Contacts of the helix formed by residues 703 - 717 (chain A) in PDB entry 6P0D
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 703 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701A THR* 3.0 2.2 + - - +
702A LYS* 1.3 76.7 - - - +
704A ILE* 1.3 64.9 + - - +
705A GLU* 2.6 48.3 + - - +
706A GLN* 3.5 37.0 + - + +
707A ILE* 3.0 25.5 + - - +
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Residues in contact with ILE 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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551A ILE* 3.9 23.2 - - + +
552A SER* 6.1 0.9 - - - +
555A LEU* 3.9 31.0 - - + -
702A LYS 3.5 4.9 + - - +
703A ASP* 1.3 74.1 + - - +
705A GLU* 1.3 59.6 + - + +
707A ILE* 3.3 8.6 + - + +
708A ALA* 2.9 30.5 + - + +
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Residues in contact with GLU 705 (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 ASP* 2.6 25.4 + - - +
704A ILE* 1.3 74.1 - - + +
706A GLN* 1.3 57.7 + - - +
708A ALA* 3.5 5.3 + - - +
709A GLU* 3.0 29.5 + - - +
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Residues in contact with GLN 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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699A LEU* 4.0 27.4 - - + +
701A THR* 3.1 27.5 + - - +
703A ASP* 3.3 28.3 + - + +
705A GLU* 1.3 79.3 - - + +
707A ILE* 1.3 52.6 + - - +
709A GLU* 3.3 5.4 + - - +
710A PHE* 2.7 37.2 + - - +
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Residues in contact with ILE 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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551A ILE* 3.7 31.2 - - + -
554A VAL* 5.9 3.4 - - + -
555A LEU* 5.4 2.7 - - + -
563A PHE* 3.9 31.9 - - + -
565A CYS* 4.2 19.3 - - - -
699A LEU* 4.9 0.4 - - - -
701A THR* 3.6 22.0 - - + +
702A LYS 4.3 4.3 - - - +
703A ASP 3.0 22.9 + - - +
704A ILE* 3.3 7.4 + - - +
706A GLN* 1.3 76.8 - - - +
708A ALA* 1.3 58.3 + - - +
710A PHE* 3.1 6.8 + - - +
711A LEU* 2.8 28.9 + - - +
722A LEU* 4.0 9.1 - - + +
724A VAL* 6.1 0.9 - - + -
745A LEU* 4.7 4.3 - - + -
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Residues in contact with ALA 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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551A ILE* 3.4 18.3 - - + +
704A ILE* 2.9 19.6 + - + +
705A GLU* 3.8 6.3 - - - +
707A ILE* 1.3 74.5 - - - +
709A GLU* 1.3 61.7 + - - +
711A LEU* 3.3 8.9 + - - +
712A GLU* 3.1 27.9 + - - +
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Residues in contact with GLU 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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705A GLU 3.0 19.3 + - - +
706A GLN* 3.7 6.3 - - - +
708A ALA* 1.3 73.4 - - - +
710A PHE* 1.3 60.8 + - - +
712A GLU* 3.2 13.8 + - - +
713A GLN* 2.9 43.3 + - + +
716A LYS* 4.8 7.3 + - - -
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Residues in contact with PHE 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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565A CYS* 3.6 34.5 - - + -
566A GLU 4.3 0.4 - - - -
567A TYR* 3.5 31.2 - + - -
697A THR* 4.0 9.4 - - + -
698A SER* 3.7 25.8 - - - -
699A LEU* 3.9 26.5 - - + -
706A GLN 2.7 22.1 + - - +
707A ILE* 3.5 6.1 - - - +
709A GLU* 1.3 74.0 - - - +
711A LEU* 1.3 56.5 + - - +
713A GLN* 3.2 7.7 + - + +
714A SER* 2.9 28.6 + - - -
722A LEU* 3.5 30.1 - - + -
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Residues in contact with LEU 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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551A ILE* 5.3 5.2 - - + -
707A ILE 2.8 16.7 + - - +
708A ALA* 3.5 13.5 - - - +
710A PHE* 1.3 73.4 - - - +
712A GLU* 1.3 65.3 + - - +
714A SER* 2.7 22.1 + - - +
715A VAL* 3.3 6.7 + - + +
721A GLY* 3.7 27.6 - - - -
722A LEU* 3.8 17.2 - - + +
745A LEU* 3.7 31.6 - - + +
747A LYS* 4.0 33.7 - - + +
750A LEU* 4.7 13.9 - - + -
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Residues in contact with GLU 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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708A ALA 3.1 16.8 + - - +
709A GLU* 3.2 20.2 + - - +
711A LEU* 1.3 78.0 - - - +
713A GLN* 1.3 63.3 + - - +
715A VAL* 3.3 9.2 + - - +
716A LYS* 3.2 36.5 + - - +
747A LYS* 3.2 43.2 + - - +
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Residues in contact with GLN 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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567A TYR* 3.3 17.3 - - - +
709A GLU* 2.9 31.3 + - + +
710A PHE* 3.2 11.9 + - + +
712A GLU* 1.3 72.9 - - - +
714A SER* 1.3 66.5 + - - +
716A LYS* 3.2 25.2 + - - +
717A ASP* 2.9 47.8 + - - +
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Residues in contact with SER 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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567A TYR* 3.5 36.7 - - - -
710A PHE 2.9 11.1 + - - -
711A LEU* 2.7 20.2 + - - -
713A GLN* 1.3 76.9 - - - +
715A VAL* 1.3 59.2 + - - +
717A ASP 3.3 7.4 + - - -
718A SER 3.4 0.3 + - - -
719A CYS* 2.9 29.2 + - - +
721A GLY* 3.3 34.5 + - - -
722A LEU* 3.8 2.9 - - - -
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Residues in contact with VAL 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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711A LEU 3.7 11.9 - - - +
712A GLU* 3.3 9.1 + - - +
713A GLN 3.2 0.6 - - - -
714A SER* 1.3 83.4 + - - +
716A LYS* 1.3 67.0 + - + +
718A SER* 3.1 13.3 + - - -
719A CYS 3.6 15.9 + - - +
720A GLU 4.6 10.3 - - - +
721A GLY* 4.7 1.8 - - - +
747A LYS* 4.3 32.8 - - + -
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Residues in contact with LYS 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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709A GLU* 4.8 8.5 + - - -
712A GLU* 3.2 27.4 + - - +
713A GLN* 3.2 33.7 + - - +
715A VAL* 1.3 77.4 - - + +
717A ASP* 1.3 59.9 + - - +
718A SER* 3.3 5.6 + - - -
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Residues in contact with ASP 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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567A TYR* 2.6 40.7 + - + -
569A TYR* 5.7 0.2 - - - -
632A ILE* 4.1 8.8 - - - +
713A GLN* 2.9 35.3 + - - +
714A SER 3.5 0.7 - - - +
715A VAL 3.1 0.8 - - - -
716A LYS* 1.3 78.9 - - - +
718A SER* 1.3 68.7 + - - +
719A CYS* 3.4 11.3 + - - -
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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