Contacts of the helix formed by residues 203 - 207 (chain O) 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 ASN 203 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50N ASP* 5.1 5.8 + - - +
51N ASP* 3.4 2.0 - - - -
104O TRP* 3.2 45.3 - - + +
201O GLY 2.9 2.8 + - - -
202O SER* 1.3 91.4 + - - +
204O HIS* 1.3 66.3 + - - +
205O SER 3.1 2.7 - - - -
206O PHE* 3.0 45.6 + - + +
207O MET* 3.7 1.9 - - - +
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Residues in contact with HIS 204 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51N ASP* 2.8 6.4 + - + +
55N ASN* 4.8 0.2 - - - -
369N ASP* 5.4 0.6 + - - -
438N ARG 3.2 15.7 + - - -
439N ARG* 3.1 27.9 - - + +
440N TYR* 3.1 33.0 + + - -
104O TRP* 3.6 0.8 - - - -
196O CYS* 3.2 32.7 - - - +
197O SER* 4.3 1.3 - - - -
198O GLU 3.1 20.2 + - - -
199O ILE* 3.8 18.7 + - + -
200O CYS* 3.4 19.7 - - - +
201O GLY 3.0 14.5 + - - +
203O ASN* 1.3 77.5 - - - +
205O SER* 1.3 58.4 + - - +
206O PHE 3.3 1.2 + - - -
207O MET* 3.7 2.1 + - - +
301O CUA 2.0 30.3 - - - -
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Residues in contact with SER 205 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N ASP* 2.6 34.2 + - - -
440N TYR* 3.2 36.7 - - - -
441N SER 3.2 13.1 + - - -
442N ASP 3.8 8.7 - - - -
135O LEU* 4.8 7.3 - - - +
195O GLN* 4.0 10.7 + - - +
204O HIS* 1.3 74.7 - - - +
206O PHE* 1.3 82.8 + - - +
207O MET 3.8 2.0 + - - -
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Residues in contact with PHE 206 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N THR* 4.7 9.9 - - - -
50N ASP* 5.1 6.5 - - + -
51N ASP* 4.0 15.3 - - - -
441N SER* 3.9 19.7 - - - -
442N ASP* 4.0 15.9 - - + -
104O TRP 4.1 6.8 - - - +
122O MET* 3.5 35.8 + - + +
135O LEU* 3.7 29.8 - - + -
202O SER 4.4 5.2 - - - -
203O ASN* 3.0 42.4 + - + +
205O SER* 1.3 96.8 - - - +
207O MET* 1.3 60.8 + - - +
208O PRO* 3.5 6.5 - - - -
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Residues in contact with MET 207 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440N TYR* 5.5 0.6 + - - -
102O HIS 3.5 11.4 - - - +
104O TRP* 3.6 44.0 - - - +
105O TYR* 3.8 12.3 - - - +
106O TRP* 2.8 49.6 + - + +
120O SER 6.0 0.9 - - - -
122O MET* 4.7 2.9 - - - +
161O HIS* 3.2 12.8 - - + +
195O GLN* 5.1 0.4 - - - -
196O CYS* 3.6 22.4 + - + -
200O CYS* 3.8 0.2 - - - -
203O ASN 3.7 9.9 - - - +
204O HIS 3.7 3.1 + - - +
205O SER 3.8 1.6 + - - -
206O PHE* 1.3 75.9 - - - +
208O PRO* 1.3 64.7 - - - +
301O CUA 2.8 27.1 - - - -
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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