Contacts of the helix formed by residues 961 - 980 (chain D) in PDB entry 3O37
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 LYS 961 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898D VAL* 6.1 0.2 - - + -
900D LEU* 3.3 13.0 - - - +
960D SER* 1.3 80.0 - - - +
962D PRO* 1.3 69.8 - - + +
963D GLU* 3.5 31.2 - - - +
964D ASP* 2.8 48.8 + - - +
965D PHE 3.8 1.9 + - - -
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Residues in contact with PRO 962 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900D LEU* 3.5 3.8 - - + -
904D ASP* 3.5 35.7 - - + +
961D LYS* 1.3 87.2 - - + +
963D GLU* 1.3 72.3 + - - +
964D ASP 2.9 1.4 + - - -
965D PHE* 3.0 20.7 + - + -
966D VAL* 2.9 27.5 + - + +
1005D TYR* 3.6 25.6 - - + +
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Residues in contact with GLU 963 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961D LYS* 3.2 35.1 + - - +
962D PRO* 1.3 85.4 - - - +
964D ASP* 1.3 57.7 + - - +
966D VAL* 3.8 8.5 - - - +
967D ALA* 3.0 30.1 + - - +
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Residues in contact with ASP 964 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958D MET 5.0 2.3 - - - +
959D TYR* 3.6 26.3 - - + -
960D SER* 3.0 30.3 + - - +
961D LYS* 2.8 41.6 + - - +
963D GLU* 1.3 80.1 - - - +
965D PHE* 1.3 58.5 + - - +
967D ALA* 3.6 14.7 + - - +
968D ASP* 3.6 5.4 + - - +
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Residues in contact with PHE 965 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900D LEU* 3.8 27.8 - - + -
904D ASP 3.8 16.4 - - - -
908D CYS* 3.5 35.7 - - + -
911D LEU* 3.9 22.9 - - + -
948D ILE* 4.6 1.1 - - + -
959D TYR* 3.7 27.3 - + + +
962D PRO* 3.0 29.2 + - + -
964D ASP* 1.3 75.8 - - - +
966D VAL* 1.3 90.1 + - + +
967D ALA 3.1 0.2 - - - -
968D ASP* 3.1 4.2 + - - +
969D PHE* 3.0 34.6 + + + -
1005D TYR* 3.4 26.2 - + - -
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Residues in contact with VAL 966 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962D PRO* 2.9 24.0 + - + +
963D GLU* 3.8 9.0 - - - +
965D PHE* 1.3 90.6 - - + +
967D ALA* 1.3 62.8 + - - +
969D PHE* 3.1 9.6 + - - +
970D ARG* 2.9 57.4 + - - +
997D PHE* 4.4 3.4 - - + -
1001D LEU* 3.9 36.1 - - + -
1005D TYR* 5.6 0.7 - - + -
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Residues in contact with ALA 967 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A GLU* 6.0 1.3 - - - +
963D GLU 3.0 17.2 + - - +
964D ASP* 3.6 8.7 - - - +
965D PHE 3.1 0.2 - - - -
966D VAL* 1.3 78.8 - - - +
968D ASP* 1.3 59.3 + - - +
970D ARG* 3.3 7.9 + - - +
971D LEU* 3.0 27.2 + - - +
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Residues in contact with ASP 968 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943D MET* 3.3 31.4 - - + +
948D ILE* 3.7 13.2 - - + -
951D ARG* 2.8 30.6 + - - -
958D MET* 5.2 0.4 - - - +
959D TYR* 2.4 39.2 + - - +
964D ASP 3.6 3.6 + - - +
965D PHE 3.1 9.6 + - - +
967D ALA* 1.3 78.7 - - - +
969D PHE* 1.3 65.2 + - - +
971D LEU* 3.2 18.5 + - - +
972D ILE* 3.3 2.9 + - - +
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Residues in contact with PHE 969 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908D CYS* 3.8 23.1 - - - -
911D LEU* 4.2 7.2 - - + -
912D LEU* 3.5 49.1 - - + -
915D LEU* 3.6 31.2 - - + -
945D LEU* 3.9 4.7 - - + -
948D ILE* 3.6 17.0 - - + -
965D PHE* 3.0 34.4 + + - -
966D VAL 3.4 2.5 - - - +
968D ASP* 1.3 74.7 - - - +
970D ARG* 1.3 63.8 + - - +
972D ILE* 3.0 21.6 + - + +
973D PHE* 3.3 14.9 - + + -
997D PHE* 3.4 38.1 - + + -
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Residues in contact with ARG 970 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859A ASN* 5.5 9.2 - - - +
966D VAL* 2.9 37.9 + - - +
967D ALA* 3.8 6.7 - - - +
969D PHE* 1.3 73.6 - - - +
971D LEU* 1.3 60.2 + - - +
973D PHE* 3.1 13.1 + - + +
974D GLN* 2.8 31.2 + - - +
994D GLU* 5.8 2.7 - - - +
997D PHE* 4.4 4.5 - - + -
998D GLU* 3.1 41.7 + - - +
1001D LEU* 3.8 13.5 - - - +
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Residues in contact with LEU 971 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A PHE 6.1 0.4 - - - +
862A SER* 4.3 10.8 - - - +
941D ASN* 3.3 42.8 - - + +
943D MET* 3.7 28.7 - - + -
967D ALA 3.0 14.1 + - - +
968D ASP* 3.3 18.2 - - - +
969D PHE 3.2 0.2 - - - -
970D ARG* 1.3 76.8 - - - +
972D ILE* 1.3 57.9 + - - +
974D GLN* 4.3 4.9 - - + -
975D ASN* 2.8 45.6 + - - +
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Residues in contact with ILE 972 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924D PHE* 3.9 33.0 - - + -
943D MET* 3.5 27.6 - - + +
944D ASP 3.5 27.1 - - - -
945D LEU* 3.7 18.2 - - + +
948D ILE* 3.7 18.8 - - + -
968D ASP 3.4 11.0 - - - +
969D PHE* 3.0 10.9 + - + +
971D LEU* 1.3 79.4 - - - +
973D PHE* 1.3 72.9 + - + +
975D ASN* 3.5 3.8 + - - +
976D CYS* 3.1 22.0 + - - +
993D LEU* 5.9 0.2 - - + -
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Residues in contact with PHE 973 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915D LEU* 4.4 10.1 - - + -
924D PHE* 6.0 1.3 - + - -
945D LEU* 6.2 0.4 - - + -
969D PHE* 3.3 22.9 - + + -
970D ARG* 3.1 13.8 + - + +
972D ILE* 1.3 85.1 - - + +
974D GLN* 1.3 60.4 + - - +
976D CYS* 3.3 6.5 + - + +
977D ALA* 3.0 29.6 + - - +
990D GLY* 3.8 12.6 - - - +
993D LEU* 3.8 25.1 - - + -
994D GLU* 3.5 55.9 - - + +
997D PHE* 3.6 46.4 - + + -
998D GLU* 5.3 0.2 - - - -
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Residues in contact with GLN 974 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859A ASN* 2.8 41.9 + - + +
860A PHE 3.2 17.2 + - - +
862A SER* 2.8 24.0 - - - +
881A ASP* 3.6 14.2 + - - +
970D ARG 2.8 17.9 + - - +
971D LEU* 3.8 7.2 - - + +
973D PHE* 1.3 75.6 - - - +
975D ASN* 1.3 64.6 + - - +
977D ALA* 3.5 8.5 + - - +
978D GLU* 3.0 51.2 + - - +
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Residues in contact with ASN 975 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862A SER* 2.8 28.5 + - - +
935D TYR* 3.3 17.6 + - - +
939D ILE* 3.3 21.4 - - + +
941D ASN 3.0 23.7 + - - +
942D PRO* 3.5 0.6 - - - +
943D MET* 3.4 21.0 + - - +
971D LEU* 2.8 30.7 + - - +
972D ILE* 3.7 5.1 - - - +
974D GLN* 1.3 75.9 - - - +
976D CYS* 1.3 63.5 + - - +
978D GLU 3.4 0.2 + - - -
979D PHE* 3.0 28.4 + - - +
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Residues in contact with CYS 976 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924D PHE* 3.4 28.9 - - + -
935D TYR* 4.8 2.4 + - - -
972D ILE 3.1 14.6 + - - +
973D PHE* 3.5 12.3 - - + +
975D ASN* 1.3 77.1 - - - +
977D ALA* 1.3 56.9 + - - +
980D ASN* 2.9 51.1 + - - +
986D VAL* 3.4 25.8 - - - -
987D ALA* 4.0 8.0 - - - -
990D GLY* 3.8 11.0 - - - -
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Residues in contact with ALA 977 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973D PHE 3.0 16.5 + - - +
974D GLN* 3.9 14.1 - - - +
976D CYS* 1.3 78.8 - - - +
978D GLU* 1.3 62.2 + - + +
980D ASN 3.5 14.5 - - - +
987D ALA* 5.7 4.7 - - - -
991D ILE* 5.6 10.3 - - + -
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Residues in contact with GLU 978 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861A PRO* 3.5 4.8 - - - +
862A SER* 2.7 38.8 + - - -
863A GLY* 3.8 9.2 + - - -
879A GLU 5.4 3.5 - - - +
881A ASP* 3.5 17.1 - - - +
938D ILE* 4.9 7.9 - - + +
939D ILE* 4.6 6.3 - - + -
974D GLN* 3.0 42.8 + - - +
975D ASN 4.0 2.2 - - - +
977D ALA* 1.3 80.3 - - + +
979D PHE* 1.3 59.5 + - - +
980D ASN 4.9 0.2 - - - -
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Residues in contact with PHE 979 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932D VAL* 5.2 13.7 - - + -
934D ASP* 4.1 11.9 - - + -
935D TYR* 3.4 64.2 - + + -
938D ILE* 4.1 24.4 - - + +
939D ILE* 3.9 6.7 - - + -
975D ASN 3.0 16.4 + - - +
978D GLU* 1.3 78.7 - - - +
980D ASN* 1.3 83.7 + - - +
981D GLU* 3.9 5.9 + - - +
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Residues in contact with ASN 980 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924D PHE* 5.4 0.2 - - - -
935D TYR* 5.5 1.4 - - - -
976D CYS* 2.9 32.7 + - - +
977D ALA 3.5 15.8 - - - +
978D GLU 4.9 0.2 - - - -
979D PHE* 1.3 101.9 - - - +
981D GLU* 1.3 66.5 + - - +
982D PRO* 3.5 3.1 - - - +
984D SER* 3.6 16.6 + - - +
986D VAL* 3.3 36.8 - - - +
987D ALA* 4.1 11.0 - - + +
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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
------------------------------------------------------------
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