Contacts of the strand formed by residues 170 - 174 (chain O) in PDB entry 3MQT
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 ALA 170 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135O PRO 4.6 1.4 + - - -
136O TYR* 3.4 12.1 - - + -
137O PHE* 3.0 24.6 + - - -
168O ALA* 3.4 1.6 - - - +
169O LYS* 1.3 82.4 - - - +
171O VAL* 1.3 68.0 + - - +
201O MET* 4.4 1.7 - - - +
202O ASP* 3.3 13.7 - - + +
204O MET* 3.5 28.5 - - + -
332O TYR* 3.6 17.9 - - + -
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Residues in contact with VAL 171 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136O TYR* 4.8 1.1 - - - -
137O PHE* 3.4 15.3 - - + +
139O LEU* 3.7 21.3 - - + -
160O ILE* 5.3 0.4 - - + -
163O ALA* 3.7 30.1 - - + -
168O ALA* 4.3 4.0 - - + -
170O ALA* 1.3 81.6 - - - +
172O LYS* 1.3 59.7 + - - +
173O VAL* 4.8 1.6 - - + -
197O ILE* 4.0 25.1 - - + -
201O MET* 3.9 25.4 - - + -
202O ASP 3.0 11.6 + - - +
203O MET* 3.5 1.2 - - - +
204O MET* 2.9 27.2 + - - +
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Residues in contact with LYS 172 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136O TYR* 3.1 28.3 + - + -
137O PHE 3.0 7.5 + - - -
138O THR* 3.5 24.3 - - - +
139O LEU* 2.8 33.5 + - - +
171O VAL* 1.3 73.9 - - - +
173O VAL* 1.3 72.7 - - - +
174O CYS* 5.1 1.1 - - - -
204O MET* 3.4 18.2 - - + +
206O ASP* 4.0 18.8 + - + +
231O PHE* 4.0 13.5 - - + -
233O GLU* 2.6 34.0 + - - +
309O HIS* 5.7 0.4 + - - -
334O GLU* 2.9 25.5 + - - -
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Residues in contact with VAL 173 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139O LEU* 4.6 9.9 - - + -
156O TYR* 3.5 33.0 - - + -
160O ILE* 4.9 3.1 - - + -
171O VAL* 4.8 1.6 - - + -
172O LYS* 1.3 79.9 - - - +
174O CYS* 1.3 63.3 + - - +
190O LEU* 4.5 4.5 - - + -
193O LEU* 3.8 24.5 - - + -
197O ILE* 4.1 21.3 - - + -
203O MET* 4.2 17.3 - - + -
204O MET 3.1 12.2 + - - +
205O VAL* 3.4 10.0 - - + +
206O ASP 3.0 22.7 + - - -
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Residues in contact with CYS 174 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138O THR* 4.7 11.9 - - - -
139O LEU 3.8 16.4 - - - -
140O TYR* 3.9 28.7 - - + -
156O TYR* 2.8 13.4 + - - +
172O LYS* 4.6 3.1 - - - -
173O VAL* 1.3 82.7 - - - +
175O ILE* 1.3 66.4 + - - +
176O ILE* 3.7 5.4 + - + +
189O TYR* 2.8 26.8 + - - -
190O LEU* 5.7 0.2 - - - -
205O VAL* 5.2 0.9 - - - -
206O ASP* 3.4 26.0 - - + +
208O LEU* 4.5 6.1 - - + -
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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
------------------------------------------------------------
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