Contacts of the strand formed by residues 735 - 740 (chain A) in PDB entry 1MUK
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 ASP 735 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584A ILE 3.6 0.5 - - - +
585A ASP* 2.6 26.5 - - - +
695A ASN* 3.9 2.4 + - - -
731A CYS* 3.2 5.5 - - - +
732A GLN 2.9 37.4 + - - +
734A ASP* 1.3 85.3 + - - +
736A GLY* 1.3 69.4 + - - +
780A GLU 4.3 6.8 - - - +
781A TYR* 3.5 16.3 - - + -
782A LEU* 2.9 37.5 + - + -
783A LYS 4.7 0.7 + - - -
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Residues in contact with GLY 736 (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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583A ASN* 3.7 2.8 - - - +
584A ILE 2.7 43.6 + - - +
695A ASN* 4.6 0.4 - - - +
729A TYR* 3.6 24.2 + - - -
730A VAL 3.4 7.6 - - - -
735A ASP* 1.3 82.3 + - - +
737A LEU* 1.3 61.0 + - - +
738A MET 4.1 0.2 - - - -
780A GLU 5.0 0.9 - - - +
781A TYR* 4.5 1.5 - - - -
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Residues in contact with LEU 737 (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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570A LEU* 4.4 10.1 - - + -
571A GLY* 5.2 5.4 - - - -
574A ALA* 4.1 9.9 - - + -
581A SER* 3.5 24.5 - - - +
582A ILE 3.7 3.1 - - - +
583A ASN* 3.5 25.1 - - - +
728A ASN 3.7 0.3 - - - +
729A TYR* 3.6 7.6 - - - -
730A VAL* 2.8 37.2 + - + +
736A GLY* 1.3 72.8 - - - -
738A MET* 1.3 58.4 + - - +
739A ILE* 3.6 29.6 + - + +
779A ALA* 4.4 7.0 - - + -
780A GLU 4.6 4.5 - - - +
781A TYR* 3.9 34.1 - - + -
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Residues in contact with MET 738 (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 SER* 3.0 7.0 - - - -
582A ILE* 2.8 61.9 + - + +
584A ILE* 4.2 14.3 - - + +
699A MET* 3.8 32.5 - - + -
703A LEU* 4.4 15.3 - - + -
723A LEU* 4.3 24.2 - - + -
728A ASN* 3.5 18.2 - - - +
729A TYR* 3.9 15.2 - - + -
736A GLY 4.1 0.6 - - - -
737A LEU* 1.3 69.2 - - - +
739A ILE* 1.3 60.4 + - - +
740A ILE* 3.7 13.4 + - + -
756A ASP* 5.8 1.6 - - - +
757A LEU* 5.9 2.0 - - + -
760A ILE* 4.8 6.7 - - + -
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Residues in contact with ILE 739 (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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299A TRP* 4.0 10.3 - - + -
570A LEU* 3.5 31.0 - - + -
573A TYR* 4.0 10.1 - - + -
574A ALA* 3.9 28.3 - - + -
579A ASN* 5.2 1.6 - - + -
580A GLN 3.6 4.3 - - - +
581A SER* 4.5 0.4 - - - +
723A LEU* 4.2 0.6 - - - +
728A ASN* 2.7 46.2 + - - +
730A VAL* 3.9 16.2 - - + -
737A LEU* 3.8 27.4 - - + +
738A MET* 1.3 72.6 - - - +
740A ILE* 1.3 62.1 + - - +
741A ASP* 3.5 16.8 + - - +
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Residues in contact with ILE 740 (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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578A PRO 4.5 0.3 - - - +
579A ASN* 3.5 1.2 - - - -
580A GLN* 2.7 44.9 + - + +
582A ILE* 4.3 12.8 - - + -
719A LEU* 4.0 20.9 - - + -
722A SER* 6.0 0.2 - - - +
723A LEU* 4.2 20.6 - - + -
738A MET* 4.4 13.2 - - + +
739A ILE* 1.3 72.0 - - - +
741A ASP* 1.3 64.8 + - - +
742A GLY* 4.5 0.3 - - - -
748A VAL* 3.5 34.8 - - + -
753A ILE* 4.0 37.7 - - + -
756A ASP* 5.7 0.9 - - - +
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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