Contacts of the helix formed by residues 709 - 728 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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693A LEU* 3.5 8.5 - - - -
707A PRO* 2.8 20.7 + - + +
708A PHE* 1.3 78.9 - - - +
710A SER* 1.3 66.0 + - - +
711A HIS* 3.7 9.2 + - - +
712A GLY 3.1 17.0 + - - -
713A LEU* 3.0 24.4 + - - +
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Residues in contact with SER 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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690A LEU* 5.0 5.4 + - - +
693A LEU* 3.3 26.6 + - - +
709A THR* 1.3 73.1 - - - +
711A HIS* 1.3 62.6 + - - +
713A LEU* 4.2 3.3 - - - +
714A ARG* 3.1 39.2 + - - +
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Residues in contact with HIS 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A THR* 3.1 10.1 + - - +
710A SER* 1.3 79.4 - - - +
712A GLY* 1.3 59.0 + - - +
714A ARG* 5.0 0.7 - - - +
715A LEU* 3.0 42.0 + - + +
746A PRO* 3.7 37.6 - - + +
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Residues in contact with GLY 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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706A PHE* 3.5 12.1 - - - +
707A PRO* 3.3 33.9 - - - -
709A THR* 3.1 13.6 + - - -
711A HIS* 1.3 77.2 + - - +
713A LEU* 1.3 54.7 + - - +
715A LEU* 3.3 8.6 + - - +
716A GLY 2.8 28.4 + - - -
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Residues in contact with LEU 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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686A LEU* 3.9 26.5 - - + +
689A ALA* 3.2 48.7 - - + +
690A LEU* 3.6 17.0 - - + +
693A LEU* 3.6 26.9 - - + -
703A ILE* 4.1 15.5 - - + +
706A PHE* 5.4 0.4 - - + -
707A PRO 3.6 8.0 + - - +
708A PHE* 4.0 8.1 - - + -
709A THR 3.0 12.6 + - - +
710A SER* 4.2 3.1 - - - +
712A GLY* 1.3 72.7 - - - +
714A ARG* 1.3 55.3 + - - +
716A GLY* 3.1 2.5 + - - -
717A VAL* 2.7 41.9 + - - +
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Residues in contact with ARG 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LEU* 3.3 29.9 - - + +
710A SER* 3.1 31.8 + - - +
711A HIS* 3.9 2.5 - - - +
713A LEU* 1.3 73.7 - - - +
715A LEU* 1.3 58.6 + - - +
717A VAL* 3.9 1.1 - - - +
718A GLU* 2.8 32.6 + - - +
743A LYS 4.1 9.1 + - - -
744A VAL* 3.2 36.6 + - + +
745A ARG 3.3 19.4 + - - -
746A PRO* 3.8 24.5 + - + +
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Residues in contact with LEU 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A PHE* 4.2 21.5 - - + -
707A PRO* 5.6 3.4 - - + -
711A HIS* 3.0 32.9 + - + +
712A GLY* 3.4 7.2 - - - +
713A LEU 3.2 0.2 - - - -
714A ARG* 1.3 77.8 - - - +
716A GLY* 1.3 55.4 + - - +
718A GLU* 3.5 12.7 - - - +
719A ALA* 2.9 32.0 + - + +
746A PRO* 3.8 19.6 - - + +
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Residues in contact with GLY 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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686A LEU* 4.0 9.9 - - - +
706A PHE* 3.5 33.1 - - - -
712A GLY 2.8 16.1 + - - -
713A LEU* 3.1 4.0 + - - -
715A LEU* 1.3 70.7 - - - +
717A VAL* 1.3 58.0 + - - +
719A ALA* 3.3 2.6 + - - +
720A SER* 2.9 33.1 + - - -
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Residues in contact with VAL 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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683A ALA* 4.6 5.8 - - + +
686A LEU* 3.7 11.8 - - + +
687A GLY* 3.6 33.4 - - - +
690A LEU* 4.3 9.2 - - + -
713A LEU 2.7 24.8 + - - +
714A ARG 3.9 3.1 - - - +
716A GLY* 1.3 66.6 - - - +
718A GLU* 1.3 67.8 + - - +
720A SER* 3.1 8.7 + - - -
721A LEU* 2.9 44.2 + - + +
744A VAL* 3.8 18.8 - - + -
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Residues in contact with GLU 718 (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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714A ARG 2.8 21.6 + - - +
715A LEU* 3.5 16.3 - - - +
717A VAL* 1.3 72.1 - - - +
719A ALA* 1.3 65.1 + - - +
721A LEU* 2.9 16.8 + - - +
722A ARG* 2.9 49.4 + - - +
741A ALA* 3.4 20.8 - - - +
744A VAL* 3.7 11.4 - - + +
745A ARG* 3.3 32.6 + - - +
746A PRO* 3.6 9.5 - - - +
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Residues in contact with ALA 719 (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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706A PHE* 4.3 15.9 - - + -
715A LEU* 2.9 19.6 + - + +
716A GLY 3.8 3.8 - - - +
717A VAL 3.3 0.2 - - - -
718A GLU* 1.3 77.0 - - - +
720A SER* 1.3 57.2 + - - +
722A ARG* 3.5 8.5 + - - +
723A SER* 3.0 29.5 + - - -
726A ARG* 5.1 0.9 + - - -
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Residues in contact with SER 720 (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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679A LEU* 3.6 16.9 - - - +
682A ARG* 4.5 6.8 + - - +
683A ALA* 3.8 31.3 + - - -
686A LEU* 3.8 15.8 - - - +
706A PHE* 5.5 1.2 - - - -
716A GLY 2.9 16.0 + - - -
717A VAL* 3.1 9.8 + - - -
719A ALA* 1.3 76.3 - - - +
721A LEU* 1.3 57.3 + - - +
723A SER* 3.3 1.3 + - - -
724A LEU* 2.9 33.5 + - - +
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Residues in contact with LEU 721 (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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434A TYR* 4.7 14.1 - - + -
683A ALA* 5.2 2.9 - - + -
717A VAL* 2.9 37.7 + - + +
718A GLU 3.5 4.5 - - - +
720A SER* 1.3 74.0 - - - +
722A ARG* 1.3 55.0 + - - +
724A LEU* 3.2 15.4 + - + +
725A ALA* 2.7 34.0 + - - +
737A LEU* 3.7 30.4 - - + +
740A MET* 3.7 44.6 - - + +
741A ALA* 3.8 9.9 - - + +
744A VAL* 3.9 5.8 - - + -
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Residues in contact with ARG 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A GLU* 2.9 48.6 + - - +
719A ALA* 3.9 7.0 - - - +
721A LEU* 1.3 74.6 - - - +
723A SER* 1.3 62.0 + - - +
725A ALA* 3.5 9.1 + - - +
726A ARG* 3.3 38.4 + - - +
738A VAL* 4.2 18.2 - - + +
741A ALA* 3.4 17.3 - - + +
742A ASN* 2.7 43.4 + - - +
745A ARG* 3.3 16.4 - - - +
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Residues in contact with SER 723 (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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679A LEU* 3.2 25.9 - - - +
719A ALA 3.0 18.4 + - - -
720A SER* 3.6 4.9 - - - -
722A ARG* 1.3 75.6 - - - +
724A LEU* 1.3 64.6 + - - +
726A ARG* 3.4 30.8 + - - +
727A VAL* 3.5 14.7 + - - +
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Residues in contact with LEU 724 (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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434A TYR* 3.8 45.5 - - + +
435A LEU* 4.3 17.4 - - + +
679A LEU* 3.6 27.1 - - + +
680A GLN* 4.2 18.6 - - + +
683A ALA* 4.1 15.3 - - + -
720A SER 2.9 19.8 + - - +
721A LEU* 3.2 15.0 + - + +
723A SER* 1.3 76.3 + - - +
725A ALA* 1.3 62.3 + - - +
727A VAL* 3.1 6.4 + - - +
728A ALA* 3.1 22.9 + - - +
737A LEU* 3.7 12.7 - - + +
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Residues in contact with ALA 725 (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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721A LEU 2.7 20.9 + - - +
722A ARG* 3.6 10.3 - - - +
723A SER 3.2 0.2 - - - -
724A LEU* 1.3 73.8 - - - +
726A ARG* 1.3 61.0 + - - +
727A VAL 3.3 0.9 + - - -
728A ALA* 3.4 13.0 + - - +
734A ARG* 3.5 28.4 + - + +
737A LEU* 3.6 24.6 - - + +
738A VAL* 4.0 23.1 - - + +
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Residues in contact with ARG 726 (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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719A ALA 5.1 0.8 + - - -
722A ARG* 3.3 37.1 + - - +
723A SER* 3.4 22.2 + - - +
724A LEU 3.2 0.8 - - - -
725A ALA* 1.3 78.4 - - - +
727A VAL* 1.3 62.5 + - + +
728A ALA 5.5 0.2 - - - -
734A ARG* 5.2 4.7 + - - +
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Residues in contact with VAL 727 (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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435A LEU* 3.6 20.2 - - + +
679A LEU* 4.1 13.0 - - + -
723A SER 3.5 12.8 - - - +
724A LEU* 3.1 17.2 + - - +
726A ARG* 1.3 80.2 - - + +
728A ALA* 1.3 64.8 + - - +
729A PRO* 3.3 10.6 - - - +
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Residues in contact with ALA 728 (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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435A LEU* 3.8 15.5 - - - +
724A LEU 3.1 10.7 + - - +
725A ALA 3.4 16.4 + - - +
726A ARG 3.6 0.4 - - - -
727A VAL* 1.3 75.9 - - - +
729A PRO* 1.3 63.0 - - + +
730A THR* 2.9 16.1 + - - +
733A HIS* 4.1 3.6 - - + +
734A ARG* 4.0 26.8 + - + +
737A LEU* 4.0 13.5 - - + -
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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