9 1.7 + - + -
155B LEU* 3.6 44.0 + - + +
179B ALA* 3.5 27.8 - - + -
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Residues in contact with LEU 150 (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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135B PHE* 4.3 17.5 - - + -
139B LEU* 5.2 0.2 - - + -
146B LEU* 3.3 18.4 - - + +
147B LYS* 3.0 7.2 + - - +
149B LEU* 1.3 77.0 - - - +
151B LEU* 1.3 66.6 + - + +
153B GLN* 3.2 14.9 + - - -
155B LEU* 4.9 13.2 - - + +
156B ALA* 4.3 6.6 + - + +
159B VAL* 4.1 22.7 - - + +
164B ALA* 4.4 15.9 - - + -
168B LEU* 4.3 27.4 - - + -
190B LEU* 4.4 17.7 - - + -
194B LEU* 4.2 30.1 - - + -
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Residues in contact with LEU 151 (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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52B LYS* 5.8 0.5 + - - -
147B LYS* 3.1 35.2 + - + +
148B ALA* 3.1 15.5 + - - +
150B LEU* 1.3 73.5 - - - +
152B ASP* 1.3 62.1 + - - +
153B GLN* 3.1 20.4 + - - +
159B VAL 4.2 8.6 - - - +
160B GLY 3.7 27.1 - - - +
161B ASN* 3.7 4.5 - - - +
164B ALA* 3.8 7.6 - - + -
253B ARG* 3.0 50.5 - - + +
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Residues in contact with ASP 152 (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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117B LEU* 5.8 0.2 - - - +
120B ARG* 3.1 27.0 + - - +
144B ARG* 2.5 41.5 + - - -
148B ALA 3.3 7.8 + - - +
149B LEU* 3.0 17.6 + - + +
151B LEU* 1.3 76.4 - - - +
153B GLN* 1.3 69.7 + - - +
154B ARG* 3.1 18.6 + - + +
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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