Contacts of the helix formed by residues 938 - 948 (chain A) in PDB entry 4B87
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 938 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935A MET* 2.8 30.1 + - - +
936A GLN* 2.9 7.0 + - - +
937A ILE* 1.3 73.1 - - - +
939A PHE* 1.3 65.9 + - - +
940A LYS* 3.4 11.1 + - - +
941A GLY* 2.9 27.6 + - - +
942A LEU* 2.9 25.4 + - - +
960A ARG* 4.7 4.5 - - - +
986A ILE* 3.8 13.9 - - - -
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Residues in contact with PHE 939 (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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938A ASN* 1.3 73.3 - - - +
940A LYS* 1.3 53.5 + - - +
942A LEU* 3.6 1.6 - - - +
943A GLN* 2.7 46.9 + - + +
979A GLN* 3.5 47.6 - - + -
980A THR 4.0 1.6 - - - -
981A LYS* 3.5 56.1 - - + -
984A ILE* 3.6 30.2 - - + +
986A ILE* 3.9 14.8 - - + -
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Residues in contact with LYS 940 (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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938A ASN* 3.4 7.0 + - - +
939A PHE* 1.3 75.3 - - - +
941A GLY* 1.4 57.7 + - - +
943A GLN* 3.1 8.3 + - + +
944A SER* 2.9 32.6 + - - -
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Residues in contact with GLY 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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936A GLN* 3.1 44.7 + - - -
938A ASN* 2.9 17.1 + - - -
940A LYS* 1.4 70.8 - - - +
942A LEU* 1.3 56.0 + - - +
944A SER* 3.3 5.4 - - - -
945A HIS* 2.8 25.3 + - - +
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Residues in contact with LEU 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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875A VAL* 4.0 26.0 - - + -
932A LEU* 4.1 13.0 - - + -
936A GLN 3.6 13.0 - - - +
937A ILE* 4.2 5.6 - - + -
938A ASN 2.9 26.7 + - - +
939A PHE 4.0 1.8 - - - +
941A GLY* 1.3 68.1 - - - -
943A GLN* 1.3 66.9 + - - +
944A SER 3.0 1.3 - - - -
945A HIS* 3.2 1.9 + - - +
946A LEU* 3.0 19.8 + - - +
956A ILE* 3.4 22.2 - - + +
958A ALA* 3.6 24.7 - - + -
984A ILE* 3.7 33.4 - - + -
986A ILE* 3.8 13.5 - - + -
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Residues in contact with GLN 943 (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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939A PHE* 2.7 34.4 + - + +
940A LYS* 3.1 6.5 + - - +
942A LEU* 1.3 73.6 - - - +
944A SER* 1.3 63.5 + - - +
946A LEU* 3.2 13.5 + - - +
947A LYS* 3.4 13.0 + - - +
981A LYS* 6.0 1.3 - - + +
983A ASN* 5.9 1.1 - - - +
984A ILE* 4.2 18.1 - - + +
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Residues in contact with SER 944 (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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936A GLN* 5.0 3.8 + - - -
940A LYS* 2.9 18.4 + - - -
941A GLY* 3.3 8.5 - - - -
943A GLN* 1.3 77.4 - - - +
945A HIS* 1.3 61.2 + - - +
947A LYS* 3.2 21.6 + - - +
948A LYS* 3.6 10.7 + - - +
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Residues in contact with HIS 945 (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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873A LEU* 3.5 22.8 - - + +
875A VAL* 4.4 4.0 - - + -
924A MET* 4.3 8.7 - - + -
930A HIS* 2.8 36.3 + + - +
932A LEU* 3.7 42.4 - - + +
936A GLN* 4.2 7.4 + - - +
941A GLY 2.8 19.2 + - - +
942A LEU* 3.2 7.4 + - - +
944A SER* 1.3 71.0 - - - +
946A LEU* 1.3 66.8 + - - +
948A LYS* 3.0 41.0 + - + +
953A TYR* 6.0 1.4 - + - -
956A ILE* 4.4 3.4 - - + -
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Residues in contact with LEU 946 (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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873A LEU* 5.1 2.2 - - + -
942A LEU 3.0 11.6 + - - +
943A GLN* 3.2 13.0 + - - +
945A HIS* 1.3 76.5 - - - +
947A LYS* 1.3 58.2 + - - +
948A LYS 3.3 8.7 - - - +
951A GLY* 4.0 13.5 - - - -
953A TYR* 3.6 42.7 + - + +
954A ASN* 4.0 6.1 - - - -
955A GLN* 4.0 5.6 - - - +
956A ILE* 3.7 21.3 - - + +
983A ASN* 3.4 31.2 - - - +
984A ILE* 3.8 21.1 - - + -
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Residues in contact with LYS 947 (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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943A GLN 3.4 9.3 + - - +
944A SER* 3.2 14.6 + - - +
945A HIS 3.2 0.8 - - - -
946A LEU* 1.3 74.9 - - - +
948A LYS* 1.3 61.1 + - + +
950A GLY* 4.1 4.2 + - - -
951A GLY* 4.0 9.5 + - - +
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Residues in contact with LYS 948 (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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944A SER 3.6 10.5 + - - +
945A HIS* 3.0 31.6 + - + +
946A LEU 3.3 10.4 - - - +
947A LYS* 1.3 79.2 - - + +
949A CYS* 1.3 64.8 + - - +
950A GLY 2.9 10.6 + - - +
951A GLY* 3.4 3.1 + - - -
952A LYS 4.6 0.5 + - - -
953A TYR* 5.2 3.5 + - - -
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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