Contacts of the helix formed by residues 169 - 172 (chain B) in PDB entry 1EN5
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 TRP 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A PHE* 3.9 23.3 - + - -
125A GLY* 3.5 30.7 - - - -
170A GLU* 3.6 22.2 - - + -
181A ARG* 5.8 2.7 - - - -
34B PHE* 5.1 3.6 - + - -
126B SER* 3.5 21.1 - - - +
127B GLY 3.4 20.3 - - - +
128B TRP* 4.2 0.9 - - - -
145B ASN* 2.8 40.5 + - + -
146B GLN* 3.2 21.6 - - - +
167B ASP* 3.2 24.3 + - - +
168B VAL* 1.3 80.9 - - - +
170B GLU* 1.3 65.2 + - - +
171B HIS* 3.6 31.4 - + + +
172B ALA* 3.1 17.5 + - - +
173B TYR* 3.4 4.0 - - - -
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Residues in contact with GLU 170 (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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30A HIS* 3.8 9.9 + - - -
126A SER* 4.9 2.4 + - - +
169A TRP* 3.7 20.1 - - + -
170A GLU* 3.4 23.0 + - + -
171A HIS* 2.7 57.6 + - - +
125B GLY 5.9 2.2 - - - +
126B SER* 5.5 1.8 + - - +
168B VAL 3.6 1.1 + - - +
169B TRP* 1.3 73.4 - - - +
171B HIS* 1.3 58.3 + - - +
172B ALA 3.0 0.4 - - - -
173B TYR* 3.1 29.9 + - + +
174B TYR* 2.8 45.1 + - + +
181B ARG* 5.4 2.7 - - - +
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Residues in contact with HIS 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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170A GLU* 2.8 38.3 + - - +
174A TYR* 3.5 44.1 + - + +
22B THR* 3.7 14.2 + - - +
26B HIS* 3.0 20.3 + + - +
30B HIS* 3.7 21.6 - + + +
34B PHE* 5.5 3.1 - + - -
81B HIS* 4.7 1.1 - + - -
146B GLN* 4.9 2.7 - - - -
167B ASP* 3.4 1.2 + - - -
169B TRP* 3.6 26.7 - + + +
170B GLU* 1.3 76.9 - - - +
172B ALA* 1.3 65.5 + - + +
173B TYR 3.2 0.6 + - - -
174B TYR 4.4 2.6 + - - -
175B LEU 5.4 0.3 + - - -
502B MN 2.3 36.0 + - - -
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Residues in contact with ALA 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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18B PHE* 5.9 1.6 - - - -
19B ASP* 5.3 1.0 - - - +
22B THR* 3.8 14.2 - - - +
26B HIS* 3.8 15.0 + - + +
84B PHE* 5.7 0.7 - - + -
167B ASP* 3.7 28.7 - - - +
169B TRP 3.1 13.5 + - - +
170B GLU 3.0 1.2 - - - -
171B HIS* 1.3 83.5 - - - +
173B TYR* 1.3 58.9 + - + +
177B PHE* 5.7 0.5 - - - -
184B TYR* 3.6 29.5 + - + +
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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