Contacts of the strand formed by residues 168 - 173 (chain D) in PDB entry 2Y05
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 LYS 168 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D GLY 4.9 2.6 + - - +
143D GLU 2.9 6.5 + - - +
144D THR* 3.4 28.8 - - + +
145D VAL* 2.8 29.8 + - - +
167D CYS* 1.3 73.9 - - - +
169D VAL* 1.3 64.0 + - - +
170D VAL* 4.2 7.6 + - - -
188D ASP* 3.4 31.9 - - + +
189D VAL* 4.8 4.5 - - - +
206D ALA 2.7 30.2 + - - -
207D SER* 4.0 10.5 + - - +
208D PRO* 5.0 3.2 - - - +
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Residues in contact with VAL 169 (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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145D VAL* 3.5 6.5 - - + +
147D VAL* 3.7 26.5 - - + -
159D GLY* 3.6 25.4 - - - +
162D ALA* 3.7 21.8 - - + -
163D LYS* 3.8 17.3 - - + +
167D CYS 4.5 0.7 - - - +
168D LYS* 1.3 75.7 - - - +
170D VAL* 1.3 68.5 + - - +
187D PHE* 3.8 26.5 - - + -
188D ASP* 2.9 29.9 + - - +
189D VAL 3.2 9.9 + - - +
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Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D THR* 4.4 9.9 - - + -
145D VAL 2.9 10.0 + - - +
146D MET* 3.4 4.6 - - - +
147D VAL* 2.8 28.8 + - - +
168D LYS* 4.6 5.6 - - - -
169D VAL* 1.3 78.3 - - - +
171D GLY* 1.3 62.2 + - - +
189D VAL* 3.3 12.6 - - + +
191D PHE* 3.8 24.9 - - + -
203D LEU* 4.5 3.8 - - + -
206D ALA* 3.8 25.4 - - + +
211D TYR* 3.6 43.3 - - + +
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Residues in contact with GLY 171 (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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147D VAL* 3.2 9.2 - - - -
150D ALA* 3.8 14.8 - - - -
169D VAL* 4.1 3.9 - - - +
170D VAL* 1.3 74.8 - - - +
172D ALA* 1.3 60.4 + - - -
187D PHE* 5.1 0.7 - - - -
189D VAL 2.9 11.0 + - - -
190D VAL* 3.3 14.0 - - - +
191D PHE* 3.0 33.0 + - - -
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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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146D MET* 4.8 2.2 - - + -
147D VAL 2.9 7.2 + - - +
148D ASN* 4.1 9.4 - - + -
149D ALA 3.3 8.8 + - - -
150D ALA 3.1 22.7 + - - -
170D VAL 4.2 0.2 + - - -
171D GLY* 1.3 71.6 - - - -
173D VAL* 1.3 62.7 + - - +
191D PHE* 3.7 19.9 - - + -
193D TYR* 4.3 7.2 - - + -
222D PHE* 3.4 36.3 - - + -
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Residues in contact with VAL 173 (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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150D ALA* 3.7 1.1 - - + -
151D ALA* 3.7 14.8 - - + +
172D ALA* 1.3 81.2 - - - +
174D GLY* 1.3 58.0 - - - +
175D SER 3.5 2.0 - - - +
178D LYS* 3.5 15.5 - - + -
179D VAL* 3.2 48.5 - - + +
182D LEU* 3.4 32.1 - - + -
190D VAL* 4.1 4.3 - - + -
191D PHE 3.1 4.6 + - - +
192D ASN* 3.2 6.8 - - - -
193D TYR* 3.0 31.1 + - - -
701D NAP 3.5 7.0 - - - +
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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