Contacts of the helix formed by residues 714 - 719 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441C ARG* 3.7 11.2 + - - +
482C SER* 4.7 5.4 - - - -
713C GLU* 1.3 73.0 - - - +
715C PRO* 1.3 65.1 - - - +
716C SER* 2.9 36.6 + - - -
717C PHE* 3.0 20.6 + - - +
689D GLU* 3.4 25.5 - - - +
691D ILE 2.8 26.1 + - - +
692D PRO* 4.4 3.0 - - + +
693D ASN 3.5 13.5 - - - +
695D VAL* 3.8 16.9 - - - +
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Residues in contact with PRO 715 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C LEU* 5.6 3.0 - - - +
354C PHE* 3.8 25.6 - - + -
355C GLN* 4.6 15.4 + - - +
481C PRO 4.8 1.3 - - - -
482C SER* 3.4 25.8 - - - +
711C PHE* 3.8 27.1 - - + -
713C GLU* 2.9 18.1 - - + +
714C ASP* 1.3 80.4 - - - +
716C SER* 1.3 57.3 + - - +
717C PHE 3.1 3.1 + - - -
718C TYR* 3.5 30.6 + - + +
719C SER 4.4 1.0 + - - -
689D GLU* 4.5 3.6 - - + -
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Residues in contact with SER 716 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C LEU* 3.7 26.4 - - - +
441C ARG* 2.4 50.6 + - - -
455C LEU* 4.2 5.2 - - - -
481C PRO* 3.7 17.0 - - - -
714C ASP* 2.9 21.0 + - - -
715C PRO* 1.3 76.1 - - - +
717C PHE* 1.3 56.3 + - - +
718C TYR 3.0 1.8 - - - -
719C SER* 3.1 18.5 + - - +
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Residues in contact with PHE 717 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441C ARG* 3.4 13.0 + - - +
713C GLU* 3.8 15.0 - - - +
714C ASP 3.0 16.2 + - - +
716C SER* 1.3 81.2 + - - +
718C TYR* 1.3 80.8 + + + +
719C SER 3.4 0.3 + - - -
296D THR* 6.0 0.7 - - + -
297D GLY* 3.7 15.3 - - - -
298D GLY* 3.6 15.5 - - - -
301D SER* 2.9 44.0 - - - -
302D LEU 3.9 9.2 - - - -
303D LYS 3.5 21.8 - - - -
304D SER* 3.3 23.4 + - - -
305D PRO* 3.8 14.8 - - + -
692D PRO* 4.0 19.3 - - + -
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Residues in contact with TYR 718 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C GLN* 5.8 6.3 - - - +
713C GLU* 2.7 37.3 + - + -
715C PRO* 3.5 24.9 - - + +
716C SER 3.0 0.4 - - - -
717C PHE* 1.3 93.7 - + + +
719C SER* 1.3 65.2 + - - -
720C ALA 3.2 2.4 + - - -
297D GLY* 5.2 2.8 - - - -
304D SER* 3.7 4.7 - - - -
305D PRO* 3.7 24.0 - - + -
306D VAL* 3.3 24.8 - - + +
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Residues in contact with SER 719 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C LEU* 3.3 34.7 - - - +
481C PRO* 5.9 2.6 - - - +
715C PRO 4.4 0.2 + - - -
716C SER* 3.1 25.4 + - - +
717C PHE 3.2 0.6 - - - -
718C TYR* 1.3 74.7 - - - +
720C ALA* 1.3 60.7 + - - +
721C ASP* 3.4 12.0 + - - +
722C SER* 3.3 11.4 + - - -
304D SER* 2.6 24.4 + - - -
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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