Contacts of the strand formed by residues 164 - 168 (chain T) in PDB entry 2AK4
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 CYS 164 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162T ASP 4.4 0.9 - - - +
163T LYS* 1.3 74.8 - - - +
165T VAL* 1.3 62.6 + - - +
166T LEU 3.7 0.5 + - - -
175T SER 3.6 0.9 - - - +
176T ASN* 3.3 6.7 - - - -
177T SER* 2.7 39.3 + - - +
174U CYS* 2.1 42.8 - - - -
175U THR 3.7 20.4 - - - -
176U ASP* 4.2 5.4 - - - +
177U PRO* 5.2 4.3 - - + -
196U ARG* 3.6 29.8 - - - +
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Residues in contact with VAL 165 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82T VAL* 4.1 32.8 - - + -
114T VAL 5.4 2.7 - - - +
115T PHE* 5.6 5.8 - - + -
116T PRO* 4.4 20.6 - - + -
163T LYS* 5.4 2.5 - - + +
164T CYS* 1.3 70.3 - - - +
166T LEU* 1.3 72.9 + - - +
167T ASP* 4.1 4.8 + - + +
174T LYS* 4.9 8.1 - - + -
175T SER 3.7 4.5 - - - +
176T ASN* 3.7 15.5 - - - +
173U VAL 4.6 2.1 - - - +
174U CYS* 2.9 22.7 - - - +
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Residues in contact with LEU 166 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164T CYS 3.7 1.7 + - - +
165T VAL* 1.3 75.2 - - - +
167T ASP* 1.3 69.6 + - - +
168T MET* 3.7 28.3 - - + +
173T PHE* 5.5 1.6 - - + +
174T LYS* 3.2 11.3 - - - +
175T SER* 2.7 54.5 + - - +
177T SER* 5.2 4.9 - - - +
145U THR* 5.6 1.1 - - + -
172U GLY* 3.7 23.6 - - - +
173U VAL 5.1 0.7 - - - -
174U CYS* 3.9 24.2 - - + +
196U ARG* 4.3 18.4 - - + -
198U ARG* 3.8 23.1 - - + -
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Residues in contact with ASP 167 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82T VAL* 6.2 0.5 - - - +
165T VAL* 4.1 5.7 + - + +
166T LEU* 1.3 78.3 - - - +
168T MET* 1.3 67.1 + - - +
169T ARG* 3.2 10.7 + - - -
172T ASP* 5.7 0.5 - - - -
173T PHE 3.6 5.7 + - - +
174T LYS* 3.4 35.2 - - + +
170U HIS 5.0 0.7 - - - +
171U SER* 4.4 1.7 - - - -
172U GLY* 3.2 20.8 + - - -
173U VAL 4.8 4.2 + - - +
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Residues in contact with MET 168 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166T LEU* 3.7 16.8 - - + +
167T ASP* 1.3 69.0 - - - +
169T ARG* 1.3 65.5 + - - +
170T SER* 3.5 2.5 - - - +
171T MET* 3.3 13.5 + - + +
172T ASP* 3.2 18.0 + - - -
173T PHE* 2.8 41.4 + - + +
143U LYS* 3.8 31.0 - - + -
171U SER* 4.6 1.8 - - - -
172U GLY* 4.1 7.2 - - - +
198U ARG* 3.8 41.7 - - - +
199U VAL* 4.4 9.9 - - - -
200U SER* 4.4 4.7 - - - +
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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