Contacts of the strand formed by residues 170 - 174 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D PRO 4.8 1.0 + - - -
136D TYR* 3.5 24.5 - - + -
137D PHE* 3.1 24.1 + - - -
168D ALA* 3.4 2.9 + - - +
169D LYS* 1.3 82.0 - - - +
171D VAL* 1.3 69.9 + - - +
201D MET* 4.4 2.3 - - - +
202D ASP* 3.3 13.2 - - + -
204D MET* 3.7 16.2 - - + -
332D TYR* 3.8 17.0 - - + -
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Residues in contact with VAL 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D TYR* 4.7 0.9 - - - -
137D PHE* 3.2 15.7 - - + +
139D LEU* 3.7 22.9 - - + -
160D ILE* 5.1 0.2 - - + -
163D ALA* 3.8 28.3 - - + -
168D ALA* 4.5 3.1 - - + -
170D ALA* 1.3 81.1 - - - +
172D LYS* 1.3 64.4 + - - +
173D VAL* 4.9 0.4 - - + -
197D ILE* 3.8 28.9 - - + -
201D MET* 4.1 19.9 - - + +
202D ASP 3.1 7.1 + - - +
203D MET* 3.6 2.3 - - - +
204D MET* 2.9 27.6 + - - +
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Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D TYR* 3.0 38.6 + - + +
137D PHE 2.9 7.1 + - - -
138D THR* 3.7 26.3 - - + +
139D LEU* 2.9 31.5 + - - +
171D VAL* 1.3 75.4 - - - +
173D VAL* 1.3 73.5 + - - +
174D CYS* 5.3 0.2 - - - -
204D MET* 3.4 15.5 - - + +
206D ASP* 3.9 18.4 - - + +
231D PHE* 4.0 11.4 - - + -
233D GLU* 2.6 36.4 + - - +
280D GLN* 4.6 0.2 - - - +
334D GLU* 3.3 17.6 + - - -
395D MG 4.3 3.2 - - - -
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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
----------------------------------------------------------
139D LEU* 5.2 1.1 - - + -
156D TYR* 3.5 25.6 - - + +
160D ILE* 4.9 3.6 - - + -
171D VAL* 4.9 3.6 - - + -
172D LYS* 1.3 79.1 - - - +
174D CYS* 1.3 63.1 + - - +
190D LEU* 4.2 5.8 - - + -
193D LEU* 3.9 30.1 - - + -
197D ILE* 4.0 23.1 - - + -
203D MET* 4.0 19.1 - - + -
204D MET 3.0 12.7 + - - +
205D VAL* 3.4 7.9 - - + -
206D ASP* 2.8 24.4 + - - +
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Residues in contact with CYS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D THR* 4.8 14.4 - - - -
139D LEU 4.1 9.4 - - - -
140D TYR* 3.7 29.2 - - + -
156D TYR* 2.8 13.5 + - - +
172D LYS* 5.1 0.7 - - - -
173D VAL* 1.3 80.3 - - - +
175D ILE* 1.3 60.9 + - - +
176D ILE* 3.7 4.3 + - + +
189D TYR* 2.7 31.9 + - - -
205D VAL* 5.5 0.4 - - - -
206D ASP* 3.4 25.4 - - - +
208D LEU* 4.0 16.6 - - + -
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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
------------------------------------------------------------
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