Contacts of the strand formed by residues 938 - 942 (chain A) in PDB entry 4EJX
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 LYS 938 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748A PHE* 3.2 6.5 - - - -
903A VAL* 3.9 19.1 - - + -
904A PHE 3.4 6.1 - - - -
905A ASP* 3.5 38.4 - - + +
934A ILE* 3.6 30.2 - - - +
935A GLU* 3.5 23.0 + - - +
936A SER 3.8 0.4 - - - -
937A ASN* 1.3 73.7 - - - +
939A MET* 1.3 53.9 + - - +
940A HIS* 2.4 45.2 + - + +
972A ILE* 4.4 21.6 - - + +
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Residues in contact with MET 939 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A TYR* 3.7 26.9 - - + -
748A PHE* 3.4 24.2 - - - +
749A LEU* 3.8 20.4 - - + -
757A GLY 3.2 23.8 - - - +
758A SER* 4.2 4.5 - - - -
760A TYR* 3.6 35.4 - - + -
904A PHE* 3.0 33.7 + - - +
906A GLU* 4.5 2.5 - - - +
936A SER 3.9 8.5 - - - +
937A ASN* 4.3 5.2 - - - -
938A LYS* 1.3 69.8 - - - +
940A HIS* 1.4 55.5 + - - +
941A ALA* 3.1 9.6 + - - +
946A MET* 3.6 18.8 - - - -
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Residues in contact with HIS 940 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A PHE* 3.1 23.1 - + - -
903A VAL* 3.9 22.6 - - + +
935A GLU* 4.8 0.2 - - - -
938A LYS* 2.4 38.1 + - + +
939A MET* 1.4 61.9 - - - +
941A ALA* 1.5 57.5 - - - +
946A MET* 3.6 10.6 - - - +
972A ILE* 5.8 1.0 - - - +
1026A HIS* 3.3 30.7 - + - -
1029A ALA* 3.2 32.8 + - + +
1031A MET* 3.4 41.9 + - + -
1107A CU 2.4 30.2 - - - -
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Residues in contact with ALA 941 (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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726A TYR* 3.9 12.8 - - + -
900A LEU 3.8 3.5 - - - +
902A LEU 3.1 20.6 + - - +
904A PHE* 3.8 7.5 - - + -
939A MET 3.1 7.1 + - - +
940A HIS* 1.5 54.2 - - - +
942A ILE* 1.3 63.5 + - - +
943A ASN 3.6 1.9 + - - -
944A GLY* 3.6 12.4 + - - -
945A ARG 3.4 26.0 - - - +
946A MET* 3.5 20.4 - - + +
1031A MET* 3.6 3.5 - - - +
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Residues in contact with ILE 942 (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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899A LEU* 3.9 24.5 - - + -
900A LEU 3.1 12.8 - - - +
901A PHE* 3.6 50.3 - - + +
941A ALA* 1.3 67.1 - - - +
943A ASN* 1.3 65.9 + - - +
944A GLY 2.8 10.0 + - - -
945A ARG 3.0 20.4 + - - +
950A LEU* 3.7 10.8 - - + +
1019A LEU* 4.1 20.9 - - + +
1020A HIS* 4.9 0.4 - - - -
1031A MET* 3.9 15.6 - - + +
1032A GLU 4.0 22.4 - - - +
1033A THR* 4.2 8.1 - - + -
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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