Contacts of the helix formed by residues 264 - 270 (chain A) in PDB entry 1UMZ
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 PRO 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A LEU* 3.7 36.5 - - + +
159A VAL* 3.6 22.0 - - + -
262A MET* 3.6 9.4 - - + +
263A PRO* 1.3 83.4 - - + +
265A GLU* 1.3 72.1 + - - +
266A CYS 3.2 0.7 + - - -
267A LYS* 4.1 13.6 - - - +
268A ARG* 4.8 1.9 + - - +
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 3.4 20.9 + - - -
151A PHE* 3.8 11.5 - - + -
152A LYS 5.1 0.7 - - - +
154A CYS* 3.9 21.1 - - - -
159A VAL* 3.6 29.2 - - + +
252A TYR* 2.6 33.7 + - - +
263A PRO* 3.3 18.9 - - - +
264A PRO* 1.3 84.5 - - - +
266A CYS* 1.3 62.9 + - - +
267A LYS 3.4 0.2 - - - -
268A ARG* 3.2 6.9 + - - +
269A ASP* 2.9 38.6 + - - +
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Residues in contact with CYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A TYR* 4.3 2.7 - - - -
253A CYS* 2.1 57.7 - - + -
262A MET* 4.1 7.4 - - - -
263A PRO* 3.4 34.1 - - - +
264A PRO 3.2 1.8 - - - -
265A GLU* 1.3 76.5 - - - +
267A LYS* 1.3 70.9 + - + +
269A ASP* 3.3 5.2 + - - -
270A ARG 3.1 17.5 + - - -
271A ASP* 3.1 11.7 + - + -
272A ILE* 3.8 7.3 + - + -
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Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ARG* 4.9 2.6 - - - +
262A MET* 2.5 53.9 - - + -
264A PRO 4.1 10.3 - - - +
266A CYS* 1.3 73.8 - - + +
268A ARG* 1.3 62.3 + - - +
270A ARG* 3.2 19.8 + - - -
272A ILE* 3.1 36.3 - - + +
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A LYS* 4.3 25.7 - - + +
153A ASN 3.6 15.9 + - - -
154A CYS* 3.7 24.3 - - - +
156A ASP* 2.8 41.9 + - - -
157A LEU* 4.4 11.0 - - - +
237A TYR* 4.6 2.9 + - - -
264A PRO 4.8 2.0 + - - +
265A GLU* 3.2 10.4 + - - +
267A LYS* 1.3 81.6 - - - +
269A ASP* 1.3 62.9 + - - +
270A ARG* 3.1 14.1 + - - +
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Residues in contact with ASP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A VAL* 3.0 31.6 + - - +
151A PHE* 3.8 12.0 - - - -
152A LYS* 2.9 35.6 + - - +
237A TYR* 5.3 0.2 - - - -
240A LEU* 3.8 14.2 - - - +
252A TYR* 4.5 2.8 + - - -
265A GLU* 2.9 37.9 + - - +
266A CYS* 3.3 3.5 + - - +
268A ARG* 1.3 73.7 - - - +
270A ARG* 1.3 71.1 + - - +
271A ASP* 3.5 20.9 + - - +
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ASP* 5.1 3.4 + - - -
234A ALA* 6.2 0.2 - - - +
237A TYR* 3.4 66.0 + - + +
240A LEU* 4.5 9.1 - - + +
241A SER* 5.8 1.0 - - - -
244A ARG* 3.7 18.0 - - - +
266A CYS 3.1 3.4 + - - -
267A LYS 3.2 12.5 + - - -
268A ARG 3.1 11.8 + - - +
269A ASP* 1.3 83.0 - - - +
271A ASP* 1.3 57.7 + - - +
272A ILE* 3.3 21.5 - - + +
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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