Contacts of the helix formed by residues 165 - 174 (chain B) in PDB entry 1E5E
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 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B THR 5.3 0.2 + - - -
135B ALA* 5.1 6.9 - - - +
163B ILE 4.3 0.4 - - - -
164B ILE* 1.3 71.0 - - - +
166B MET* 1.3 60.3 + - - +
167B GLU* 3.5 10.4 + - - +
168B ARG* 3.3 31.8 + - + +
169B VAL* 3.2 23.2 + - - +
300B ILE* 3.5 38.8 - - + +
303B LYS* 4.1 9.5 + - - -
304B GLN* 4.1 1.4 - - - +
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Residues in contact with MET 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PHE* 3.5 38.8 - - + -
155B THR* 3.8 11.7 - - + -
164B ILE* 3.0 8.0 + - - +
165B ASP* 1.3 72.4 - - - +
167B GLU* 1.3 62.1 + - - +
169B VAL* 3.2 7.5 + - - +
170B CYS* 2.9 27.5 + - - -
183B ALA* 4.5 0.4 - - - -
193B THR* 3.8 22.2 - - + -
195B PRO* 4.0 21.5 - - + -
198B PHE* 3.6 35.2 - - + -
200B VAL* 4.2 5.2 - - + -
304B GLN* 2.7 31.1 + - + +
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Residues in contact with GLU 167 (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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165B ASP* 3.4 2.9 + - - +
166B MET* 1.3 78.6 - - - +
168B ARG* 1.3 63.7 + - - +
170B CYS* 3.2 2.1 + - - +
171B LYS* 3.0 52.8 + - + +
198B PHE* 3.4 31.5 - - + +
303B LYS* 2.5 41.1 + - - +
304B GLN* 4.2 1.2 + - - -
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Residues in contact with ARG 168 (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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137B PRO* 3.6 35.6 - - + +
138B GLY* 3.5 24.3 - - - +
141B LYS* 5.1 5.7 - - - +
165B ASP* 3.3 32.1 + - + +
166B MET 3.2 0.4 - - - -
167B GLU* 1.3 76.9 - - - +
169B VAL* 1.3 65.8 + - + +
171B LYS* 3.3 11.9 + - - +
172B ASP* 3.1 50.3 + - - +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 3.6 30.3 - - - +
140B VAL* 4.1 11.5 - - + +
151B VAL* 3.7 29.6 - - + -
153B PHE* 3.9 19.7 - - + -
164B ILE* 3.7 13.5 - - + -
165B ASP 3.2 13.7 + - - +
166B MET 3.2 7.8 + - - +
168B ARG* 1.3 80.2 - - + +
170B CYS* 1.3 57.3 + - - +
172B ASP* 3.3 7.8 + - - +
173B ALA* 2.9 26.3 + - - +
181B VAL* 4.6 4.5 - - + -
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Residues in contact with CYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 2.9 20.8 + - - +
167B GLU 3.8 1.8 - - - +
169B VAL* 1.3 76.5 - - - +
171B LYS* 1.3 56.3 + - + +
174B HIS* 2.7 51.4 + - - +
181B VAL* 3.8 23.8 - - - -
198B PHE 3.7 13.7 - - - +
199B GLY* 3.5 30.3 - - - +
200B VAL* 3.6 18.6 - - - -
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Residues in contact with LYS 171 (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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141B LYS* 4.3 4.1 + - - +
167B GLU* 3.0 45.7 + - + +
168B ARG* 3.4 15.5 - - - +
170B CYS* 1.3 79.6 - - + +
172B ASP* 1.3 67.3 + - - +
174B HIS* 3.7 3.8 - - - -
175B SER* 3.1 22.5 + - - -
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Residues in contact with ASP 172 (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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138B GLY* 3.6 20.3 + - - -
140B VAL* 3.7 19.2 + - + +
141B LYS* 3.3 45.3 + - + +
144B MET* 3.6 8.8 - - - +
168B ARG* 3.1 37.9 + - - +
169B VAL* 3.6 7.0 - - - +
171B LYS* 1.3 81.6 - - - +
173B ALA* 1.3 62.1 + - - +
175B SER* 2.7 23.9 + - - -
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Residues in contact with ALA 173 (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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140B VAL* 4.3 0.6 - - + +
144B MET* 3.5 16.1 - - - +
151B VAL* 3.6 22.2 - - + -
169B VAL 2.9 20.6 + - - +
170B CYS 3.9 0.7 - - - +
172B ASP* 1.3 72.7 - - - +
174B HIS* 1.3 61.5 + - + +
175B SER 3.2 3.8 + - - -
176B GLN 3.5 1.7 - - - +
179B VAL* 3.3 30.1 - - + +
181B VAL* 3.5 28.5 - - + -
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Residues in contact with HIS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B CYS* 2.7 28.6 + - + +
171B LYS* 3.7 3.6 - - - +
173B ALA* 1.3 72.5 - - - +
175B SER* 1.3 59.5 + - - +
176B GLN 3.1 13.6 + - - +
177B GLU* 5.5 0.2 - - - -
179B VAL* 3.3 21.2 + - + -
181B VAL* 3.9 13.4 - - + +
199B GLY* 3.1 29.3 - - - -
201B ASP* 2.7 29.0 + - - -
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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