Contacts of the helix formed by residues 703 - 713 (chain A) in PDB entry 3E0D
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 GLU 703 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A GLY 3.3 19.8 + - - +
701A PRO 2.8 5.6 + - - +
702A MET* 1.3 77.7 - - - +
704A HIS* 1.3 81.1 + - + +
705A ILE 3.1 1.1 - - - -
706A PRO* 3.0 20.8 - - - +
707A THR* 4.1 5.2 + - - -
811A TYR* 6.1 2.2 - - - -
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Residues in contact with HIS 704 (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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696A LEU* 4.6 11.0 - - + -
700A GLY 5.4 0.2 + - - -
701A PRO* 2.7 38.8 + - + +
703A GLU* 1.3 93.4 + - + +
705A ILE* 1.3 55.8 + - - +
706A PRO 3.6 0.2 - - - -
707A THR* 3.4 14.3 + - - +
708A TYR* 3.1 25.3 + - - +
740A ILE* 3.6 25.3 - - + +
741A PRO 5.4 0.7 - - - -
808A PHE* 3.0 43.6 - + - -
811A TYR* 5.6 7.3 - - + +
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Residues in contact with ILE 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A THR* 3.4 28.7 - - + +
682A LEU* 5.6 1.3 - - + -
693A LEU* 4.1 13.7 - - + -
696A LEU* 4.3 18.8 - - + -
697A TYR* 3.4 50.3 - - + +
701A PRO 4.4 0.2 - - - +
702A MET* 3.3 18.6 - - - +
703A GLU 3.1 0.2 - - - -
704A HIS* 1.3 76.0 - - - +
706A PRO* 1.4 65.0 - - + +
708A TYR* 3.1 11.3 + - + +
709A ILE* 2.8 42.1 + - + +
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Residues in contact with PRO 706 (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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702A MET 3.9 3.1 - - - +
703A GLU* 3.0 20.9 - - - +
705A ILE* 1.4 93.8 - - + +
707A THR* 1.3 61.5 - - - +
709A ILE* 3.2 11.9 + - + +
710A ARG* 3.0 43.8 + - - +
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Residues in contact with THR 707 (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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703A GLU 4.1 3.8 + - - -
704A HIS* 3.4 22.4 + - - -
705A ILE 3.2 0.4 - - - -
706A PRO* 1.3 77.7 - - - +
708A TYR* 1.3 64.6 + - - +
710A ARG* 3.4 16.8 + - - +
711A ARG* 3.1 64.5 + - - +
716A GLU* 3.8 7.9 - - - +
740A ILE* 4.3 7.4 - - + -
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Residues in contact with TYR 708 (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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682A LEU* 4.0 31.0 - - + -
688A GLU 4.8 1.7 + - - -
689A ASP* 4.0 14.4 + - - -
692A ALA* 3.7 26.1 - - + +
696A LEU* 3.8 19.3 - - + -
704A HIS 3.1 14.5 + - - +
705A ILE* 3.2 16.2 - - + +
707A THR* 1.3 76.9 - - - +
709A ILE* 1.3 52.6 + - + +
711A ARG* 3.4 4.9 + - - +
712A HIS* 2.7 40.9 + - + +
736A GLU 4.5 7.4 + - - -
737A THR* 3.5 24.4 - - - -
738A TYR* 3.8 33.0 - + - -
740A ILE* 3.7 17.4 - - + +
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Residues in contact with ILE 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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678A THR* 4.6 4.9 - - + +
681A GLY* 4.1 10.8 - - - +
682A LEU* 3.9 38.8 - - + +
705A ILE* 2.8 40.7 + - + +
706A PRO* 3.2 8.7 + - + +
708A TYR* 1.3 71.4 - - + +
710A ARG* 1.3 59.1 + - + +
712A HIS* 3.1 6.6 + - - +
713A HIS* 2.7 62.8 + - + +
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Residues in contact with ARG 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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706A PRO* 3.0 38.3 + - - +
707A THR* 3.7 20.2 + - - +
709A ILE* 1.3 79.3 - - + +
711A ARG* 1.3 60.9 + - - +
713A HIS* 3.6 9.1 + - + -
715A GLN* 3.4 29.6 + - + +
716A GLU* 3.4 36.2 + - + +
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Residues in contact with ARG 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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707A THR* 3.1 37.5 + - - +
708A TYR 3.7 3.8 - - - +
710A ARG* 1.3 74.6 - - - +
712A HIS* 1.3 65.1 + - - +
714A GLY* 3.1 15.8 + - - -
716A GLU* 2.9 50.4 + - + +
717A PRO 4.4 6.4 + - - -
718A VAL* 4.6 13.8 - - + +
719A SER 6.0 0.9 - - - -
738A TYR* 2.9 55.1 + - + -
739A GLY* 4.4 4.2 - - - -
740A ILE* 3.7 18.2 - - - +
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Residues in contact with HIS 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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682A LEU* 4.2 25.6 + - + +
683A LYS 4.7 4.0 + - - -
685A ARG* 2.9 48.1 + - - -
686A ARG* 5.9 2.9 - - - -
689A ASP* 3.7 26.7 + - - -
708A TYR* 2.7 28.5 + + + +
709A ILE* 3.1 6.9 + - - +
711A ARG* 1.3 74.0 - - - +
713A HIS* 1.3 68.5 + + - +
714A GLY 3.2 5.7 + - - -
738A TYR* 2.9 43.5 + + + -
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Residues in contact with HIS 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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681A GLY 3.8 9.7 + - - -
682A LEU 3.8 20.6 - - - -
683A LYS* 5.0 7.6 - - + -
685A ARG* 5.2 4.6 + - - +
709A ILE* 2.7 42.5 + - + +
710A ARG* 3.6 7.8 + - + +
711A ARG 3.3 0.8 - - - -
712A HIS* 1.3 79.5 - + - +
714A GLY* 1.8 48.4 + - - -
715A GLN* 3.3 31.5 + - - +
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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