Contacts of the helix formed by residues 716 - 729 (chain A) in PDB entry 1SO2
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 PRO 716 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714A LYS 3.5 8.9 - - - +
715A ILE* 1.3 82.2 - - + +
717A THR* 1.3 65.4 + - - +
718A GLN 3.4 0.8 + - - +
719A GLN* 3.2 38.6 - - - +
720A PHE* 3.1 20.1 + - - +
870A PHE* 3.5 24.7 - - - +
872A LEU* 3.9 13.9 - - + -
873A HIS* 4.8 3.6 - - + +
968D ASN 6.0 1.1 - - - +
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Residues in contact with THR 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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701A TYR* 4.1 28.8 + - + +
710A LEU* 5.0 7.5 - - - +
715A ILE* 3.3 5.4 + - - -
716A PRO* 1.3 71.2 - - - +
718A GLN* 1.3 67.1 + - - +
720A PHE* 3.1 7.8 + - - +
721A MET* 2.9 37.3 + - + +
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Residues in contact with GLN 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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716A PRO* 3.4 1.0 - - + +
717A THR* 1.3 81.9 - - - +
719A GLN* 1.3 66.4 + - + +
721A MET* 3.4 3.0 + - - +
722A ASN* 2.7 67.0 + - - +
725A ARG* 4.6 11.7 - - - +
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Residues in contact with GLN 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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716A PRO* 3.2 33.1 + - + +
717A THR 3.4 0.2 - - - -
718A GLN* 1.3 81.9 - - + +
720A PHE* 1.3 66.9 + - - +
722A ASN* 3.8 2.8 - - - +
723A TYR* 3.2 16.1 + - - +
866A PRO 4.5 1.8 + - - +
867A GLU* 3.0 37.4 - - - +
868A TYR 3.6 10.7 - - - +
869A ASN 4.3 9.0 + - - +
870A PHE* 3.7 21.3 - - + +
872A LEU* 4.9 1.6 - - - +
968D ASN 4.7 4.0 + - - -
969D LEU* 4.4 32.5 + - - +
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Residues in contact with PHE 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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697A SER 4.9 0.4 - - - -
700A MET* 4.1 12.3 - - + -
701A TYR* 3.8 31.4 - + - -
704A PHE* 3.4 47.1 - + + -
710A LEU* 4.3 7.0 - - + -
715A ILE* 3.7 23.1 - - + -
716A PRO 3.1 18.3 + - - +
717A THR* 3.1 7.7 + - - +
719A GLN* 1.3 81.1 - - - +
721A MET* 1.3 78.7 + - - +
723A TYR* 3.9 0.3 - - - +
724A PHE* 3.2 58.8 + + + -
870A PHE* 3.6 15.4 - + - +
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Residues in contact with MET 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A SER* 3.8 20.6 - - - +
698A GLN* 3.4 30.5 - - - +
701A TYR* 3.8 31.0 - - + -
717A THR* 2.9 32.4 + - + +
718A GLN* 3.9 4.5 - - - +
720A PHE* 1.3 86.7 - - + +
722A ASN* 1.3 65.0 + - - +
724A PHE* 4.7 1.8 - - - +
725A ARG* 2.9 65.3 + - - +
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Residues in contact with ASN 722 (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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718A GLN* 2.7 57.4 + - - +
719A GLN* 3.8 1.9 - - - +
720A PHE 3.3 0.2 - - - -
721A MET* 1.3 77.0 - - - +
723A TYR* 1.3 57.8 + - - +
725A ARG* 3.7 10.1 + - - +
726A ALA* 3.0 29.6 + - - +
867A GLU* 3.2 40.3 + - + +
868A TYR* 3.7 15.2 - - + -
866C PRO* 5.8 0.5 - - - +
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Residues in contact with TYR 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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719A GLN 3.2 15.1 + - - +
720A PHE 3.9 2.7 - - - +
722A ASN* 1.3 79.3 - - - +
724A PHE* 1.3 83.7 + + - +
726A ALA* 2.9 5.2 + - - +
727A LEU* 2.7 40.0 + - + +
820A MET* 3.2 26.6 - - + +
858A ALA* 2.8 29.6 + - - +
861A LEU* 3.9 14.1 - - + -
862A TYR* 3.5 38.4 - + + -
868A TYR* 3.7 27.3 - + + +
870A PHE* 3.6 24.2 - + + -
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Residues in contact with PHE 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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696A LEU* 5.3 2.7 - - + +
697A SER* 3.9 22.0 - - - +
700A MET* 4.3 19.7 - - + -
704A PHE* 5.3 0.2 - + - -
720A PHE* 3.2 55.8 + + + +
721A MET* 4.6 1.6 - - - +
723A TYR* 1.3 90.5 - + - +
725A ARG* 1.3 60.8 + - - +
727A LEU* 3.8 24.0 - - + +
728A GLU* 3.1 28.9 + - - +
816A VAL* 4.3 21.1 - - + -
819A ALA* 4.1 12.6 - - + -
820A MET* 5.5 0.2 - - + -
870A PHE* 3.5 39.5 - + - -
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Residues in contact with ARG 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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694A ARG* 3.6 43.1 - - - +
697A SER* 3.9 15.9 - - - +
698A GLN* 4.6 4.2 - - - +
718A GLN* 4.6 13.3 - - - +
721A MET* 2.9 58.5 + - - +
722A ASN* 3.7 9.7 + - - +
724A PHE* 1.3 77.1 - - - +
726A ALA* 1.3 61.6 + - - +
728A GLU* 3.5 21.1 - - - +
729A ASN* 3.1 20.1 + - - -
866C PRO* 4.3 20.7 - - + +
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Residues in contact with ALA 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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722A ASN 3.0 17.1 + - - +
723A TYR 2.9 4.8 + - - +
725A ARG* 1.3 75.2 - - - +
727A LEU* 1.3 65.0 + - - +
729A ASN* 3.5 16.9 + - - +
730A GLY* 3.6 6.8 + - - -
823A TYR* 4.6 0.9 + - - -
861A LEU* 4.0 18.7 - - + +
868A TYR* 3.7 26.9 - - + +
866C PRO* 5.1 4.0 - - + +
869C ASN* 5.1 5.6 - - - +
872C LEU* 5.8 2.6 - - - +
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Residues in contact with LEU 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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696A LEU* 4.6 4.3 - - + -
723A TYR* 2.7 41.4 + - + +
724A PHE* 3.8 31.6 - - + +
725A ARG 3.3 0.2 - - - -
726A ALA* 1.3 71.2 - - - +
728A GLU* 1.3 57.5 + - - +
730A GLY* 2.7 27.0 + - - -
731A TYR* 3.7 6.3 + - + -
819A ALA* 3.7 32.8 - - + +
820A MET* 3.9 9.0 - - + +
823A TYR* 3.4 40.9 - - + -
858A ALA* 3.9 11.7 - - + -
861A LEU* 3.9 7.3 - - + +
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Residues in contact with GLU 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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693A GLY 3.4 17.3 - - - +
694A ARG* 2.7 38.7 - - - +
695A ILE 3.1 0.3 + - - -
696A LEU* 2.8 26.9 + - + -
697A SER* 2.7 35.0 + - - +
724A PHE 3.1 16.2 + - - +
725A ARG* 3.5 17.3 - - - +
727A LEU* 1.3 78.3 - - - +
729A ASN* 1.3 56.9 + - - +
730A GLY 2.8 10.0 + - - -
731A TYR* 2.8 26.4 + - - +
739A ARG* 3.2 17.7 + - + +
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Residues in contact with ASN 729 (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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693A GLY 4.5 2.4 - - - +
725A ARG 3.1 17.0 + - - -
726A ALA* 4.0 9.0 - - - +
727A LEU 3.3 0.6 - - - -
728A GLU* 1.3 80.5 - - - +
730A GLY* 1.3 58.3 + - - +
731A TYR 3.3 6.0 - - - +
739A ARG* 2.7 31.0 + - - +
716C PRO* 5.6 1.7 - - - +
719C GLN* 3.4 31.9 + - + +
866C PRO* 3.2 39.8 + - - +
867C GLU* 4.2 8.4 - - - +
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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