Contacts of the helix formed by residues 169 - 172 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C PHE* 4.0 18.4 - + - -
125C GLY* 3.6 31.0 - - - -
170C GLU* 3.7 14.4 - - + -
181C ARG* 5.8 3.4 - - - -
34D PHE* 5.1 4.0 - + - -
126D SER* 3.4 21.8 - - - +
127D GLY 3.3 22.2 - - - +
128D TRP* 4.2 1.3 - - - -
145D ASN* 2.8 44.1 + - + -
146D GLN* 3.2 23.0 - - + +
167D ASP* 3.1 23.8 + - - +
168D VAL* 1.3 81.1 - - - +
170D GLU* 1.3 66.0 + - - +
171D HIS* 3.5 36.8 - + + +
172D ALA* 3.1 17.2 + - - +
173D TYR* 3.4 4.0 - - - -
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Residues in contact with GLU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C HIS* 3.9 9.0 - - - -
126C SER* 5.1 1.8 + - - +
169C TRP* 3.7 19.8 - - + -
170C GLU* 3.4 23.7 + - + +
171C HIS* 2.8 56.9 + - - +
125D GLY 6.0 2.7 - - - +
126D SER* 5.3 2.0 + - - +
168D VAL 3.6 1.1 + - - +
169D TRP* 1.3 73.3 - - - +
171D HIS* 1.3 57.8 + - - +
172D ALA 3.0 0.9 + - - -
173D TYR* 3.1 28.0 + - + +
174D TYR* 2.8 43.4 + - + +
181D ARG* 5.5 2.9 - - - +
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Residues in contact with HIS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C GLU* 2.7 37.4 + - - +
174C TYR* 3.4 47.1 + - + +
22D THR* 3.8 14.6 + - - +
26D HIS* 3.1 20.5 + + - +
30D HIS* 3.6 19.6 - + + +
34D PHE* 5.5 3.4 - + - -
81D HIS* 4.7 1.3 - + - -
146D GLN* 4.9 3.1 - - - -
167D ASP* 3.5 0.8 + - - -
169D TRP* 3.5 28.0 - + + +
170D GLU* 1.3 75.1 - - - +
172D ALA* 1.3 65.1 + - + +
173D TYR 3.2 0.7 + - - -
174D TYR 4.4 1.8 + - - -
175D LEU 5.4 0.5 + - - -
504D MN 2.3 36.0 + - - -
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Residues in contact with ALA 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 5.9 1.0 - - - -
19D ASP* 5.4 1.2 - - - +
22D THR* 3.8 14.7 - - - +
26D HIS* 3.9 13.9 + - + -
84D PHE* 5.6 0.4 - - + -
167D ASP* 3.8 28.9 - - + +
169D TRP 3.1 12.7 + - - +
170D GLU 3.0 1.2 - - - -
171D HIS* 1.3 84.0 - - - +
173D TYR* 1.3 59.7 + - + +
177D PHE* 5.7 0.2 - - - -
184D TYR* 3.6 30.4 + - + +
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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