Contacts of the strand formed by residues 170 - 173 (chain f) in PDB entry 5M32
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 170 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145f LEU* 5.3 1.3 - - + -
148f VAL* 3.7 35.0 - - - -
149f ILE* 4.6 2.0 - - - -
169f GLY* 1.3 78.3 - - - -
171f LEU* 1.3 60.7 + - - +
172f LEU* 4.0 3.9 - - + +
276f ILE* 3.4 21.8 - - + +
277f MET 3.1 26.0 + - - +
295f LEU* 3.9 6.8 - - - +
297f ARG* 3.3 30.3 - - - +
299f ILE* 3.7 20.2 - - + -
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Residues in contact with LEU 171 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170f CYS* 1.3 74.1 - - - +
172f LEU* 1.3 59.3 + - - +
173f TYR* 3.0 42.7 + - + +
235f ILE* 5.1 2.2 - - + -
277f MET* 3.4 24.2 - - + +
279f THR* 4.3 10.5 - - + -
282f PRO* 4.4 4.7 - - + -
285f LEU* 4.0 29.4 - - + -
289f LEU* 5.7 0.2 - - + -
290f LEU* 4.8 4.3 - - + -
295f LEU* 3.8 27.8 - - + +
297f ARG 3.8 4.9 + - - -
298f LYS* 3.8 26.3 - - + +
299f ILE 2.9 23.0 + - - +
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Residues in contact with LEU 172 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145f LEU* 3.7 33.2 - - + -
170f CYS* 4.8 5.4 - - + +
171f LEU* 1.3 68.8 - - - +
173f TYR* 1.3 55.6 + - - +
180f LYS* 2.4 42.0 + - + +
183f LEU* 4.2 12.6 - - + -
184f ALA* 5.8 1.6 - - + -
231f PHE* 5.1 1.1 - - + -
276f ILE* 4.6 15.7 - - + -
277f MET 2.8 13.1 + - - +
278f ALA* 3.7 27.4 - - + -
279f THR 3.4 8.7 + - - +
299f ILE* 3.5 29.2 - - + -
301f ILE* 3.7 22.0 - - + -
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Residues in contact with TYR 173 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409e LYS* 5.3 13.3 - - + +
171f LEU* 3.0 36.0 + - + -
172f LEU* 1.3 73.3 - - - +
174f GLY* 1.3 59.2 + - - +
180f LYS* 3.2 1.3 - - - -
279f THR 3.7 7.6 - - - +
282f PRO* 3.7 32.5 - - + -
298f LYS* 3.6 29.4 + - + +
299f ILE 3.1 28.6 + - - +
300f HIS* 3.3 37.3 + + + +
301f ILE 3.3 20.6 + - - -
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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