Contacts of the helix formed by residues 936 - 945 (chain A) in PDB entry 5M64
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 SER 936 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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754A LYS* 4.9 10.4 + - - +
929A ALA* 3.9 10.4 - - - +
932A GLY* 5.2 2.4 - - - -
935A GLY* 1.3 81.7 + - - -
937A ASN* 1.3 63.5 + - - +
938A VAL* 3.1 14.4 - - - -
939A ASN* 2.9 21.6 + - - +
940A VAL* 3.0 20.0 + - - +
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Residues in contact with ASN 937 (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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754A LYS* 4.5 17.4 + - - +
756A LYS* 6.0 2.8 - - - +
759A TYR* 5.3 2.5 + - - -
908A VAL* 4.7 5.6 - - + +
930A LEU* 4.0 23.7 - - - +
936A SER* 1.3 77.6 - - - +
938A VAL* 1.3 57.1 + - - +
940A VAL* 3.4 18.3 - - + +
941A SER* 3.0 30.8 + - - -
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Residues in contact with VAL 938 (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 SER* 4.2 13.8 - - - -
937A ASN* 1.3 78.4 - - - +
939A ASN* 1.3 73.8 + - - +
941A SER* 2.7 18.1 + - - +
942A GLN* 3.4 23.4 + - - +
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Residues in contact with ASN 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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925A MET* 5.5 1.6 - - + -
935A GLY* 3.3 26.4 - - - -
936A SER 2.9 11.5 + - - +
938A VAL* 1.3 89.9 - - - +
940A VAL* 1.3 65.6 + - + +
941A SER 3.1 1.6 - - - -
942A GLN* 3.3 14.6 + - - +
943A ILE* 3.1 24.8 + - - +
955B PRO* 3.3 23.7 + - + +
956B SER* 4.1 12.2 + - - +
958B MET* 5.2 4.8 - - + +
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Residues in contact with VAL 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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908A VAL* 5.3 1.6 - - + -
912A VAL* 4.9 22.1 - - + +
925A MET* 4.6 9.9 - - + -
926A GLN* 5.5 8.3 - - + +
929A ALA* 3.6 28.5 - - + -
930A LEU* 5.3 1.1 - - + +
936A SER 3.0 14.5 + - - +
937A ASN* 3.4 28.3 - - + +
939A ASN* 1.3 73.8 - - + +
941A SER* 1.3 64.5 + - - +
943A ILE* 3.6 11.2 - - + -
944A MET* 3.0 40.1 + - + +
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Residues in contact with SER 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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908A VAL* 3.6 30.3 - - - -
937A ASN 3.0 14.9 + - - -
938A VAL* 2.7 29.5 + - - +
940A VAL* 1.3 79.2 - - - +
942A GLN* 1.3 62.4 + - - +
945A CYS* 3.3 8.3 + - - -
946A LEU 2.8 35.8 + - - +
947A LEU 5.0 2.5 + - - -
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Residues in contact with GLN 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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938A VAL* 3.4 28.1 + - - +
939A ASN* 3.3 13.4 + - - +
941A SER* 1.3 79.7 - - - +
943A ILE* 1.3 59.8 + - - +
944A MET 3.7 0.2 + - - -
946A LEU 4.4 1.6 + - - -
947A LEU* 3.6 48.2 + - + +
985A ARG* 3.0 24.6 + - - -
986A PHE* 5.0 6.5 - - + -
998A HIS* 5.9 0.3 + - - -
711B GLN* 4.4 7.8 + - - -
958B MET* 4.4 19.8 - - + +
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Residues in contact with ILE 943 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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832A ASP* 5.0 1.6 - - - +
833A LEU* 3.3 20.5 - - + +
925A MET* 3.8 25.8 - - + -
939A ASN 3.1 19.4 + - - +
940A VAL* 3.6 12.6 - - - +
942A GLN* 1.3 76.2 - - - +
944A MET* 1.3 73.2 + - + +
985A ARG* 2.3 45.1 + - - +
954B PHE 5.7 0.7 - - - +
958B MET* 3.6 33.0 - - + -
960B ILE* 3.6 30.1 - - + -
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Residues in contact with MET 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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832A ASP* 3.3 30.1 - - - +
833A LEU* 3.8 17.4 - - + +
834A ARG 5.9 0.2 - - - +
835A LEU* 5.2 13.3 - - - +
843A ARG* 4.9 1.0 + - - -
911A CYS* 4.8 10.1 - - - -
912A VAL* 5.1 12.8 - - + -
916A THR* 4.6 13.5 - - - -
925A MET* 5.1 0.7 - - - -
926A GLN* 3.1 29.8 - - + +
940A VAL* 3.0 27.0 + - + +
943A ILE* 1.3 111.2 - - + +
945A CYS* 1.3 64.6 + - + +
985A ARG* 3.7 12.4 + - - +
987A TYR* 6.1 0.5 - - - -
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Residues in contact with CYS 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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835A LEU* 6.4 0.4 - - - -
843A ARG* 2.4 44.8 + - + +
907A VAL* 4.0 26.2 - - + +
908A VAL* 4.2 9.2 - - - -
911A CYS* 3.6 35.2 - - + -
941A SER* 3.3 16.0 + - - -
944A MET* 1.3 80.2 - - - +
946A LEU* 1.3 75.0 + - + +
985A ARG* 3.6 9.4 - - - -
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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