Contacts of the helix formed by residues 708 - 719 (chain A) in PDB entry 1OEC
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 708 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668A LYS* 4.9 0.4 - - - +
706A GLY 3.6 10.3 - - - +
707A ILE* 1.3 87.5 - - - +
709A VAL* 1.3 66.3 + - - +
710A GLU* 3.1 28.1 + - + +
711A GLU* 3.1 36.0 + - + +
712A LEU* 3.5 6.9 + - - +
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Residues in contact with VAL 709 (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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667A VAL* 3.5 31.7 - - + +
668A LYS* 3.9 22.6 - - + +
707A ILE 3.8 1.2 + - - -
708A PRO* 1.3 70.4 - - - +
710A GLU* 1.3 81.0 + - - +
712A LEU* 3.1 22.3 + - - +
713A PHE* 3.7 16.1 - - + -
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Residues in contact with GLU 710 (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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708A PRO* 3.4 26.4 - - + +
709A VAL* 1.3 98.2 + - + +
711A GLU* 1.3 57.3 + - + +
712A LEU 3.5 0.2 - - - -
713A PHE* 3.6 24.2 + - + +
714A LYS* 6.2 0.3 - - - +
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Residues in contact with GLU 711 (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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706A GLY 4.7 1.2 - - - +
707A ILE* 3.3 29.1 - - + +
708A PRO* 3.1 35.1 + - + +
710A GLU* 1.3 77.4 - - + +
712A LEU* 1.3 64.2 + - - +
713A PHE 3.2 3.8 + - - -
714A LYS* 3.4 8.7 + - - +
715A LEU* 3.4 33.4 + - - +
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Residues in contact with LEU 712 (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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667A VAL* 4.1 27.4 - - + +
668A LYS* 4.1 17.0 - - + -
675A LEU* 4.9 5.4 - - + -
704A TYR* 3.5 46.9 - - + -
707A ILE* 4.5 6.5 - - + -
708A PRO 3.5 3.9 + - - +
709A VAL 3.1 17.4 + - - +
711A GLU* 1.3 76.4 - - - +
713A PHE* 1.3 64.7 + - + +
715A LEU* 4.3 10.5 - - + -
716A LEU* 3.0 52.9 + - + +
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Residues in contact with PHE 713 (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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667A VAL* 4.4 21.1 - - + -
675A LEU* 4.0 33.0 - - + -
676A PHE* 3.7 24.2 - + + -
709A VAL* 3.7 17.7 - - + -
710A GLU* 3.6 24.9 - - - +
711A GLU 3.2 0.8 - - - -
712A LEU* 1.3 80.7 - - + +
714A LYS* 1.3 69.5 + - + +
716A LEU* 3.9 0.6 + - - -
717A LYS* 3.6 23.6 + - - +
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Residues in contact with LYS 714 (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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710A GLU 6.2 0.2 - - - +
711A GLU* 3.4 8.3 + - - +
712A LEU 3.3 0.2 - - - -
713A PHE* 1.3 83.0 - - + +
715A LEU* 1.3 68.0 + - + +
717A LYS* 3.2 28.6 + - + +
718A GLU* 3.1 34.6 + - - +
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Residues in contact with LEU 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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704A TYR* 6.3 0.2 - - + -
707A ILE* 3.6 43.5 - - + -
711A GLU* 3.4 30.4 + - - +
712A LEU* 3.9 7.6 - - + +
714A LYS* 1.3 79.5 - - + +
716A LEU* 1.3 64.0 + - + +
718A GLU* 3.1 20.8 + - + +
720A HIS* 3.1 45.3 + - + +
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Residues in contact with LEU 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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670A MET 4.1 13.0 - - - +
672A PRO* 4.1 25.9 - - + +
675A LEU* 3.6 30.1 - - + -
676A PHE* 4.8 7.4 - - + -
687A TRP* 4.2 12.3 - - + -
704A TYR* 3.9 25.6 - - + +
712A LEU* 3.0 33.8 + - + +
713A PHE 4.1 4.7 - - - +
715A LEU* 1.3 77.3 - - + +
717A LYS* 1.3 61.4 + - - +
719A GLY* 3.4 8.1 + - - -
720A HIS* 4.1 15.5 - - + +
721A ARG* 3.8 11.2 + - - +
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Residues in contact with LYS 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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676A PHE* 3.7 42.8 - - + -
713A PHE 3.6 13.2 + - - +
714A LYS* 3.2 29.8 + - + +
715A LEU 3.2 0.4 - - - -
716A LEU* 1.3 74.9 - - - +
718A GLU* 1.3 65.2 + - - +
719A GLY* 3.0 6.7 + - - -
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Residues in contact with GLU 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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714A LYS* 3.1 26.4 + - - +
715A LEU* 3.1 20.4 + - + +
717A LYS* 1.3 79.9 - - - +
719A GLY* 1.3 59.1 + - - +
720A HIS* 4.5 3.6 - - + +
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Residues in contact with GLY 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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715A LEU 3.3 1.8 + - - -
716A LEU 3.4 2.6 + - - -
717A LYS 3.0 6.5 - - - -
718A GLU* 1.3 79.4 - - - +
720A HIS* 1.3 67.0 + - - +
721A ARG* 3.5 27.6 + - - +
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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