Contacts of the helix formed by residues 706 - 719 (chain B) in PDB entry 4ZG9
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 TYR 706 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675B GLN* 3.4 30.1 - - + -
676B MET* 3.5 20.5 - - + -
705B MET* 1.3 75.0 - - - +
707B PRO* 1.3 70.6 - - + +
708B ALA 4.0 5.2 - - - +
709B PHE* 3.3 3.8 + - - +
710B LYS* 3.1 20.8 + - - +
755B GLN* 3.0 28.5 + - - -
764B VAL* 4.5 3.1 - - + +
798B HIS* 3.2 54.5 + + - +
799B ARG 3.8 5.4 - - - +
800B PRO* 3.6 50.6 - - + +
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Residues in contact with PRO 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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674B LYS 6.0 0.7 - - - +
675B GLN 3.2 22.9 - - - +
676B MET 5.5 0.2 - - - -
677B SER* 4.3 12.6 - - - -
705B MET 4.2 2.9 - - - +
706B TYR* 1.3 84.7 - - + +
708B ALA* 1.3 64.9 + - - +
710B LYS* 3.3 20.2 + - + +
711B ARG* 3.3 17.3 + - - +
800B PRO 5.8 1.1 - - - +
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Residues in contact with ALA 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706B TYR* 3.2 1.4 - - - +
707B PRO* 1.3 79.8 - - - +
709B PHE* 1.3 62.2 + - - +
711B ARG* 3.5 15.5 + - - +
712B VAL* 3.8 4.0 + - - +
799B ARG 3.7 4.9 - - - +
800B PRO 3.4 28.2 + - - +
801B ASP* 3.6 22.4 - - - -
802B ASN* 3.4 29.1 + - - +
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Residues in contact with PHE 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705B MET* 3.7 28.5 - - + -
706B TYR* 3.3 12.8 + - + +
707B PRO 3.2 0.2 - - - -
708B ALA* 1.3 78.9 - - - +
710B LYS* 1.3 59.5 + - - +
712B VAL* 3.2 14.4 + - + +
713B TRP* 2.8 39.2 + + + +
768B TYR* 3.5 35.9 - + + -
796B LEU* 3.8 31.6 - - + -
797B PRO 3.6 25.4 - - - -
798B HIS* 3.7 32.1 - + + +
799B ARG 4.2 6.1 + - - +
802B ASN* 5.5 0.2 - - - -
819B LEU* 6.5 0.2 - - + -
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Residues in contact with LYS 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B SER* 3.6 22.9 - - - +
678B TYR 2.9 29.8 + - - +
679B GLY* 4.1 6.9 - - - -
680B PHE* 6.1 1.2 - - - -
705B MET* 4.0 17.9 - - + +
706B TYR 3.1 19.0 + - - +
707B PRO* 3.3 12.0 + - + +
709B PHE* 1.3 77.8 - - - +
711B ARG* 1.3 56.8 + - - +
713B TRP* 4.2 6.7 - - + -
714B ASN* 2.7 58.7 + - - +
718B ARG* 6.0 0.8 - - - +
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Residues in contact with ARG 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B PRO 3.3 13.9 + - - +
708B ALA* 3.7 9.0 - - - +
709B PHE 3.2 0.6 - - - -
710B LYS* 1.3 78.5 - - - +
712B VAL* 1.3 62.4 + - - +
714B ASN* 4.3 3.7 - - - +
715B TYR* 3.3 20.8 + - - +
802B ASN* 3.9 15.3 - - - +
808B SER* 2.7 34.7 + - - -
809B SER* 4.7 4.0 + - - +
810B GLU 3.2 15.0 + - - -
811B ASP* 5.1 0.2 - - - +
812B GLU* 3.0 37.9 + - + +
815B TRP* 3.7 21.0 - - + +
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Residues in contact with VAL 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708B ALA 3.8 10.1 + - - +
709B PHE* 3.2 17.8 + - + +
711B ARG* 1.3 77.6 - - - +
713B TRP* 1.3 58.2 + - - +
715B TYR* 3.3 5.7 + - - +
716B PHE* 3.1 25.1 + - + +
796B LEU* 4.0 28.5 - - + -
802B ASN* 4.1 4.7 - - - +
815B TRP* 3.8 30.1 - - + -
816B VAL* 3.8 24.7 - - + +
819B LEU* 3.8 20.2 - - + -
820B MET* 4.9 2.2 - - + -
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Residues in contact with TRP 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B GLY* 5.3 1.6 - - - -
680B PHE 3.0 27.2 + - - -
681B LEU* 4.1 13.7 - - + -
705B MET* 3.4 34.1 - - + +
709B PHE* 2.8 41.4 + + + +
710B LYS* 4.0 4.7 - - + +
712B VAL* 1.3 71.2 - - - +
714B ASN* 1.3 68.7 + - - +
716B PHE* 3.3 24.8 + + - +
717B GLN* 3.1 57.9 + - + +
735B SER* 3.8 26.9 - - - -
768B TYR* 4.3 18.2 - + + -
769B TYR 4.6 3.8 - - - -
770B SER* 4.1 6.5 - - - -
794B PHE* 4.9 3.8 - + - -
796B LEU* 4.4 12.1 - - + -
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Residues in contact with ASN 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710B LYS* 2.7 53.5 + - - +
711B ARG* 4.3 3.9 - - - +
713B TRP* 1.3 73.7 - - - +
715B TYR* 1.3 61.0 + - - +
717B GLN* 3.1 9.1 + - - +
718B ARG* 2.8 80.7 + - - +
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Residues in contact with TYR 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711B ARG 3.3 17.1 + - - +
712B VAL 3.3 5.7 + - - +
714B ASN* 1.3 79.2 - - - +
716B PHE* 1.3 62.3 + - - +
718B ARG* 5.1 0.2 - - - -
719B VAL* 3.1 59.1 + - + +
720B LEU* 3.2 34.2 + - + +
811B ASP* 5.3 1.1 - - - -
812B GLU* 3.8 25.8 - - + -
813B SER* 3.7 30.4 - - - -
816B VAL* 3.7 23.3 - - + -
817B GLU* 3.6 20.1 + - + -
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Residues in contact with PHE 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634B TYR* 5.2 1.6 - - - -
712B VAL* 3.1 15.0 + - + +
713B TRP* 3.6 33.9 - + + +
714B ASN 3.1 0.2 - - - -
715B TYR* 1.3 76.1 - - - +
717B GLN* 1.3 69.0 + - + +
720B LEU* 3.4 16.5 + - + -
721B VAL* 3.0 52.0 + - + +
724B TYR* 3.9 16.8 - + - -
733B VAL* 4.8 5.6 - - + -
735B SER* 4.6 3.1 - - - -
770B SER* 3.6 29.4 - - - -
772B ILE* 4.1 8.7 - - + -
794B PHE* 3.8 21.8 - + - -
796B LEU* 5.9 1.3 - - + -
820B MET* 4.0 24.7 - - + -
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Residues in contact with GLN 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634B TYR* 4.5 4.3 + - - +
680B PHE* 2.8 26.7 + - - +
681B LEU 2.9 20.8 + - - -
683B PRO* 3.4 35.9 - - + +
684B PRO* 5.6 0.2 - - - +
685B TYR* 4.6 0.6 - - - -
686B LEU* 4.2 17.0 - - - +
713B TRP* 3.1 45.6 + - - +
714B ASN* 4.0 8.3 - - - +
716B PHE* 1.3 92.3 - - + +
718B ARG* 1.3 69.4 + - + +
721B VAL* 4.0 19.0 - - - +
722B LYS 4.9 0.7 + - - -
735B SER* 5.3 0.2 + - - -
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Residues in contact with ARG 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683B PRO* 6.0 0.7 - - + -
685B TYR* 3.7 61.5 + - + +
710B LYS* 6.0 0.6 - - - +
714B ASN* 2.8 58.7 + - - +
715B TYR* 5.1 0.4 - - - -
717B GLN* 1.3 83.9 - - + +
719B VAL* 1.3 64.6 + - + +
722B LYS* 4.7 8.0 - - - +
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Residues in contact with VAL 719 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715B TYR* 3.1 53.2 + - + +
718B ARG* 1.3 85.1 - - + +
720B LEU* 1.3 71.4 + - + +
721B VAL 3.5 1.2 + - - -
722B LYS* 3.6 5.9 + - - +
723B LYS* 3.3 22.8 + - + +
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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