Contacts of the helix formed by residues 262 - 268 (chain E) in PDB entry 6S7T
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 SER 262 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723A TYR* 5.7 0.7 - - - -
724A ARG* 4.5 15.3 - - - -
758A GLU* 3.6 20.6 - - - -
148E GLN* 3.4 16.2 + - - -
260E PRO* 3.9 5.2 + - - -
261E PHE* 1.3 72.6 - - - +
263E ARG* 1.3 65.7 + - - +
264E TYR 4.5 3.6 - - - -
265E ASP* 2.8 36.8 + - - +
266E TYR 3.2 7.8 + - - -
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Residues in contact with ARG 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A GLU* 4.1 6.2 + - - -
758A GLU* 4.4 5.3 + - - -
760A PHE* 3.9 13.9 - - - -
761A THR* 2.5 35.4 + - + +
762A SER 3.2 20.5 + - - -
763A GLU* 3.9 21.6 - - - +
765A TRP* 4.1 10.1 - - - +
261E PHE* 3.8 25.3 + - + -
262E SER* 1.3 69.2 - - - +
264E TYR* 1.3 60.4 + - - +
266E TYR* 3.1 30.4 + - + +
267E GLN* 2.9 50.6 + - + +
317E ARG* 6.0 1.6 - - - +
321E PRO* 3.6 27.5 - - - +
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Residues in contact with TYR 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724A ARG* 3.6 37.5 - - + -
727A GLU* 3.1 56.5 + - + +
728A MET* 3.7 20.2 - - + -
765A TRP* 3.7 24.4 - + + -
262E SER* 3.2 1.0 - - - -
263E ARG* 1.3 78.7 - - - +
265E ASP* 1.3 65.6 + - - +
267E GLN* 4.6 2.7 - - - -
268E ARG* 3.0 59.7 + - + +
269E GLN* 6.5 0.4 - - + -
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Residues in contact with ASP 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724A ARG* 4.0 25.6 + - - -
148E GLN* 4.4 10.3 - - + +
149E SER* 6.4 1.8 - - - -
262E SER* 2.8 25.7 + - - +
264E TYR* 1.3 84.0 - - - +
266E TYR* 1.3 56.0 + - - +
267E GLN 3.4 0.2 + - - -
269E GLN* 3.1 40.8 - - - +
272E SER* 2.6 25.6 + - - -
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Residues in contact with TYR 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E GLN* 3.4 14.5 - - - +
261E PHE* 4.3 4.9 - + + -
262E SER 3.2 6.7 + - - +
263E ARG* 3.1 41.1 + - + +
265E ASP* 1.3 77.3 - - - +
267E GLN* 1.3 61.5 + - + +
269E GLN 4.9 1.8 - - - +
272E SER* 3.4 23.7 + - - +
273E GLY 5.0 0.4 - - - -
276E SER* 4.6 8.5 - - - -
278E ARG* 2.5 53.0 + - - +
321E PRO* 3.6 24.1 - - + +
323E PHE* 3.6 34.3 - + - -
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Residues in contact with GLN 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728A MET* 4.5 16.2 - - + +
763A GLU* 4.1 18.6 + - - +
765A TRP* 3.9 12.3 + - - -
263E ARG* 2.9 39.1 + - + +
264E TYR* 4.3 2.2 - - - +
266E TYR* 1.3 84.2 - - + +
268E ARG* 1.3 70.2 + - + +
269E GLN 3.7 1.3 - - - -
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Residues in contact with ARG 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727A GLU 5.0 2.9 - - - -
728A MET* 3.4 31.1 - - - +
729A GLN 3.3 28.2 + - - +
730A LEU* 4.3 10.3 - - - +
731A ASP* 3.9 20.2 + - - +
264E TYR* 3.0 48.7 + - + +
267E GLN* 1.3 86.4 - - + +
269E GLN* 1.3 61.1 + - - +
270E PRO* 4.3 4.2 - - - +
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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