Contacts of the helix formed by residues 895 - 902 (chain A) in PDB entry 4X7J
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 ASN 895 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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893A LYS 3.4 3.0 + - - -
894A GLU* 1.3 75.4 - - - +
896A LEU* 1.3 59.8 + - - +
897A LYS* 3.0 11.7 + - - +
898A ASP* 2.9 33.0 + - - +
899A TRP* 2.8 27.9 + - - +
940A PRO 4.0 3.8 - - - +
941A SER* 3.6 27.2 + - - +
943A ILE 3.3 13.7 - - - +
944A PHE* 3.6 34.0 - - + +
945A PHE* 4.1 3.4 - - - -
958A LEU* 5.8 2.2 + - - +
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Residues in contact with LEU 896 (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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895A ASN* 1.3 69.7 - - - +
897A LYS* 1.3 62.0 + - - +
899A TRP* 3.3 10.1 + - + +
900A MET* 3.0 37.9 + - + +
917A ILE* 4.1 7.9 - - + -
921A ILE* 3.9 17.0 - - + -
940A PRO* 3.3 20.0 - - + +
943A ILE* 2.8 46.3 + - + +
945A PHE* 3.8 26.8 - - + -
1013A ILE* 4.4 10.8 - - + -
1017A LEU* 4.0 23.6 - - + -
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Residues in contact with LYS 897 (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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895A ASN* 3.0 11.1 + - - +
896A LEU* 1.3 78.8 - - - +
898A ASP* 1.3 61.5 + - - +
900A MET* 3.4 7.0 + - + +
901A ASN* 3.0 49.3 + - - +
940A PRO* 3.5 26.2 + - + +
941A SER* 4.2 14.8 - - - +
1024A GLN* 4.8 10.2 + - - +
1027A ARG* 3.9 33.4 - - - +
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Residues in contact with ASP 898 (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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893A LYS 3.8 5.2 - - - +
894A GLU* 3.5 29.8 - - + +
895A ASN* 2.9 34.0 + - - +
897A LYS* 1.3 79.4 - - - +
899A TRP* 1.3 65.7 + - - +
901A ASN* 3.3 11.3 + - - +
902A GLY* 3.1 20.3 + - - -
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Residues in contact with TRP 899 (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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892A ARG* 4.9 2.2 - - - -
894A GLU* 3.6 24.1 - - - +
895A ASN 2.8 17.3 + - - +
896A LEU* 3.6 12.6 - - + +
897A LYS 3.3 0.2 - - - -
898A ASP* 1.3 76.1 - - - +
900A MET* 1.3 76.3 + - + +
902A GLY* 3.4 8.5 + - - -
903A ARG* 3.2 51.6 + - - +
908A GLU 4.6 3.6 - - - -
909A ARG* 4.4 10.5 - - - -
913A VAL* 4.4 12.1 - - + -
914A CYS* 5.1 6.3 - - - -
917A ILE* 3.5 29.6 - - + -
945A PHE* 3.9 23.9 - + + -
1017A LEU* 4.1 15.0 - - + -
1102A TLA 3.1 32.0 + - - +
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Residues in contact with MET 900 (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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896A LEU* 3.0 23.7 + - + +
897A LYS* 3.9 5.4 - - - +
899A TRP* 1.3 92.5 - - + +
901A ASN* 1.3 61.6 + - - +
903A ARG 3.0 19.1 + - - +
904A CYS* 4.2 2.4 - - - -
909A ARG* 3.0 33.4 + - - +
940A PRO* 3.7 28.7 - - + -
1013A ILE* 5.3 1.1 - - + +
1016A GLU* 3.7 57.0 - - + +
1017A LEU* 4.0 16.8 - - + -
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Residues in contact with ASN 901 (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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897A LYS* 3.0 43.1 + - - +
898A ASP* 3.3 12.7 + - - +
900A MET* 1.3 76.8 - - - +
902A GLY* 1.3 56.6 + - - +
903A ARG 3.3 0.9 - - - -
904A CYS* 3.1 23.2 - - - -
1024A GLN* 5.2 9.7 + - - +
1027A ARG* 5.4 6.4 - - - -
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Residues in contact with GLY 902 (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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898A ASP 3.1 12.9 + - - -
899A TRP 3.4 3.8 + - - -
900A MET 3.1 0.6 - - - -
901A ASN* 1.3 76.3 - - - +
903A ARG* 1.3 66.5 + - - +
904A CYS* 3.9 1.8 - - - -
908A GLU* 3.8 9.4 - - - +
1102A TLA 5.1 1.6 - - - +
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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