Contacts of the helix formed by residues 696 - 715 (chain D) in PDB entry 6AH0
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 LYS 696 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D GLY* 6.1 2.0 - - - -
694D GLU* 3.5 7.7 - - - +
695D LYS* 1.3 74.9 - - - +
697D ALA* 1.3 64.7 + - - +
698D ILE 3.3 2.9 - - - +
699D LYS* 3.7 4.0 + - - +
700D ARG* 3.4 15.6 + - - -
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Residues in contact with ALA 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ASP 4.6 8.7 + - - -
131D ILE* 4.4 22.0 - - - +
134D GLY* 5.3 3.2 - - - -
694D GLU 5.7 0.2 - - - -
695D LYS 3.3 6.0 + - - -
696D LYS* 1.3 71.7 - - - +
698D ILE* 1.3 58.5 + - - +
700D ARG* 3.2 2.8 + - - +
701D PHE* 2.9 27.7 + - - -
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Residues in contact with ILE 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ILE* 4.8 5.9 + - - +
134D GLY* 5.2 3.3 - - - -
135D ALA* 5.0 16.5 - - - +
696D LYS* 3.3 1.6 - - - +
697D ALA* 1.3 79.6 - - - +
699D LYS* 1.3 58.6 + - - +
701D PHE* 3.8 6.4 + - - -
702D GLN* 4.1 4.5 + - - -
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Residues in contact with LYS 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696D LYS 3.7 6.0 + - - -
697D ALA 3.3 0.2 - - - -
698D ILE* 1.3 74.4 - - - +
700D ARG* 1.3 60.2 + - - +
701D PHE 3.2 0.4 - - - -
702D GLN* 3.1 5.1 + - - +
703D ILE* 3.0 22.9 + - - -
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Residues in contact with ARG 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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694D GLU* 5.8 5.6 - - - +
696D LYS 3.4 12.3 + - - -
697D ALA* 3.2 8.8 + - - +
699D LYS* 1.3 72.7 - - - +
701D PHE* 1.3 55.5 + - - +
702D GLN 3.0 4.9 - - - -
703D ILE* 4.3 2.2 - - - +
704D MET* 2.9 30.0 + - - -
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Residues in contact with PHE 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697D ALA 2.9 14.4 + - - -
698D ILE 3.8 5.3 + - - -
699D LYS 3.2 0.4 - - - -
700D ARG* 1.3 74.9 - - - +
702D GLN* 1.3 58.1 + - - +
704D MET 4.7 1.1 - - - -
705D ASN* 4.5 7.7 + - - +
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Residues in contact with GLN 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698D ILE 4.1 3.2 + - - -
699D LYS 3.1 7.7 + - - -
700D ARG 3.0 0.6 - - - -
701D PHE* 1.3 78.2 - - - +
703D ILE* 1.3 66.1 + - - +
704D MET 3.2 1.3 - - - -
705D ASN* 2.9 13.9 + - - +
706D GLU* 3.0 10.7 + - - -
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Residues in contact with ILE 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699D LYS 3.0 13.6 + - - -
700D ARG* 3.2 3.8 + - - +
702D GLN* 1.3 74.6 - - - +
704D MET* 1.3 56.4 + - - +
706D GLU* 3.2 3.3 + - - +
707D ILE* 2.9 25.1 + - - -
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Residues in contact with MET 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700D ARG 2.9 14.7 + - - -
701D PHE 5.5 0.2 - - - -
703D ILE* 1.3 71.5 - - - +
705D ASN* 1.3 65.1 + - - +
707D ILE* 3.3 2.2 + - - +
708D VAL* 2.9 20.4 + - - -
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Residues in contact with ASN 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701D PHE 4.5 8.6 + - - -
702D GLN 2.9 9.5 + - - -
704D MET* 1.3 75.9 - - - +
706D GLU* 1.3 57.1 + - - +
708D VAL* 3.2 4.0 + - - -
709D TYR* 2.9 23.0 + - - -
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Residues in contact with GLU 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702D GLN 3.0 12.7 + - - -
703D ILE* 3.2 4.0 + - - +
705D ASN* 1.3 72.1 - - - +
707D ILE* 1.3 59.8 + - - +
709D TYR* 3.2 2.2 + - - +
710D GLU* 2.9 26.0 + - - -
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Residues in contact with ILE 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703D ILE 2.9 14.4 + - - -
704D MET* 3.8 3.4 - - - +
705D ASN 3.3 0.2 - - - -
706D GLU* 1.3 72.0 - - - +
708D VAL* 1.3 65.9 + - - +
710D GLU* 3.4 1.0 + - - +
711D LYS* 2.9 23.0 + - - -
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Residues in contact with VAL 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704D MET 2.9 14.1 + - - -
705D ASN 3.5 4.7 - - - -
707D ILE* 1.3 75.9 - - - +
709D TYR* 1.3 56.8 + - - +
711D LYS* 3.3 0.9 + - - +
712D ILE* 2.9 28.1 + - - -
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Residues in contact with TYR 709 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705D ASN 2.9 14.5 + - - -
706D GLU* 3.2 4.4 + - - +
708D VAL* 1.3 75.1 - - - +
710D GLU* 1.3 57.1 + - - +
712D ILE* 3.2 1.8 + - - +
713D MET* 2.9 27.2 + - - -
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Residues in contact with GLU 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706D GLU 2.9 15.0 + - - -
707D ILE* 4.0 0.9 - - - +
709D TYR* 1.3 74.6 - - - +
711D LYS* 1.3 56.2 + - - +
713D MET* 3.3 1.5 + - - +
714D GLU* 3.0 25.8 + - - -
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Residues in contact with LYS 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707D ILE 2.9 16.6 + - - -
708D VAL* 3.8 1.1 - - - +
710D GLU* 1.3 76.1 - - - +
712D ILE* 1.3 61.0 + - - +
714D GLU* 3.4 9.3 + - - +
715D HIS* 3.6 8.1 + - - -
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Residues in contact with ILE 712 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708D VAL 2.9 16.4 + - - -
709D TYR* 3.7 1.3 - - - +
711D LYS* 1.3 76.5 - - - +
713D MET* 1.3 58.7 + - - +
714D GLU 3.2 0.2 - - - -
715D HIS* 3.2 5.0 + - - +
716D ALA* 3.1 23.2 + - - -
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Residues in contact with MET 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709D TYR 2.9 15.4 + - - -
710D GLU* 3.8 2.0 - - - +
712D ILE* 1.3 74.0 - - - +
714D GLU* 1.3 65.3 + - - +
716D ALA* 3.2 14.1 + - - +
717D GLY 4.8 0.5 + - - -
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Residues in contact with GLU 714 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710D GLU 3.0 14.8 + - - -
711D LYS* 3.4 6.0 + - - +
712D ILE 3.2 0.6 - - - -
713D MET* 1.3 78.5 - - - +
715D HIS* 1.3 56.2 + - - +
716D ALA 3.4 0.2 - - - -
717D GLY 4.7 2.3 + - - -
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Residues in contact with HIS 715 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711D LYS 3.6 7.5 + - - -
712D ILE 3.2 9.1 + - - -
713D MET 3.2 0.2 - - - -
714D GLU* 1.3 73.9 - - - +
716D ALA* 1.3 56.8 + - - +
717D GLY 2.9 22.1 + - - +
718D LYS 4.7 0.2 - - - -
719D ASN* 4.3 16.5 - - - +
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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