Contacts of the helix formed by residues 705 - 719 (chain B) in PDB entry 4Z7I
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 ALA 705 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620B THR* 6.2 0.2 - - - -
621B VAL 3.3 6.1 + - - -
622B GLN* 3.6 25.3 - - + +
704B TYR* 1.3 76.5 - - - +
706B ASP* 1.3 59.0 + - - +
707B ASP* 3.4 4.0 - - - +
708B ASP* 3.0 19.5 + - - +
709B TRP* 2.7 32.4 + - - +
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Residues in contact with ASP 706 (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 ALA* 1.3 73.2 - - - +
707B ASP* 1.3 75.7 + - - +
709B TRP* 3.5 2.6 + - - +
710B GLU* 3.1 40.6 + - - +
748B ARG* 2.6 40.4 + - - +
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Residues in contact with ASP 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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705B ALA* 3.4 2.7 - - + +
706B ASP* 1.3 92.4 + - - +
708B ASP* 1.3 63.8 + - - +
710B GLU* 3.5 6.3 + - - +
711B ALA* 2.8 28.6 + - - +
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Residues in contact with ASP 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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621B VAL 4.6 0.2 - - - +
622B GLN* 3.5 2.9 - - - +
623B LYS* 3.1 60.7 + - - +
624B LYS* 5.8 0.5 - - - +
690B VAL* 5.1 5.6 + - + +
704B TYR* 3.9 22.7 - - + -
705B ALA* 3.0 27.1 + - - +
707B ASP* 1.3 79.7 - - - +
709B TRP* 1.3 67.2 + - - +
711B ALA* 3.7 8.0 - - - +
712B LEU* 3.4 26.5 + - - +
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Residues in contact with TRP 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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702B VAL* 3.8 17.0 - - + -
703B HIS* 3.2 18.5 + + - -
704B TYR* 3.1 62.9 + + + +
705B ALA 2.7 13.8 + - - +
706B ASP* 3.7 4.7 - - - +
708B ASP* 1.3 76.3 - - - +
710B GLU* 1.3 57.4 + - - +
711B ALA 3.0 0.4 - - - -
712B LEU* 2.9 10.1 + - + +
713B ILE* 2.9 34.1 + - + +
731B LEU* 3.8 24.9 - - + -
734B ASN* 4.9 3.1 - - + -
735B ILE* 3.9 34.8 - - + -
738B LEU* 3.8 16.4 - - + -
744B VAL* 3.9 9.2 - - + +
748B ARG* 4.2 23.1 - - - -
752B LEU* 3.8 17.5 - - + -
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Residues in contact with GLU 710 (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 ASP* 3.1 28.2 + - - +
707B ASP* 3.8 7.0 - - - +
709B TRP* 1.3 78.7 - - - +
711B ALA* 1.3 56.6 + - - +
713B ILE* 4.0 13.4 - - - +
714B HIS* 3.1 29.6 + - - +
748B ARG* 3.8 30.2 + - - +
751B ASP* 5.3 5.6 - - - +
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Residues in contact with ALA 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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623B LYS* 6.0 0.4 - - - -
688B LEU* 3.2 38.5 - - + +
689B TRP* 4.6 4.3 - - - -
707B ASP 2.8 18.6 + - - +
708B ASP* 3.7 11.4 - - - +
709B TRP 3.0 0.4 - - - -
710B GLU* 1.3 78.0 - - - +
712B LEU* 1.3 58.5 + - - +
714B HIS* 3.9 2.4 - - - +
715B GLN* 3.0 30.3 + - - +
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Residues in contact with LEU 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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689B TRP* 3.7 33.4 - - + -
690B VAL 3.2 30.1 - - - +
691B LYS* 3.9 11.9 - - + +
704B TYR* 3.5 31.9 - - + +
708B ASP 3.4 14.3 + - - +
709B TRP* 2.9 9.9 + - + +
711B ALA* 1.3 77.1 - - - +
713B ILE* 1.3 61.5 + - + +
715B GLN* 3.3 6.6 + - + +
716B LEU* 3.0 34.6 + - + +
723B LEU* 5.0 4.9 - - + -
731B LEU* 4.5 17.7 - - + -
752B LEU* 6.2 0.4 - - + -
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Residues in contact with ILE 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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709B TRP* 2.9 26.9 + - + +
710B GLU* 4.2 14.8 - - - +
712B LEU* 1.3 76.2 - - + +
714B HIS* 1.3 62.7 + - - +
716B LEU* 3.3 19.8 + - - +
717B LYS* 3.4 22.2 + - - +
735B ILE* 4.5 3.4 - - + -
748B ARG* 3.8 41.3 - - + +
751B ASP* 3.3 32.1 - - + +
752B LEU* 3.6 30.0 - - + +
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Residues in contact with HIS 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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688B LEU* 5.9 2.5 - - + -
710B GLU* 3.1 18.7 + - - +
711B ALA* 3.9 4.7 - - - +
713B ILE* 1.3 76.2 - - - +
715B GLN* 1.3 65.6 + - - +
717B LYS* 3.0 23.6 + - - +
718B ILE* 3.2 18.8 + - + +
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Residues in contact with GLN 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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688B LEU* 4.0 18.0 - - + +
689B TRP* 3.3 45.2 - - + +
711B ALA 3.0 18.2 + - - +
712B LEU* 3.5 11.2 - - + +
713B ILE 3.3 0.2 - - - -
714B HIS* 1.3 76.8 - - - +
716B LEU* 1.3 61.5 + - + +
718B ILE* 3.1 24.8 - - + +
719B ASN* 3.0 35.4 + - - +
722B VAL* 3.9 16.8 - - + +
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Residues in contact with LEU 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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712B LEU* 3.0 21.6 + - + +
713B ILE* 3.5 9.4 - - - +
714B HIS 3.2 0.2 - - - -
715B GLN* 1.3 76.9 - - + +
717B LYS* 1.3 61.0 + - - +
719B ASN 5.4 0.2 - - - +
720B PRO* 3.3 35.3 - - + +
722B VAL* 6.2 0.2 - - + -
723B LEU* 3.8 29.4 - - + -
728B ARG* 4.0 17.7 - - + +
731B LEU* 4.7 16.2 - - + -
732B ILE* 6.3 0.2 - - + -
752B LEU* 3.9 27.1 - - + +
755B TYR* 3.7 41.2 - - + +
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Residues in contact with LYS 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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713B ILE* 3.4 19.3 + - - +
714B HIS* 3.0 14.2 + - - +
716B LEU* 1.3 79.2 - - - +
718B ILE* 1.3 61.7 + - + +
720B PRO* 5.4 0.9 - - - +
751B ASP* 3.3 31.1 + - - +
752B LEU 5.6 0.2 - - - -
754B ASN* 3.6 30.5 - - + +
755B TYR* 4.4 18.4 - - + +
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Residues in contact with ILE 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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688B LEU* 5.1 6.5 - - + -
714B HIS* 3.2 12.7 + - + +
715B GLN* 3.1 40.4 - - + +
717B LYS* 1.3 84.3 - - + +
719B ASN* 1.3 69.7 + - + +
720B PRO* 3.8 5.7 - - - +
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Residues in contact with ASN 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 GLN* 3.0 23.7 + - - +
716B LEU* 5.4 0.3 - - - +
718B ILE* 1.3 89.2 + - + +
720B PRO* 1.3 64.9 - - - +
721B TYR* 3.2 19.9 + - - +
722B VAL* 3.2 31.0 + - + +
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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