Contacts of the strand formed by residues 672 - 676 (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 PHE 672 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A LYS* 3.6 42.8 - - + -
607A LEU* 3.8 23.6 - - + -
629A ASP* 3.8 11.4 + - + +
630A LEU* 3.3 25.9 - - + -
631A SER 2.9 24.1 + - - -
671A ASP* 1.3 79.6 - - - +
673A TYR* 1.3 68.9 + - - +
674A PHE* 4.4 1.7 - + + -
698A LYS* 4.8 5.6 - - + -
796A LEU* 3.8 39.7 - - + -
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Residues in contact with TYR 673 (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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602A ASP 3.8 22.4 - - - -
603A ARG* 4.3 2.2 - - - -
604A PHE 4.2 10.5 + - - -
605A PRO* 3.9 6.7 - - + -
606A LYS* 2.7 32.5 + - - +
607A LEU 3.4 4.2 + - - -
631A SER* 3.0 32.1 - - - +
662A PHE* 3.7 33.4 - + + -
663A PRO* 3.2 46.7 + - + +
664A ILE 4.0 9.7 + - - -
670A SER* 4.6 9.2 + - - -
671A ASP* 4.6 10.1 - - - -
672A PHE* 1.3 90.8 - - - +
674A PHE* 1.3 60.5 + - - +
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Residues in contact with PHE 674 (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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605A PRO* 4.2 2.0 - - - -
607A LEU* 3.3 31.0 - - + +
609A ILE* 4.1 17.0 - - + -
621A TYR* 3.7 33.2 - + - -
624A LEU* 3.9 18.2 - - + -
625A GLY* 3.7 24.0 - - - -
630A LEU* 3.9 19.1 - - + -
631A SER 3.1 34.9 + - - -
632A SER* 3.5 25.9 - - - -
633A ASN* 3.4 13.5 + - - +
662A PHE* 4.0 5.1 - - - -
672A PHE* 4.4 2.2 - + + -
673A TYR* 1.3 78.2 - - - +
675A GLU* 1.3 62.1 + - - +
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Residues in contact with GLU 675 (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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605A PRO* 4.4 0.6 - - + +
607A LEU 3.3 3.3 + - - +
608A LEU* 3.6 12.9 - - + -
609A ILE* 3.1 25.3 + - - +
621A TYR* 4.8 1.8 - - - -
633A ASN* 3.6 8.3 - - - +
643A ILE* 3.6 29.9 + - + +
658A TYR* 2.8 32.0 + - - +
662A PHE* 3.9 6.3 - - + -
674A PHE* 1.3 77.4 - - - +
676A LYS* 1.3 69.9 + - - +
677A SER* 2.7 25.6 + - - -
680A TYR* 2.5 34.1 + - + -
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Residues in contact with LYS 676 (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 4.5 1.0 + - - -
609A ILE* 3.4 25.6 - - + +
617A THR* 3.1 49.3 + - - +
618A THR* 3.3 13.7 + - - -
621A TYR* 3.6 30.1 - - + -
633A ASN* 4.4 1.0 + - - -
641A GLU* 2.9 24.6 + - + +
642A GLU* 2.8 59.2 + - - +
675A GLU* 1.3 77.2 + - - +
677A SER* 1.3 67.1 + - - +
678A ALA* 4.1 6.9 - - - +
833A LYS* 5.5 1.2 - - - +
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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