Contacts of the helix formed by residues 686 - 693 (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 ALA 686 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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646A PHE* 3.8 30.6 - - + +
647A ASN* 4.2 1.3 - - - +
680A TYR* 4.0 6.1 - - + +
683A SER* 3.4 26.6 + - - +
685A VAL* 1.3 81.2 - - - +
687A PRO* 1.4 60.2 - - + +
689A ARG* 3.3 0.6 + - - +
690A ALA* 2.8 35.3 + - - +
764A TRP* 4.0 15.9 - - + -
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Residues in contact with PRO 687 (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 SER 3.2 22.4 - - - +
684A GLU 3.5 8.7 - - - +
685A VAL 3.3 4.5 - - - -
686A ALA* 1.4 92.1 - - + +
688A ARG* 1.3 57.2 + - - +
690A ALA* 3.8 2.1 - - - +
691A ALA* 2.9 28.8 + - - +
763A ARG* 3.5 31.9 - - + +
764A TRP* 3.7 37.2 - - + +
767A ALA* 3.4 10.5 - - + +
768A TYR* 4.0 2.1 - - - -
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Residues in contact with ARG 688 (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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581A LEU* 4.2 14.7 - - + +
684A GLU 5.2 5.2 + - - +
685A VAL* 3.4 41.9 + - - +
687A PRO* 1.3 76.1 - - - +
689A ARG* 1.3 72.1 + - + +
691A ALA* 3.8 6.3 - - - +
692A ALA* 2.9 30.3 + - - +
767A ALA* 4.2 5.8 - - + +
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Residues in contact with ARG 689 (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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579A ASP* 4.6 18.0 - - - +
580A PRO* 5.1 2.4 + - - +
581A LEU* 4.0 9.9 - - + -
646A PHE* 2.8 39.8 + - + -
647A ASN 3.6 3.0 + - - -
648A GLY* 3.6 12.3 + - - -
651A TYR* 3.6 65.5 + - + +
685A VAL* 3.0 48.7 + - + +
686A ALA 3.7 2.7 - - - +
688A ARG* 1.3 90.5 - - + +
690A ALA* 1.3 61.9 + - - +
692A ALA* 3.6 2.9 + - - +
693A LEU* 3.4 17.7 + - - +
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Residues in contact with ALA 690 (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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608A LEU* 4.0 11.7 - - + -
646A PHE* 3.6 33.4 - - + -
686A ALA 2.8 17.7 + - - +
687A PRO 3.8 3.4 - - - +
689A ARG* 1.3 76.3 - - - +
691A ALA* 1.3 56.8 + - - +
693A LEU 3.3 0.2 + - - -
694A LEU* 2.8 34.1 + - - +
764A TRP* 4.2 9.0 - - + -
768A TYR* 3.2 15.6 + - - +
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Residues in contact with ALA 691 (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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687A PRO 2.9 19.7 + - - +
688A ARG* 3.8 5.4 - - - +
690A ALA* 1.3 78.3 - - - +
692A ALA* 1.3 60.5 + - - +
695A PRO* 3.2 28.6 - - + +
767A ALA* 3.5 31.9 - - + +
768A TYR* 3.6 14.1 + - + -
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Residues in contact with ALA 692 (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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581A LEU* 3.7 28.7 - - + -
582A TRP 3.5 14.6 - - - +
583A GLN* 3.5 15.4 + - - +
584A ASP* 3.0 22.5 + - - +
688A ARG 2.9 17.5 + - - +
689A ARG 3.8 3.6 - - - +
691A ALA* 1.3 80.4 - - - +
693A LEU* 1.3 58.6 + - - +
695A PRO* 3.9 3.6 - - - +
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Residues in contact with LEU 693 (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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582A TRP* 3.6 17.0 - - + +
583A GLN 3.5 7.2 - - - +
584A ASP* 3.7 14.4 - - - +
585A PRO* 3.5 26.9 - - + +
604A PHE* 3.8 23.0 - - + -
645A PHE* 4.2 13.2 - - + -
646A PHE* 4.1 22.2 - - + -
651A TYR* 6.0 0.2 - - + -
655A ILE* 4.4 15.5 - - + -
658A TYR* 4.3 8.3 - - + -
689A ARG 3.4 11.9 + - - +
690A ALA 3.3 3.4 + - - +
692A ALA* 1.3 76.3 - - - +
694A LEU* 1.3 70.1 + - + +
695A PRO* 3.1 12.4 - - - +
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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