Contacts of the strand formed by residues 201 - 206 (chain D) in PDB entry 1YY9
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 ILE 201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160D TRP* 3.2 11.6 - - - -
161D ASN* 2.9 38.1 + - - +
199D THR* 3.8 24.5 - - + -
200D TYR* 1.3 75.0 - - - +
202D CYS* 1.3 63.0 + - - +
203D ASN* 3.5 23.1 + - - +
214D ASP* 4.1 17.7 - - + +
215D LYS 3.4 9.0 - - - +
216D ARG* 4.5 13.2 - - + -
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Residues in contact with CYS 202 (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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127D VAL* 5.2 0.2 - - + -
146D CYS* 2.0 53.8 - - - -
158D VAL* 4.3 10.8 - - - -
159D SER 4.2 0.9 - - - -
160D TRP* 3.5 20.6 - - + -
201D ILE* 1.3 74.2 - - - +
203D ASN* 1.3 63.3 + - - +
204D VAL* 3.5 10.6 + - + +
213D VAL 3.3 2.8 - - - +
214D ASP* 3.1 26.0 - - - -
215D LYS* 2.8 20.8 + - + +
217D VAL* 5.0 0.2 - - + -
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Residues in contact with ASN 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D THR* 3.6 1.7 + - - +
158D VAL* 3.5 4.8 - - - +
159D SER* 2.9 59.3 + - - +
161D ASN* 3.2 9.3 - - - +
162D SER* 2.7 40.4 + - - +
201D ILE* 3.5 16.9 + - - +
202D CYS* 1.3 71.3 - - - +
204D VAL* 1.3 61.4 - - - +
205D ASN* 3.8 2.4 + - - +
213D VAL 3.9 0.2 - - - -
214D ASP* 3.2 23.2 - - - +
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Residues in contact with VAL 204 (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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125D PRO* 4.5 7.9 - - + -
127D VAL* 4.0 26.7 - - + -
148D VAL* 3.7 38.6 - - + -
156D VAL* 3.6 23.3 - - + -
157D THR 3.4 5.4 - - - +
158D VAL* 4.7 4.9 - - + +
202D CYS* 4.3 16.4 - - - +
203D ASN* 1.3 72.3 - - - +
205D ASN* 1.3 62.8 + - - +
211D THR 3.6 1.6 - - - +
212D LYS* 3.5 3.3 - - - +
213D VAL* 2.9 44.1 + - + +
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Residues in contact with ASN 205 (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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156D VAL* 3.1 6.2 - - - +
157D THR* 2.8 51.4 + - - +
203D ASN 3.8 3.2 + - - +
204D VAL* 1.3 74.1 - - - +
206D HIS* 1.3 63.8 + - - +
207D LYS* 3.1 41.5 + - - +
210D ASN* 5.5 1.7 - - - +
211D THR 3.7 4.9 + - - +
212D LYS* 3.1 43.4 + - + +
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Residues in contact with HIS 206 (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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123D LYS 2.9 25.9 + - - -
125D PRO* 3.6 23.1 - - + -
151D TYR* 3.5 18.5 - + - -
152D PHE 3.6 6.7 + - - -
153D PRO 2.9 29.2 - - - -
155D PRO 3.3 13.6 + - - -
156D VAL* 4.2 3.0 - - + +
205D ASN* 1.3 74.2 - - - +
207D LYS* 1.3 51.5 + - - +
208D PRO* 3.4 13.7 - - + +
209D SER* 2.8 30.2 + - - -
210D ASN* 2.7 30.4 + - - -
211D THR* 3.0 26.6 + - - +
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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