Contacts of the helix formed by residues 742 - 755 (chain A) in PDB entry 1NST
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 SER 742 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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741A SER* 1.3 75.9 + - - +
743A LYS* 1.3 61.6 + - - -
745A ARG* 3.2 9.9 + - - +
746A ALA* 2.8 29.2 + - - +
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Residues in contact with LYS 743 (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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724A VAL* 3.5 26.7 - - + +
741A SER* 3.0 8.1 + - - +
742A SER* 1.3 77.7 - - - +
744A LEU* 1.3 61.6 + - - +
746A ALA* 3.4 8.0 + - - +
747A LEU* 3.0 28.2 + - - +
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Residues in contact with LEU 744 (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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724A VAL* 3.5 9.3 - - + +
728A TYR* 3.6 57.4 - - + +
732A GLU* 4.2 5.4 - - + +
733A VAL* 4.0 29.6 - - + -
736A ALA* 3.9 11.4 - - + -
740A ALA* 3.6 25.6 - - + -
741A SER* 3.4 16.1 + - - +
742A SER 3.2 0.4 - - - -
743A LYS* 1.3 75.6 - - - +
745A ARG* 1.3 67.1 + - - +
747A LEU* 3.3 2.3 + - - +
748A GLN* 3.1 19.4 + - - +
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Residues in contact with ARG 745 (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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736A ALA* 4.6 4.9 - - + +
737A GLY* 3.6 23.5 + - - +
738A SER* 4.3 12.1 + - - +
740A ALA* 3.8 22.3 + - + -
741A SER 3.1 22.4 + - - +
742A SER* 3.5 8.1 - - - +
744A LEU* 1.3 76.9 - - - +
746A ALA* 1.3 62.5 + - - +
748A GLN* 2.9 29.8 + - - +
749A ASN* 3.0 13.0 + - - +
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Residues in contact with ALA 746 (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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742A SER 2.8 16.9 + - - +
743A LYS* 3.5 9.4 - - - +
744A LEU 3.3 0.2 - - - -
745A ARG* 1.3 76.9 - - - +
747A LEU* 1.3 62.2 + - - +
749A ASN* 3.3 9.0 + - - +
750A ARG* 3.1 27.7 + - + +
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Residues in contact with LEU 747 (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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713A TRP* 4.5 7.6 - - - +
714A TYR* 4.6 4.5 - - + -
717A GLN* 4.0 20.6 - - + +
722A ASP* 3.9 17.9 - - - +
724A VAL* 3.6 17.9 - - + -
725A ALA* 3.6 31.0 - - + +
733A VAL* 3.7 25.8 - - + -
743A LYS 3.0 17.1 + - - +
744A LEU 3.6 5.4 - - - +
745A ARG 3.2 0.2 - - - -
746A ALA* 1.3 76.1 - - - +
748A GLN* 1.3 61.7 + - - +
750A ARG* 3.3 7.8 + - + +
751A CYS* 3.1 29.3 + - - -
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Residues in contact with GLN 748 (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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733A VAL* 3.0 30.9 - - - +
734A ILE* 3.0 26.6 + - - -
735A THR 4.4 0.2 - - - -
736A ALA* 3.7 24.2 + - + +
744A LEU 3.1 10.6 + - - +
745A ARG* 2.9 18.2 + - - +
747A LEU* 1.3 75.3 - - - +
749A ASN* 1.3 59.9 + - - +
751A CYS* 3.1 2.0 + - - +
752A LEU* 2.9 55.0 + - + +
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Residues in contact with ASN 749 (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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745A ARG 3.0 10.4 + - - +
746A ALA* 3.5 11.7 - - - +
748A GLN* 1.3 77.5 + - - +
750A ARG* 1.3 72.4 + - - +
752A LEU* 5.1 1.1 - - - -
753A VAL* 2.8 66.5 + - - +
754A PRO* 3.2 1.4 - - - +
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Residues in contact with ARG 750 (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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613A GLN* 2.6 31.3 + - - +
679A ASN* 5.0 3.6 + - - -
682A ASP* 3.9 12.7 + - - +
709A ARG* 3.7 7.7 + - - +
713A TRP* 3.4 48.2 + - + +
746A ALA* 3.1 15.4 + - + +
747A LEU* 3.6 11.7 - - + +
748A GLN 3.2 0.4 - - - -
749A ASN* 1.3 86.5 + - - +
751A CYS* 1.3 56.6 + - - +
754A PRO* 3.4 39.7 - - - +
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Residues in contact with CYS 751 (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 PRO 4.8 0.5 - - - +
709A ARG* 2.8 23.8 + - - +
710A ALA* 3.2 43.7 - - + +
713A TRP* 3.8 16.4 - - - -
714A TYR* 4.0 17.3 - - - -
730A PHE* 4.6 4.3 - - + -
733A VAL* 4.1 16.6 - - + -
734A ILE* 5.2 0.2 - - + -
747A LEU* 3.1 20.8 + - - +
748A GLN* 3.1 8.9 + - - +
750A ARG* 1.3 78.8 - - - +
752A LEU* 1.3 64.4 + - + +
852A TYR* 4.2 1.4 + - - -
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Residues in contact with LEU 752 (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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710A ALA* 4.3 6.5 - - + -
734A ILE* 3.9 22.7 - - + +
748A GLN* 2.9 49.8 + - + +
749A ASN* 5.1 0.7 - - - -
751A CYS* 1.3 80.6 - - + +
753A VAL* 1.3 61.0 + - + +
754A PRO* 3.4 2.2 - - - -
755A GLY* 2.8 20.3 + - - -
756A TRP* 3.7 6.7 - - - -
847A PHE* 5.9 1.1 - - + -
848A LEU* 3.8 27.6 - - + -
851A TYR* 4.4 26.0 - - + +
852A TYR* 2.8 22.5 + - + +
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Residues in contact with VAL 753 (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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682A ASP* 4.5 8.1 - - - +
749A ASN* 2.8 56.4 + - - +
752A LEU* 1.3 72.4 - - + +
754A PRO* 1.3 60.9 - - + +
755A GLY 2.9 5.4 + - - -
756A TRP* 3.0 52.0 + - + +
760A HIS* 3.0 25.0 - - - +
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Residues in contact with PRO 754 (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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612A PRO* 4.5 9.0 - - + +
613A GLN* 5.9 0.2 - - - +
681A PHE* 3.7 14.0 - - - -
682A ASP* 3.7 25.6 - - + +
709A ARG* 3.4 25.8 - - - +
749A ASN* 3.2 13.2 - - - +
750A ARG* 3.4 40.8 - - - +
752A LEU 3.4 4.0 - - - -
753A VAL* 1.3 90.1 - - + +
755A GLY* 1.3 56.7 + - - +
756A TRP 3.3 2.0 + - - -
757A TYR* 3.5 16.9 - - - -
760A HIS* 3.8 1.1 + - - -
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Residues in contact with GLY 755 (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 PRO* 3.9 13.0 - - - +
709A ARG* 4.3 7.6 - - - +
752A LEU 2.8 13.0 + - - -
754A PRO* 1.3 76.0 - - - +
756A TRP* 1.3 55.8 + - - +
757A TYR* 2.9 31.9 + - - -
852A TYR* 3.6 27.5 - - - -
855A HIS* 4.9 2.1 - - - +
856A ASN* 5.4 0.7 - - - +
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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