Contacts of the helix formed by residues 706 - 719 (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 PRO 706 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704A ILE 2.9 5.8 - - - +
705A ASN* 1.3 88.9 - - - +
707A ALA* 1.3 55.0 + - - +
709A ARG* 3.3 4.2 + - + +
710A ALA* 2.8 30.8 + - - +
751A CYS 4.8 0.2 - - - +
755A GLY* 3.9 18.5 - - - +
757A TYR* 3.8 14.6 - - + +
852A TYR* 3.4 47.6 + - + +
856A ASN* 3.9 15.3 - - - +
873A TRP* 3.5 20.6 - - + -
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Residues in contact with ALA 707 (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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705A ASN* 3.0 15.0 + - - +
706A PRO* 1.3 78.6 - - - +
708A ASP* 1.3 60.1 + - - +
710A ALA* 3.3 4.1 + - - +
711A TYR* 2.9 26.9 + - - +
840A MET* 3.6 13.1 - - + +
845A ARG* 4.9 9.2 - - + +
848A LEU* 3.7 40.3 - - + +
849A LYS* 5.3 0.7 - - - +
852A TYR* 3.9 6.8 - - + -
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Residues in contact with ASP 708 (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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704A ILE* 4.2 9.6 - - + -
705A ASN* 3.0 37.2 + - + +
707A ALA* 1.3 74.3 - - - +
709A ARG* 1.3 61.4 + - - +
711A TYR* 3.5 3.8 - - + +
712A SER* 2.8 31.0 + - - -
837A TYR* 5.1 0.7 + - - -
840A MET* 3.7 8.3 - - - +
845A ARG* 2.7 32.5 + - - -
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Residues in contact with ARG 709 (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 6.5 - - - +
613A GLN* 3.0 47.2 + - - +
614A LYS* 4.2 2.7 - - - +
615A THR* 3.9 11.0 - - + -
704A ILE* 3.5 22.8 - - + +
705A ASN 3.0 7.5 + - - +
706A PRO 3.5 8.7 - - - +
707A ALA 3.2 0.2 - - - -
708A ASP* 1.3 78.0 - - - +
710A ALA* 1.3 61.8 + - - +
712A SER* 3.6 5.1 + - - -
713A TRP* 3.2 33.3 + - - +
750A ARG* 3.7 7.3 + - - +
751A CYS* 2.8 30.7 + - - +
754A PRO* 3.4 35.7 - - - +
755A GLY* 4.3 6.5 - - - +
757A TYR* 3.6 28.0 - - - +
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Residues in contact with ALA 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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706A PRO 2.8 16.9 + - - +
707A ALA* 3.5 7.9 - - - +
709A ARG* 1.3 76.3 - - - +
711A TYR* 1.3 64.3 + - - +
713A TRP* 3.2 4.9 + - - +
714A TYR* 3.1 18.4 + - - +
730A PHE* 3.9 10.8 - - + -
751A CYS* 3.2 44.6 - - + +
752A LEU* 4.3 11.7 - - + -
848A LEU* 5.0 0.9 - - + -
852A TYR* 4.7 1.6 - - - +
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Residues in contact with TYR 711 (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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707A ALA 2.9 17.5 + - - +
708A ASP* 3.3 6.9 + - + +
710A ALA* 1.3 77.7 - - - +
712A SER* 1.3 56.3 + - - +
714A TYR* 3.2 9.7 + + - +
715A GLN* 2.8 59.4 + - + +
730A PHE* 3.4 42.8 - + + -
837A TYR* 3.5 22.9 - + - -
838A PRO* 2.6 36.7 + - - +
839A GLU* 4.0 1.5 + - - -
840A MET* 3.4 41.4 - - + -
845A ARG* 5.8 0.4 - - - -
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Residues in contact with SER 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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301A A3P 2.5 27.0 + - - -
614A LYS* 3.3 34.6 + - - +
704A ILE* 5.5 1.3 - - - -
708A ASP 2.8 17.5 + - - -
709A ARG* 3.8 2.7 - - - -
710A ALA 3.3 0.2 - - - -
711A TYR* 1.3 76.9 - - - +
713A TRP* 1.3 57.2 + - - +
715A GLN* 3.4 3.5 + - - +
716A HIS* 2.7 29.5 + - - +
835A ARG* 5.2 0.3 + - - -
837A TYR* 3.8 12.9 + - - -
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Residues in contact with TRP 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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613A GLN* 3.8 32.3 - - + -
614A LYS* 3.7 22.8 - - + +
709A ARG* 3.2 22.3 + - - +
710A ALA* 3.2 10.2 + - - +
711A TYR 3.2 0.8 - - - -
712A SER* 1.3 76.4 - - - +
714A TYR* 1.3 56.2 + - - +
716A HIS* 2.9 28.7 + + - +
717A GLN* 2.8 70.5 + - + +
747A LEU* 4.5 2.9 - - + +
750A ARG* 3.4 61.3 - - + +
751A CYS* 3.8 12.6 - - - -
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Residues in contact with TYR 714 (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 3.1 12.1 + - - +
711A TYR* 3.4 16.4 - + - +
713A TRP* 1.3 78.3 - - - +
715A GLN* 1.3 74.5 + - - +
717A GLN* 3.1 7.2 + - - +
718A ARG* 3.0 53.5 + - - +
725A ALA* 3.2 26.3 + - + -
728A TYR 2.7 24.6 + - - -
729A THR* 3.4 8.7 - - - -
730A PHE* 3.5 37.6 + + + -
733A VAL* 3.9 25.6 - - + -
747A LEU* 4.6 3.6 - - + -
751A CYS* 4.0 10.5 - - - -
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Residues in contact with GLN 715 (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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711A TYR* 2.8 52.4 + - + +
712A SER 3.7 2.9 - - - +
714A TYR* 1.3 83.5 - - - +
716A HIS* 1.3 58.0 + - - +
718A ARG* 3.4 20.7 + - - +
719A ALA* 3.0 28.6 + - - +
835A ARG* 4.4 4.9 - - - -
837A TYR* 3.5 58.6 - - + +
838A PRO* 4.2 4.4 - - - +
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Residues in contact with HIS 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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614A LYS* 2.9 34.1 + - + +
712A SER 2.7 15.5 + - - +
713A TRP* 2.9 33.8 + + - +
715A GLN* 1.3 76.0 - - - +
717A GLN* 1.3 84.0 + - - +
719A ALA* 3.3 2.8 + - - +
720A HIS* 3.2 51.9 + + - -
832A SER 5.4 0.2 - - - -
833A LYS* 5.4 4.2 + - - -
835A ARG* 3.1 25.2 + - - +
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Residues in contact with GLN 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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713A TRP* 2.8 51.8 + - - +
714A TYR 3.7 7.4 - - - +
716A HIS* 1.3 92.9 + - - +
718A ARG* 1.3 57.1 + - - +
720A HIS* 3.4 12.7 + - - +
722A ASP* 2.7 65.7 + - + +
725A ALA* 3.7 8.1 - - + -
747A LEU* 4.0 9.9 - - + -
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Residues in contact with ARG 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 TYR* 3.0 54.1 + - + +
715A GLN* 3.6 20.9 - - - +
716A HIS 3.2 0.2 - - - -
717A GLN* 1.3 73.6 - - - +
719A ALA* 1.3 58.7 + - - +
721A ASP* 2.7 30.0 + - - +
722A ASP 4.3 2.0 - - - +
725A ALA* 3.2 31.9 + - + +
726A LEU* 3.5 44.0 + - + +
728A TYR 4.4 1.6 + - - -
729A THR* 5.7 0.4 - - - +
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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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715A GLN 3.0 14.8 + - - +
716A HIS 3.3 4.7 + - - +
718A ARG* 1.3 78.6 - - - +
720A HIS* 1.3 57.9 + - - +
721A ASP* 3.0 10.6 + - - +
835A ARG* 3.2 39.3 - - - +
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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