Contacts of the helix formed by residues 177 - 181 (chain A) in PDB entry 1DS1
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 VAL 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ALA 4.1 1.0 + - - -
176A SER* 1.3 71.3 - - - +
178A ARG* 1.3 66.6 + - + +
180A ALA* 4.3 7.6 - - + +
181A LEU* 2.9 36.8 + - + +
221A LEU* 3.7 30.3 - - + -
228A PRO* 3.4 31.6 - - + +
230A LEU* 3.9 22.6 - - + +
251A LEU* 5.5 2.9 - - + -
255A LEU* 4.8 0.2 - - - -
276A ARG* 2.8 38.5 + - + +
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Residues in contact with ARG 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU 2.9 28.7 + - - -
57A GLY* 3.6 3.4 - - - -
58A SER* 3.2 34.6 + - - +
59A GLU* 3.6 44.2 + - - +
176A SER* 3.1 3.5 + - - +
177A VAL* 1.3 87.2 - - + +
179A LYS* 1.3 59.2 + - - +
181A LEU* 4.9 2.8 - - - +
182A PRO* 3.6 16.6 - - - +
227A ASP* 2.9 42.8 + - - +
276A ARG* 3.3 32.1 - - - +
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Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 3.6 24.5 - - + +
60A ASP* 4.6 7.2 - - + +
176A SER* 3.1 13.0 + - - +
178A ARG* 1.3 79.1 - - - +
180A ALA* 1.3 62.2 + - - +
182A PRO* 3.4 10.4 - - - +
183A LEU* 4.0 7.6 - - - +
258A VAL* 2.9 55.5 + - + +
259A THR 4.7 0.6 + - - -
260A GLU* 2.8 36.3 + - - +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A SER 3.0 15.2 + - - +
177A VAL* 4.1 4.3 - - + +
179A LYS* 1.3 78.1 - - - +
181A LEU* 1.3 64.6 + - - +
183A LEU* 3.0 21.3 + - - +
184A LEU* 3.7 4.1 + - - +
251A LEU* 5.1 6.3 - - + -
254A ALA* 3.8 22.8 - - + +
255A LEU* 3.8 24.5 - - + -
258A VAL* 3.9 15.0 - - + +
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A VAL* 2.9 21.1 + - + +
178A ARG* 4.9 2.5 - - - +
180A ALA* 1.3 75.7 - - - +
182A PRO* 1.3 68.0 - - + +
184A LEU* 2.9 31.3 + - + +
189A ARG* 3.5 51.1 - - + +
221A LEU* 3.9 31.0 - - + -
225A ALA 4.4 0.2 - - - +
226A ASP 4.5 6.3 - - - +
228A PRO* 3.6 32.3 - - + -
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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