Contacts of the helix formed by residues 976 - 994 (chain D) in PDB entry 4AY6
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 976 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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972D LYS* 2.9 31.5 + - + +
973D LEU 4.4 1.8 - - - -
975D THR* 1.3 78.4 + - - +
977D LEU* 1.3 50.3 + - - +
978D GLU* 3.5 11.8 + - - +
979D TYR* 2.8 33.4 + - + +
980D LEU* 2.8 32.9 + - - +
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Residues in contact with LEU 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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720D TYR* 6.2 4.5 - - + -
832D ILE* 4.2 24.9 - - + -
974D GLY 4.3 7.9 - - - +
975D THR 3.1 15.4 + - - +
976D ASP* 1.3 71.0 - - - +
978D GLU* 1.3 61.3 - - - +
980D LEU* 3.5 14.4 - - + +
981D LYS* 3.1 28.4 + - - +
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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
----------------------------------------------------------
976D ASP* 3.1 10.0 + - - +
977D LEU* 1.3 78.3 - - - +
979D TYR* 1.3 63.6 - - - +
981D LYS* 3.3 29.6 + - - +
982D LYS* 3.1 21.5 + - - +
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Residues in contact with TYR 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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957D GLU* 3.5 33.2 + - + +
958D LEU* 6.4 0.2 - - + -
969D ILE* 5.4 5.0 - - + +
972D LYS* 3.7 48.1 + - + -
973D LEU* 3.8 29.2 - - + -
976D ASP* 2.8 27.6 + - + +
978D GLU* 1.3 74.0 - - - +
980D LEU* 1.3 70.1 + - - +
982D LYS* 3.1 21.1 + - + +
983D VAL* 3.0 37.6 + - + +
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Residues in contact with LEU 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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832D ILE* 4.2 22.9 - - + -
909D ASP* 4.2 16.4 - - + +
910D VAL* 4.0 24.0 - - + -
932D PRO* 5.1 1.1 - - + -
973D LEU* 3.4 39.2 + - + +
974D GLY* 5.2 0.4 - - - -
976D ASP 2.8 8.1 + - - +
977D LEU* 3.5 18.2 - - + +
979D TYR* 1.3 80.0 - - - +
981D LYS* 1.3 59.0 + - - +
983D VAL* 3.1 1.4 + - - +
984D ARG* 2.9 52.1 + - + +
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Residues in contact with LYS 981 (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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719D ILE* 5.0 9.1 + - - +
977D LEU 3.1 13.2 + - - +
978D GLU* 3.6 29.6 + - - +
979D TYR 3.3 0.2 - - - -
980D LEU* 1.3 79.6 - - - +
982D LYS* 1.3 63.2 + - - +
984D ARG* 4.0 7.5 - - - +
985D GLY* 3.0 20.4 + - - -
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Residues in contact with LYS 982 (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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978D GLU 3.1 14.2 + - - +
979D TYR* 3.1 27.8 + - + +
981D LYS* 1.3 78.0 - - - +
983D VAL* 1.3 58.7 + - + +
985D GLY* 3.4 1.6 + - - -
986D LYS* 3.1 31.7 + - + +
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Residues in contact with VAL 983 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932D PRO* 4.0 12.6 - - + -
955D CYS* 5.5 1.1 - - - -
957D GLU* 4.8 13.9 - - + +
958D LEU* 3.9 35.2 - - + -
973D LEU* 3.9 9.2 - - + -
979D TYR* 3.0 48.3 + - + +
980D LEU 3.7 4.0 - - - +
982D LYS* 1.3 73.9 - - + +
984D ARG* 1.3 67.1 + - - +
986D LYS* 2.9 21.3 + - + +
987D VAL* 3.0 15.6 + - + +
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Residues in contact with ARG 984 (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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708D LYS* 4.6 9.5 - - - +
721D ASP* 2.9 37.7 + - - +
722D ASN* 4.1 3.3 - - - +
746D MET* 5.5 0.7 - - - -
906D GLN 3.7 14.5 + - - -
908D ALA 3.2 22.0 + - - -
909D ASP* 2.8 38.3 + - - -
929D ALA 4.9 1.6 + - - -
930D GLY 3.9 17.6 + - - +
931D THR* 3.6 11.1 + - - -
932D PRO* 3.6 27.7 - - + +
980D LEU* 2.9 38.8 + - + +
981D LYS* 4.0 6.7 - - - +
983D VAL* 1.3 72.5 - - - +
985D GLY* 1.3 57.2 + - - +
987D VAL* 3.5 3.0 + - - +
988D TRP* 3.0 29.2 + - - +
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Residues in contact with GLY 985 (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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746D MET* 4.2 24.6 - - - +
981D LYS 3.0 16.2 + - - -
982D LYS 3.7 3.8 - - - -
984D ARG* 1.3 74.7 - - - +
986D LYS* 1.3 64.2 + - - +
988D TRP* 3.6 2.9 + - - +
989D LYS* 3.1 23.4 + - - +
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Residues in contact with LYS 986 (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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954D GLY 3.4 21.5 + - - -
955D CYS* 3.8 10.5 - - - -
957D GLU* 2.7 35.5 + - - +
982D LYS* 3.1 18.2 + - + +
983D VAL* 2.9 15.2 + - + +
985D GLY* 1.3 73.2 - - - +
987D VAL* 1.3 55.4 + - - +
989D LYS* 3.0 6.7 + - - +
990D GLN* 2.6 54.1 + - + +
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Residues in contact with VAL 987 (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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927D LEU* 3.9 17.9 - - + +
930D GLY* 3.5 29.8 - - - +
931D THR 3.9 7.4 - - - +
932D PRO* 3.8 26.5 - - + -
950D LEU* 6.1 0.4 - - + -
953D LEU* 4.6 13.0 - - + +
955D CYS* 4.6 12.5 - - - -
958D LEU* 4.7 3.6 - - + -
983D VAL* 3.0 15.4 + - + +
984D ARG 3.6 6.5 - - - +
986D LYS* 1.3 74.1 - - - +
988D TRP* 1.3 65.9 + - - +
990D GLN* 3.1 6.1 + - - -
991D ARG* 2.9 27.0 + - + +
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Residues in contact with TRP 988 (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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705D LEU 3.8 12.8 - - - -
706D LYS 3.3 12.1 + - - -
707D LYS* 4.0 1.6 - - + -
708D LYS* 3.1 61.2 - - + -
746D MET* 3.8 32.0 - - + -
762D LEU* 4.6 18.3 - - - +
763D ASN 5.5 0.8 + - - +
906D GLN* 4.3 5.2 - - - -
929D ALA* 3.8 20.2 - - - -
930D GLY* 4.0 7.2 - - - -
984D ARG 3.0 15.6 + - - +
985D GLY* 3.6 9.4 - - - +
987D VAL* 1.3 79.2 - - - +
989D LYS* 1.3 64.5 + - + +
991D ARG* 2.9 59.5 + - - +
992D ILE* 4.6 3.3 + - - +
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Residues in contact with LYS 989 (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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762D LEU 5.3 10.5 - - - +
985D GLY 3.1 12.3 + - - +
986D LYS* 3.0 9.0 + - - +
988D TRP* 1.3 81.2 - - + +
990D GLN* 1.3 78.0 + - - +
992D ILE* 3.2 17.0 + - - +
993D SER* 3.2 32.6 + - - +
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Residues in contact with GLN 990 (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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953D LEU* 3.3 40.5 + - + +
954D GLY* 5.1 2.9 - - - +
955D CYS* 4.8 3.6 - - - -
986D LYS* 2.6 42.1 + - + +
987D VAL* 3.8 2.0 - - - +
989D LYS* 1.3 90.4 + - - +
991D ARG* 1.3 58.4 + - - +
993D SER* 3.5 16.7 + - - -
994D SER* 2.7 46.9 + - - +
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Residues in contact with ARG 991 (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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705D LEU 3.2 18.4 + - - -
706D LYS* 2.9 29.8 + - - +
927D LEU 3.7 14.1 - - - +
928D TRP* 2.8 54.7 + - + +
930D GLY 4.5 1.8 - - - +
953D LEU* 3.5 13.6 - - + +
987D VAL* 2.9 13.0 + - + +
988D TRP* 2.9 57.1 + - - +
990D GLN* 1.3 75.1 - - - +
992D ILE* 1.3 74.9 - - + +
994D SER* 4.4 2.3 + - - +
997D PHE* 3.4 47.8 + - + +
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Residues in contact with ILE 992 (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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706D LYS* 3.9 24.0 - - + +
928D TRP* 3.9 31.0 - - + -
988D TRP 4.6 4.3 - - - +
989D LYS* 3.2 8.8 + - - +
990D GLN 3.1 0.2 - - - -
991D ARG* 1.3 92.0 - - + +
993D SER* 1.3 68.2 + - - +
994D SER 3.3 8.5 - - - +
998D ASN* 5.7 3.5 + - - +
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Residues in contact with SER 993 (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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989D LYS* 3.2 37.8 + - - +
990D GLN* 3.5 17.5 + - - -
992D ILE* 1.3 83.4 - - - +
994D SER* 1.3 61.9 + - - +
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Residues in contact with SER 994 (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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952D CYS 3.5 9.9 - - - -
953D LEU* 3.4 31.5 - - - +
990D GLN* 2.7 30.2 + - - +
991D ARG* 4.4 3.3 - - - +
992D ILE 3.3 10.2 - - - +
993D SER* 1.3 78.8 + - - +
995D PRO* 1.3 75.8 - - - +
996D LEU* 3.2 12.2 + - - +
997D PHE 4.5 1.2 + - - -
998D ASN* 4.6 4.5 + - - +
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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
------------------------------------------------------------
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