Contacts of the helix formed by residues 931 - 945 (chain A) in PDB entry 5V4R
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 ASP 931 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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898A GLN* 2.5 24.0 + - + +
902A VAL* 4.7 9.6 - - + +
929A ASP 3.9 0.6 + - - -
930A ILE* 1.3 71.9 - - - +
932A PRO* 1.3 76.9 - - - +
933A LYS* 2.8 27.9 + - - +
934A LEU* 2.9 26.2 + - + +
935A GLN* 2.9 11.3 + - - +
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Residues in contact with PRO 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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930A ILE 3.2 8.0 - - - +
931A ASP* 1.3 87.6 - - - +
933A LYS* 1.3 61.1 - - - +
935A GLN* 3.4 12.8 + - + +
936A GLU* 3.2 20.1 + - - +
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Residues in contact with LYS 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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902A VAL* 3.7 21.5 - - - +
906A GLU* 2.9 24.9 + - - +
931A ASP* 2.8 20.1 + - - +
932A PRO* 1.3 76.2 - - - +
934A LEU* 1.3 62.9 + - - +
936A GLU* 3.3 14.2 + - - +
937A TYR* 3.1 46.1 + - + +
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Residues in contact with LEU 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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898A GLN* 3.8 30.1 - - + +
901A THR* 3.8 24.9 - - + -
902A VAL* 4.0 13.8 - - + +
913A LEU* 3.9 15.7 - - + -
916A PHE* 3.6 36.8 - - + -
930A ILE* 4.2 2.5 - - + -
931A ASP* 2.9 19.3 + - + +
933A LYS* 1.3 75.9 - - - +
935A GLN* 1.3 60.3 + - - +
937A TYR* 3.0 11.7 + - + -
938A LEU* 2.8 42.5 + - + +
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Residues in contact with GLN 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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928A LEU 5.6 1.6 + - - -
930A ILE* 3.6 44.6 + - + +
931A ASP 2.9 10.0 + - - +
932A PRO* 3.6 13.1 - - - +
933A LYS 3.4 0.2 - - - -
934A LEU* 1.3 75.1 - - - +
936A GLU* 1.3 63.8 + - - +
938A LEU* 3.2 13.7 + - + +
939A GLY* 3.1 17.7 + - - -
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Residues in contact with GLU 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 PRO 3.2 10.1 + - - +
933A LYS* 3.4 15.9 - - - +
934A LEU 3.2 0.6 - - - -
935A GLN* 1.3 79.1 - - - +
937A TYR* 1.3 81.4 + - + +
939A GLY* 3.0 15.0 + - - -
940A LYS 4.1 1.6 + - - -
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Residues in contact with TYR 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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902A VAL* 4.2 11.9 - - + -
905A TYR* 3.3 53.4 + + + -
906A GLU* 2.8 36.3 + - + +
913A LEU* 3.8 22.4 - - + +
933A LYS* 3.1 32.2 + - + +
934A LEU* 3.0 18.2 + - + +
936A GLU* 1.3 95.1 - - + +
938A LEU* 1.3 63.1 + - - +
939A GLY 3.1 1.4 + - - -
940A LYS* 3.2 20.1 + - - +
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Residues in contact with LEU 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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913A LEU* 3.4 37.0 - - + +
916A PHE* 3.8 26.7 - - + -
917A TRP* 4.0 28.2 - - + +
920A LEU* 3.8 26.0 - - + -
930A ILE* 4.7 6.3 - - + -
934A LEU* 2.8 23.4 + - + +
935A GLN* 3.2 15.5 + - + +
937A TYR* 1.3 75.4 - - - +
939A GLY* 1.3 61.8 + - - +
940A LYS 3.2 0.2 - - - -
941A PHE* 3.1 17.5 + - + +
942A ARG* 3.3 10.5 + - - +
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Residues in contact with GLY 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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935A GLN 3.1 7.9 + - - -
936A GLU* 3.0 13.7 + - - -
938A LEU* 1.3 75.3 - - - +
940A LYS* 1.3 65.4 + - - +
942A ARG* 3.2 17.7 + - - +
943A ARG* 3.4 12.5 + - - +
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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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905A TYR* 4.8 8.5 - - + +
910A LEU* 4.1 12.0 - - + +
913A LEU* 5.0 0.7 - - + -
936A GLU 4.1 1.6 + - - -
937A TYR 3.2 12.5 + - - +
938A LEU 3.2 0.4 - - - -
939A GLY* 1.3 77.6 - - - +
941A PHE* 1.3 84.0 + - + +
942A ARG 3.5 0.2 + - - -
943A ARG* 3.6 7.2 + - - +
944A LEU* 3.3 30.1 - - + +
833B GLN* 2.8 55.9 + - + +
836B ASN* 4.0 9.1 - - - +
837B THR* 3.5 25.0 - - + +
840B ARG* 5.9 0.6 - - - +
872B TYR* 5.5 1.6 + - - -
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Residues in contact with PHE 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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910A LEU* 4.3 13.7 - - + -
913A LEU* 3.8 26.0 - - + -
914A GLU* 3.7 48.0 - - + -
917A TRP* 3.7 40.8 - + + +
938A LEU* 3.1 11.3 + - + +
940A LYS* 1.3 108.0 - - + +
942A ARG* 1.3 65.1 + - - +
944A LEU* 3.2 23.7 + - + +
945A GLU* 3.5 19.1 - - - +
840B ARG* 6.0 1.3 - - - -
872B TYR* 5.4 4.0 - - - -
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Residues in contact with ARG 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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917A TRP* 4.3 18.8 - - + -
938A LEU 3.3 8.4 + - - +
939A GLY* 3.2 14.1 + - - +
941A PHE* 1.3 78.0 - - - +
943A ARG* 1.3 62.2 + - - +
944A LEU 3.3 0.7 + - - -
945A GLU* 3.4 21.2 + - - +
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Residues in contact with ARG 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 GLY 3.4 8.0 + - - +
940A LYS* 4.0 8.7 - - - +
941A PHE 3.3 0.6 - - - -
942A ARG* 1.3 78.2 - - - +
944A LEU* 1.3 64.7 + - + +
945A GLU 3.6 2.3 + - - -
795B MET 4.9 7.2 - - - +
796B GLN* 4.8 2.8 - - - -
797B HIS* 3.7 27.3 + - + +
800B HIS* 5.1 1.0 - - - +
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Residues in contact with LEU 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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940A LYS* 3.3 36.6 - - + +
941A PHE* 3.2 21.2 + - + +
942A ARG 3.1 1.0 - - - -
943A ARG* 1.3 83.9 - - + +
945A GLU* 1.3 60.0 + - + +
797B HIS* 4.1 24.7 - - + -
799B SER* 4.4 7.9 - - - +
800B HIS* 3.4 27.6 - - - +
837B THR* 4.2 18.2 - - + -
840B ARG* 3.7 49.8 + - - +
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Residues in contact with GLU 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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917A TRP* 3.3 26.7 + - - -
921A LYS* 2.9 34.2 + - - -
941A PHE* 3.5 13.9 - - - +
942A ARG* 3.4 13.6 + - - +
943A ARG 4.7 1.8 - - - -
944A LEU* 1.3 85.6 - - + +
800B HIS* 4.4 18.4 - - - -
840B ARG* 4.8 13.1 + - - +
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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