Contacts of the helix formed by residues 924 - 937 (chain A) in PDB entry 5A31
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 924 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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925A SER* 1.3 72.6 + - - +
926A LEU* 3.2 10.0 - - - +
927A ALA* 3.2 14.6 + - - +
928A GLU* 3.0 24.2 + - - +
965A GLN* 6.0 9.0 - - - -
1827A GLN* 6.2 2.2 - - - +
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Residues in contact with SER 925 (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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924A SER* 1.3 83.2 + - - +
926A LEU* 1.3 52.9 + - - +
928A GLU* 3.5 15.1 + - - +
929A ARG* 2.8 44.3 + - - +
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Residues in contact with LEU 926 (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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879A LEU* 4.0 17.3 - - - +
880A TYR* 3.5 47.6 - - + +
881A ILE 5.8 0.4 - - - -
882A LEU* 5.2 7.6 - - - +
924A SER 4.2 7.2 - - - +
925A SER* 1.3 77.9 - - - +
927A ALA* 1.3 64.3 + - + +
929A ARG* 3.3 21.3 - - - +
930A LEU* 3.3 8.5 + - - +
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Residues in contact with ALA 927 (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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880A TYR* 4.1 20.0 - - + +
924A SER* 3.2 15.1 + - - +
926A LEU* 1.3 85.4 - - + +
928A GLU* 1.3 62.3 + - - +
930A LEU* 3.1 15.1 + - - +
931A VAL* 3.2 15.3 + - - +
958A ALA* 4.1 7.6 - - - +
961A HIS* 4.2 23.8 - - + -
962A CYS* 4.8 6.1 - - - +
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Residues in contact with GLU 928 (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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924A SER 3.0 15.5 + - - +
925A SER* 3.8 14.2 + - - +
927A ALA* 1.3 72.9 - - - +
929A ARG* 1.3 59.7 + - - +
931A VAL* 3.5 1.8 + - + +
932A VAL* 2.9 34.2 + - + +
962A CYS* 3.7 17.8 - - - -
967A ALA* 4.7 12.2 - - - +
968A SER* 6.0 1.6 - - - -
970A TRP* 3.1 44.1 + - + +
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Residues in contact with ARG 929 (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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879A LEU* 3.8 32.0 - - + +
925A SER* 2.8 27.1 + - - +
926A LEU* 3.3 13.9 - - - +
928A GLU* 1.3 76.1 - - - +
930A LEU* 1.3 62.7 + - - +
932A VAL* 3.4 10.7 - - - +
933A TRP* 2.9 34.2 + - - +
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Residues in contact with LEU 930 (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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876A SER* 3.7 35.0 - - - +
879A LEU* 4.4 14.6 - - + +
880A TYR* 3.9 26.5 - - + -
926A LEU 3.3 7.1 + - - +
927A ALA 3.1 9.6 + - - +
929A ARG* 1.3 80.7 - - - +
931A VAL* 1.3 63.2 + - - +
933A TRP* 3.6 16.9 - - + +
934A MET* 3.1 30.3 + - + +
954A PRO 4.5 0.4 - - - +
955A ILE* 4.1 20.2 - - + -
958A ALA* 3.6 24.7 - - + -
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Residues in contact with VAL 931 (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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927A ALA 3.2 9.6 + - - +
928A GLU* 3.8 7.2 - - + +
930A LEU* 1.3 76.6 - - - +
932A VAL* 1.3 67.1 + - + +
934A MET* 3.0 13.2 + - + +
935A THR* 3.0 21.1 + - - -
958A ALA* 4.1 9.4 - - + +
959A ILE* 3.8 27.8 - - + -
962A CYS* 3.8 25.8 - - + -
970A TRP* 5.9 0.2 - - + -
974A VAL* 3.8 28.0 - - + -
977A LEU* 4.0 9.7 - - + +
978A ILE* 4.0 14.6 - - + -
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Residues in contact with VAL 932 (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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928A GLU* 2.9 25.5 + - + +
929A ARG* 3.4 15.5 - - - +
931A VAL* 1.3 80.6 - - + +
933A TRP* 1.3 61.0 + - - +
935A THR* 3.4 2.4 + - - -
936A ASN* 2.7 45.8 + - - +
970A TRP* 4.8 14.8 - - + -
971A PRO* 4.9 7.9 - - + -
974A VAL* 4.1 20.6 - - + -
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Residues in contact with TRP 933 (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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871A ARG* 6.0 1.3 - - - -
872A LEU* 3.5 36.1 - - + -
875A LEU* 3.6 33.5 - - + +
876A SER* 4.0 15.5 - - - -
879A LEU* 3.8 19.9 - - + +
929A ARG* 2.9 25.8 + - - +
930A LEU* 3.6 17.9 - - + +
932A VAL* 1.3 78.1 - - + +
934A MET* 1.3 78.9 + - + +
936A ASN* 3.1 15.1 + - + +
937A VAL* 2.9 49.9 + - + +
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Residues in contact with MET 934 (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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872A LEU* 4.2 13.5 - - + -
876A SER* 5.6 0.4 - - - -
930A LEU* 3.1 21.2 + - + +
931A VAL* 3.0 10.9 + - + +
933A TRP* 1.3 90.5 - - + +
935A THR* 1.3 61.8 + - - +
937A VAL* 2.7 27.6 + - - +
939A PHE* 3.1 50.8 - - + +
955A ILE* 3.5 38.8 - - + +
959A ILE* 4.2 8.3 - - + -
977A LEU* 4.1 20.6 - - + -
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Residues in contact with THR 935 (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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931A VAL 3.0 7.7 + - - -
932A VAL 3.6 4.9 - - - -
933A TRP 3.3 0.2 - - - -
934A MET* 1.3 77.0 - - - +
936A ASN* 1.3 67.1 + - - +
937A VAL 2.9 12.3 - - - +
939A PHE 4.3 6.6 - - - +
940A ILE* 5.8 1.4 - - - +
971A PRO* 4.6 6.3 - - + -
973A ALA* 3.4 31.4 + - + +
974A VAL* 3.2 42.0 + - + +
977A LEU* 3.7 15.8 - - - +
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Residues in contact with ASN 936 (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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932A VAL* 2.7 35.0 + - - +
933A TRP* 3.1 13.1 + - + +
935A THR* 1.3 82.0 - - - +
937A VAL* 1.3 65.3 + - + +
938A GLY* 3.8 0.5 + - - -
971A PRO* 5.3 3.5 - - - +
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Residues in contact with VAL 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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868A GLU 6.0 0.9 - - - +
871A ARG* 6.2 3.1 - - + -
872A LEU* 4.4 26.7 - - + -
933A TRP* 2.9 52.8 + - + +
934A MET* 2.7 21.2 + - - +
935A THR 2.9 10.6 - - - +
936A ASN* 1.3 76.4 - - + +
938A GLY* 1.3 67.1 + - - +
939A PHE 3.2 2.4 - - - +
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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