Contacts of the helix formed by residues 709 - 723 (chain B) in PDB entry 2PZI
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 THR 709 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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693B LEU* 3.5 10.5 - - - -
700B THR* 4.1 23.3 - - + -
707B PRO* 2.7 20.6 + - + +
708B PHE* 1.3 77.9 - - - +
710B SER* 1.3 64.1 + - - +
711B HIS* 3.6 6.5 + - - +
712B GLY* 2.8 30.0 + - - -
713B LEU* 2.9 25.6 + - - +
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Residues in contact with SER 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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690B LEU* 3.3 31.8 - - - +
693B LEU* 3.4 13.2 - - - +
709B THR* 1.3 72.4 - - - +
711B HIS* 1.3 61.6 + - - +
714B ARG* 3.3 34.3 + - - -
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Residues in contact with HIS 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B THR* 3.2 6.2 + - - +
710B SER* 1.3 77.7 + - - +
712B GLY* 1.3 66.1 + - - +
714B ARG* 3.2 19.4 + - + +
715B LEU* 3.2 52.7 + - + +
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Residues in contact with GLY 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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706B PHE* 3.6 10.8 - - - +
707B PRO* 3.5 24.7 - - - -
709B THR* 2.8 22.5 + - - -
711B HIS* 1.3 75.0 + - - +
713B LEU* 1.3 55.4 + - - +
715B LEU* 3.3 16.9 + - - +
716B GLY 2.9 21.7 + - - -
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Residues in contact with LEU 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B LEU* 3.6 31.7 - - + +
689B ALA* 3.6 14.6 - - + -
690B LEU* 3.6 40.6 - - + +
693B LEU* 3.8 14.1 - - + -
703B ILE* 3.8 20.4 - - + -
706B PHE* 4.9 1.3 - - + +
707B PRO 3.7 12.6 - - - +
708B PHE* 3.9 10.8 - - + -
709B THR 2.9 21.7 + - - +
712B GLY* 1.3 72.8 - - - +
714B ARG* 1.3 56.6 + - - +
716B GLY* 3.1 3.1 + - - +
717B VAL* 2.8 39.4 + - - +
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Residues in contact with ARG 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B LEU* 4.0 26.4 - - + +
710B SER* 3.3 36.2 + - - +
711B HIS* 3.2 20.2 + - + +
713B LEU* 1.3 78.1 - - - +
715B LEU* 1.3 62.6 + - + +
717B VAL* 3.4 5.7 + - - +
718B GLU* 3.1 23.8 + - - +
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Residues in contact with LEU 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B PHE* 4.0 13.2 - - + -
707B PRO* 5.9 2.2 - - + -
711B HIS* 3.2 46.4 + - + +
712B GLY* 3.4 13.0 - - - +
714B ARG* 1.3 80.6 - - + +
716B GLY* 1.3 58.0 + - - +
718B GLU* 3.6 5.5 + - + +
719B ALA* 3.1 30.3 + - - +
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Residues in contact with GLY 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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686B LEU* 3.6 11.2 - - - -
706B PHE* 3.4 32.9 - - - -
712B GLY 2.9 11.0 + - - -
713B LEU* 3.1 5.3 + - - -
715B LEU* 1.3 75.6 - - - +
717B VAL* 1.3 56.2 + - - +
719B ALA* 3.5 1.0 + - - +
720B SER* 2.7 36.7 + - - -
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Residues in contact with VAL 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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683B ALA* 4.4 6.7 - - + +
686B LEU* 4.0 5.4 - - + +
687B GLY* 3.6 35.9 - - - +
690B LEU* 5.0 8.3 - - + -
713B LEU 2.8 24.3 + - - +
714B ARG* 3.7 8.1 - - - +
716B GLY* 1.3 69.7 - - - +
718B GLU* 1.3 67.3 + - - +
720B SER* 3.2 4.6 + - - -
721B LEU* 3.0 46.5 + - + +
729B PRO* 4.7 11.4 - - + -
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Residues in contact with GLU 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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714B ARG 3.1 16.5 + - - +
715B LEU* 3.9 6.7 - - - +
716B GLY 3.4 0.4 - - - -
717B VAL* 1.3 78.5 - - - +
719B ALA* 1.3 57.9 + - - +
721B LEU* 3.4 6.4 + - - +
722B ARG* 3.0 32.7 + - - +
726B ARG 4.5 0.5 - - - +
727B VAL* 3.1 40.0 - - - +
729B PRO* 4.7 8.2 - - - +
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Residues in contact with ALA 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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706B PHE* 3.8 21.5 - - + -
715B LEU 3.1 18.3 + - - +
716B GLY 4.0 0.4 - - - +
718B GLU* 1.3 74.9 - - - +
720B SER* 1.3 60.8 + - - +
722B ARG* 3.6 29.7 + - - +
723B SER* 3.0 26.2 + - - -
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Residues in contact with SER 720 (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 LEU* 4.8 3.5 - - - +
682B ARG* 4.7 16.4 + - - -
683B ALA* 3.9 27.3 + - - -
686B LEU* 3.3 15.1 - - - +
706B PHE* 4.8 3.5 - - - -
716B GLY 2.7 22.2 + - - -
717B VAL 3.8 2.9 - - - -
719B ALA* 1.3 75.3 - - - +
721B LEU* 1.3 64.0 + - - +
723B SER* 3.4 19.6 - - - -
724B LEU* 3.7 14.6 - - - +
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Residues in contact with LEU 721 (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 ALA* 4.3 17.0 - - + -
717B VAL* 3.0 37.1 + - + +
718B GLU* 3.8 6.3 - - - +
720B SER* 1.3 71.8 - - - +
722B ARG* 1.3 59.4 + - - +
723B SER 3.1 2.0 - - - -
724B LEU* 2.7 32.2 + - + +
726B ARG* 3.0 55.1 + - + +
727B VAL* 4.1 2.5 - - - -
728B ALA* 3.9 16.8 - - + +
729B PRO* 3.8 22.4 - - + -
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Residues in contact with ARG 722 (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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718B GLU* 3.0 20.5 + - - +
719B ALA* 3.7 30.5 - - - +
721B LEU* 1.3 74.3 - - - +
723B SER* 1.3 62.9 + - - +
725B ALA* 3.0 15.0 + - - +
726B ARG 3.3 10.2 + - - +
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Residues in contact with SER 723 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B LEU* 4.8 20.1 - - - +
719B ALA 3.0 15.0 + - - -
720B SER* 3.4 13.7 - - - -
721B LEU 3.1 0.4 - - - -
722B ARG* 1.3 79.3 - - - +
724B LEU* 1.3 61.0 - - - +
725B ALA 3.4 1.2 + - - -
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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