Contacts of the helix formed by residues 714 - 719 (chain A) in PDB entry 2C11
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 ASP 714 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A ARG* 3.4 13.1 + - - +
482A SER* 4.5 5.0 - - - -
713A GLU* 1.3 73.6 - - - +
715A PRO* 1.3 67.4 - - - +
716A SER* 2.6 39.5 + - - -
717A PHE* 2.9 21.0 + - - +
689B GLU* 3.5 20.5 - - - +
691B ILE 2.6 26.5 + - - +
692B PRO* 4.2 3.5 - - + +
693B ASN 3.9 7.2 - - - +
695B VAL* 3.8 26.1 - - - +
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Residues in contact with PRO 715 (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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334A LEU* 5.6 2.4 - - - +
354A PHE* 3.8 20.9 - - + -
355A GLN* 4.5 16.4 + - - +
481A PRO 4.7 2.0 - - - -
482A SER* 3.4 24.7 - - - +
711A PHE* 3.5 32.1 - - + -
713A GLU* 2.9 16.7 - - + +
714A ASP* 1.3 82.8 - - - +
716A SER* 1.3 57.4 + - - +
717A PHE 3.2 2.7 + - - -
718A TYR* 3.6 30.4 + - + +
719A SER 4.4 0.9 + - - -
689B GLU* 4.5 2.5 - - + -
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Residues in contact with SER 716 (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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440A LEU* 3.6 26.1 - - - +
441A ARG* 2.6 37.3 + - - -
455A LEU* 4.2 4.3 - - - -
481A PRO* 3.7 17.3 - - - -
714A ASP* 2.6 33.7 + - - -
715A PRO* 1.3 76.5 - - - +
717A PHE* 1.3 57.6 + - - +
718A TYR 2.9 2.5 - - - -
719A SER* 2.9 19.8 + - - +
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Residues in contact with PHE 717 (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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441A ARG* 3.3 14.0 + - - +
713A GLU* 3.7 15.3 - - - +
714A ASP 2.9 14.8 + - - +
716A SER* 1.3 80.5 + - - +
718A TYR* 1.3 77.8 + + + +
719A SER 3.2 0.2 - - - -
297B GLY* 3.7 16.2 - - - -
298B GLY* 3.7 13.9 - - - -
301B SER* 3.1 37.5 - - - -
302B LEU 4.0 9.4 - - - -
303B LYS 3.6 25.4 - - - -
304B SER* 3.1 26.2 + - - -
305B PRO* 3.7 15.9 - - + -
692B PRO* 3.9 20.6 - - + -
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Residues in contact with TYR 718 (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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355A GLN* 5.9 4.3 - - - +
713A GLU* 2.6 39.0 + - + -
715A PRO* 3.6 24.2 - - + +
716A SER 2.9 0.6 - - - -
717A PHE* 1.3 94.2 - + + +
719A SER* 1.3 66.1 + - - +
720A ALA 3.2 2.4 + - - -
297B GLY* 5.0 4.0 - - - -
304B SER* 3.5 5.2 - - - -
305B PRO* 3.5 24.7 - - + -
306B VAL* 3.3 25.6 - - + +
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Residues in contact with SER 719 (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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455A LEU* 3.4 29.3 - - - +
481A PRO* 5.8 3.2 - - - +
715A PRO 4.4 0.4 + - - -
716A SER* 2.9 24.6 + - - +
717A PHE 3.2 1.0 - - - -
718A TYR* 1.3 75.8 - - - +
720A ALA* 1.3 60.4 + - - +
721A ASP* 3.0 18.2 + - - +
722A SER* 3.3 12.1 + - - -
304B SER* 2.6 24.3 + - - -
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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