Contacts of the strand formed by residues 545 - 547 (chain A) in PDB entry 1N7D
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 ILE 545 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A ALA* 4.1 18.5 - - + +
501A ILE* 4.7 0.7 - - - +
502A VAL* 3.6 34.2 - - + +
511A TYR* 6.2 1.8 - - + -
512A TRP* 4.4 10.5 - - - +
513A THR* 4.0 15.7 - - + +
521A ILE* 4.2 20.6 - - + -
542A PRO* 6.4 0.9 - - + -
543A ASN 5.9 0.7 - - - +
544A GLY* 1.3 77.6 - - - +
546A THR* 1.3 67.5 + - - +
554A LEU* 5.7 4.7 - - + -
555A TYR 3.3 21.5 - - - +
556A TRP* 3.5 15.3 - - + -
589A SER 4.6 0.8 - - - -
590A LEU* 3.7 16.3 + - - +
630A ASP* 5.5 2.9 - - - +
631A MET 5.6 0.7 - - - +
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Residues in contact with THR 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A VAL* 4.4 5.6 - - - -
545A ILE* 1.3 83.0 - - - +
547A LEU* 1.3 72.1 + - - +
554A LEU* 4.5 0.7 - - - +
555A TYR* 3.2 27.3 + - + +
590A LEU* 3.4 39.2 + - + +
591A ALA* 3.8 5.2 - - - +
592A VAL* 3.7 31.7 + - + +
632A VAL* 6.2 0.3 - - - -
633A LEU* 5.7 5.7 + - - +
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Residues in contact with LEU 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A VAL* 3.9 31.5 - - + +
503A VAL 4.6 5.6 - - - +
504A ASP* 4.6 24.9 - - + +
511A TYR* 4.8 9.9 - - + -
546A THR* 1.3 86.1 + - - +
548A ASP* 1.3 67.7 + - - +
549A LEU* 3.5 9.9 + - + +
552A GLY 3.8 22.2 - - - +
553A ARG 4.5 10.1 - - - +
554A LEU* 4.6 7.4 - - + +
555A TYR* 5.8 0.4 - - - -
569A VAL* 4.4 13.5 - - + -
592A VAL* 4.8 10.4 - - - +
638A THR* 4.5 15.8 - - - +
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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
------------------------------------------------------------
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