Contacts of the helix formed by residues 177 - 181 (chain N) in PDB entry 2DYS
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 SER 177 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14G ARG* 5.1 1.2 + - - -
172N LYS* 3.7 5.8 - - - +
175N ALA 3.5 2.5 + - - -
176N MET* 1.3 83.3 - - - +
178N GLN* 1.3 64.4 + - - +
179N TYR* 3.1 24.0 + - - +
180N GLN* 3.0 42.0 + - - +
181N THR* 3.7 1.6 - - - +
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Residues in contact with GLN 178 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ASP* 3.3 44.9 + - - +
9G GLY* 4.0 8.1 - - - -
168N ILE* 3.3 34.1 + - - +
169N ILE* 4.0 4.0 - - - +
172N LYS* 2.8 36.1 - - - +
177N SER* 1.3 74.8 - - - +
179N TYR* 1.3 59.2 - - + +
180N GLN 3.1 2.1 + - - -
181N THR* 2.8 27.1 + - - -
186N TRP* 2.9 41.1 + - + -
189N MET* 3.8 8.6 - - + +
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Residues in contact with TYR 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ASP* 3.7 15.6 + - - +
14G ARG* 3.7 43.8 + - + +
15G THR* 2.8 47.3 + - - +
18G PHE* 3.7 29.8 - + - -
177N SER* 3.0 16.9 - - - +
178N GLN* 1.3 76.6 - - - +
180N GLN* 1.3 58.4 + - - +
186N TRP* 3.8 27.8 - + - -
270N TYR* 3.2 12.3 - - - -
271N MET* 3.8 21.5 - - + +
274N VAL* 5.2 0.7 - - + -
278N MET* 5.7 1.5 - - + +
66S ASN 4.7 0.2 - - - -
67S SER* 3.4 26.0 - - - -
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Residues in contact with GLN 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G ARG* 4.7 3.6 + - - -
175N ALA 3.6 12.1 + - - -
176N MET* 3.7 19.1 - - + +
177N SER* 3.0 43.8 + - - +
178N GLN 3.1 1.0 - - - -
179N TYR* 1.3 79.2 - - - +
181N THR* 1.3 66.8 + - - +
182N PRO* 4.1 2.1 - - - +
270N TYR* 4.0 0.2 - - - -
61S ILE* 4.0 18.7 - - + +
65S ASP* 4.5 7.8 + - - +
66S ASN 2.9 30.8 + - - +
67S SER 3.6 14.5 - - - +
69S VAL* 3.8 28.8 - - + +
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Residues in contact with THR 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87N ILE* 4.3 6.1 - - + -
168N ILE* 5.4 0.2 - - - +
172N LYS* 3.1 36.3 - - + -
176N MET* 3.6 14.1 - - - -
177N SER 3.7 6.5 - - - +
178N GLN* 2.8 25.0 + - - +
180N GLN* 1.3 80.6 - - - +
182N PRO* 1.3 73.0 + - - +
185N VAL* 4.2 14.8 - - + +
186N TRP* 3.4 14.4 + - - -
270N TYR* 2.5 30.0 + - - -
67S SER 5.5 0.2 - - - -
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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