Contacts of the helix formed by residues 958 - 980 (chain D) in PDB entry 6M6C
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 GLU 958 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956D ILE 4.5 5.1 - - - +
957D PRO* 1.3 74.8 - - - +
959D GLU* 1.3 70.7 + - - +
960D LYS 3.0 6.6 + - - -
961D LYS* 3.3 17.8 + - - +
962D GLN* 3.7 17.7 + - - +
1010D ASN* 5.1 6.2 - - - +
1014D ASN* 5.9 0.5 + - - -
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Residues in contact with GLU 959 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957D PRO* 3.3 11.7 - - + +
958D GLU* 1.3 89.2 + - - +
960D LYS* 1.3 56.3 + - - +
961D LYS 3.3 0.4 - - - -
962D GLN* 3.3 22.4 + - - +
963D TYR* 2.9 59.3 + - + +
1006D ALA* 4.1 23.2 - - + +
1009D LYS* 4.4 15.9 + - - -
1010D ASN* 5.1 4.6 - - - +
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Residues in contact with LYS 960 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956D ILE* 4.2 16.6 - - + -
957D PRO* 3.7 19.4 + - + +
958D GLU 3.0 1.6 + - - -
959D GLU* 1.3 78.4 - - - +
961D LYS* 1.3 58.8 + - - +
963D TYR* 3.4 3.2 + - - +
964D LEU* 2.9 53.2 + - + +
1003D VAL* 4.1 27.3 - - + +
1006D ALA* 5.7 0.4 - - - +
1039D CYS 4.6 3.6 + - - +
1040D GLY* 3.2 32.0 + - - +
1041D LEU* 4.5 4.9 - - + -
1058D ARG 3.6 18.8 + - - -
1060D SER* 4.2 2.0 + - - +
1063D GLU* 3.3 33.5 + - - +
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Residues in contact with LYS 961 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957D PRO 4.9 0.2 + - - -
958D GLU 3.3 10.3 + - - +
959D GLU 3.3 0.6 - - - -
960D LYS* 1.3 79.5 - - - +
962D GLN* 1.3 60.4 + - + +
964D LEU* 3.3 8.5 + - - +
965D GLU* 2.9 58.5 + - + +
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Residues in contact with GLN 962 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958D GLU* 3.7 25.4 + - - +
959D GLU* 3.8 22.7 - - - +
960D LYS 3.3 0.2 - - - -
961D LYS* 1.3 77.1 - - + +
963D TYR* 1.3 64.1 + - + +
965D GLU* 3.3 14.2 + - - +
966D GLU* 2.9 30.8 + - - +
969D ARG* 5.5 0.5 + - - -
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Residues in contact with TYR 963 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959D GLU* 2.9 42.7 + - + +
960D LYS* 3.7 4.9 - - - +
962D GLN* 1.3 84.0 - - + +
964D LEU* 1.3 59.2 + - + +
966D GLU* 3.4 18.1 + - - +
967D ALA* 2.9 29.6 + - - +
999D THR* 4.5 17.2 + - + +
1002D LYS* 3.8 47.7 + - + +
1003D VAL* 4.2 21.5 - - + -
1006D ALA* 4.0 7.8 - - + +
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Residues in contact with LEU 964 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960D LYS* 2.9 46.1 + - + +
961D LYS* 3.7 6.3 - - - +
963D TYR* 1.3 76.3 - - + +
965D GLU* 1.3 59.5 + - + +
967D ALA* 3.3 2.6 + - - +
968D ASP* 2.9 35.6 + - - +
996D TRP* 4.3 22.2 - - + -
999D THR* 4.4 6.5 - - + -
1041D LEU* 4.0 23.1 - - + -
1058D ARG* 4.3 35.8 + - + +
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Residues in contact with GLU 965 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961D LYS* 2.9 45.7 + - + +
962D GLN* 3.7 13.8 - - - +
964D LEU* 1.3 78.4 - - + +
966D GLU* 1.3 62.9 + - - +
968D ASP* 3.2 10.2 + - - +
969D ARG* 3.0 35.8 + - - +
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Residues in contact with GLU 966 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962D GLN 2.9 16.5 + - - +
963D TYR* 3.7 22.2 - - - +
965D GLU* 1.3 75.9 - - - +
967D ALA* 1.3 57.9 + - - +
969D ARG* 3.3 30.3 + - - +
970D LYS* 2.9 45.3 + - + +
1002D LYS* 4.5 17.4 + - - -
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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
----------------------------------------------------------
963D TYR 2.9 17.2 + - - +
964D LEU* 3.7 6.7 - - - +
965D GLU 3.3 0.2 - - - -
966D GLU* 1.3 75.8 - - - +
968D ASP* 1.3 58.1 + - - +
970D LYS* 3.3 1.9 + - - +
971D LEU* 2.9 29.7 + - - +
995D LEU* 3.8 19.7 - - + +
996D TRP* 4.1 25.4 - - + -
999D THR* 3.7 20.4 - - + +
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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
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964D LEU* 2.9 22.8 + - - +
965D GLU* 3.2 9.7 + - - +
967D ALA* 1.3 76.9 - - - +
969D ARG* 1.3 56.8 + - - +
971D LEU* 3.2 9.7 + - - +
972D LEU* 2.9 27.9 + - - +
996D TRP* 4.5 4.9 - - - -
1058D ARG* 2.8 40.2 + - - -
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Residues in contact with ARG 969 (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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962D GLN 5.5 0.4 + - - -
965D GLU* 3.0 19.4 + - - +
966D GLU* 3.4 51.7 - - - +
968D ASP* 1.3 77.2 - - - +
970D LYS* 1.3 65.4 + - + +
972D LEU* 3.3 9.2 + - - +
973D GLN* 2.9 48.4 + - - +
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Residues in contact with LYS 970 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966D GLU* 2.9 33.6 + - + +
967D ALA 3.6 4.3 - - - +
969D ARG* 1.3 80.8 - - + +
971D LEU* 1.3 56.7 + - - +
973D GLN* 3.3 24.7 + - - +
974D ILE* 2.9 41.4 + - + +
995D LEU* 4.0 30.8 - - + +
998D GLU* 5.6 3.6 + - - -
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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
----------------------------------------------------------
967D ALA 2.9 16.3 + - - +
968D ASP* 3.6 9.4 - - - +
970D LYS* 1.3 75.4 - - - +
972D LEU* 1.3 61.3 + - - +
974D ILE* 3.2 8.2 + - - +
975D GLU* 2.9 41.6 + - + +
992D ILE* 4.9 22.4 - - + -
995D LEU* 4.1 8.2 - - + +
996D TRP* 3.9 34.5 - - + +
1054D GLU 5.6 1.6 - - - +
1055D VAL* 6.2 4.7 - - + -
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Residues in contact with LEU 972 (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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968D ASP 2.9 14.2 + - - +
969D ARG* 3.6 11.9 - - - +
970D LYS 3.3 0.2 - - - -
971D LEU* 1.3 79.9 - - - +
973D GLN* 1.3 67.3 + - + +
975D GLU* 3.3 6.5 + - - +
976D GLN* 2.9 31.9 + - + +
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Residues in contact with GLN 973 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969D ARG* 2.9 36.8 + - - +
970D LYS* 3.5 25.6 - - - +
972D LEU* 1.3 80.8 - - + +
974D ILE* 1.3 56.8 + - + +
976D GLN* 3.3 15.9 + - - +
977D ALA* 2.9 30.4 + - - +
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Residues in contact with ILE 974 (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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970D LYS* 2.9 28.6 + - + +
971D LEU* 3.2 6.7 + - - +
973D GLN* 1.3 75.8 - - + +
975D GLU* 1.3 60.5 + - + +
977D ALA* 3.3 6.6 + - - +
978D TYR* 2.9 27.2 + - - +
983D LEU* 4.6 4.4 - - + +
988D ARG* 4.4 20.2 - - + +
991D GLN* 4.1 46.2 - - + +
992D ILE* 4.3 22.2 - - + +
995D LEU* 4.6 16.6 - - + -
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Residues in contact with GLU 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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971D LEU* 2.9 34.3 + - + +
972D LEU* 3.7 7.2 - - + +
974D ILE* 1.3 78.6 - - + +
976D GLN* 1.3 62.2 + - - +
978D TYR* 3.1 12.3 + - - +
979D GLU* 2.9 27.0 + - - +
988D ARG* 2.7 45.4 + - - -
992D ILE* 4.4 6.1 - - + +
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Residues in contact with GLN 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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972D LEU* 2.9 25.3 + - + +
973D GLN* 3.7 16.1 - - - +
975D GLU* 1.3 75.4 - - - +
977D ALA* 1.3 62.1 + - - +
979D GLU* 3.2 38.7 - - - +
980D MET* 3.4 28.8 + - + +
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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 GLN 2.9 18.0 + - - +
974D ILE* 3.8 7.0 - - - +
976D GLN* 1.3 77.5 - - - +
978D TYR* 1.3 60.6 + - - +
980D MET* 3.7 8.9 + - - -
982D PHE* 3.4 35.6 + - + +
983D LEU* 3.8 11.2 - - + -
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Residues in contact with TYR 978 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974D ILE 2.9 17.9 + - - +
975D GLU* 3.1 14.6 + - - +
977D ALA* 1.3 72.6 - - - +
979D GLU* 1.3 66.7 + - + +
980D MET 3.0 4.7 - - - -
981D GLY* 2.9 21.8 + - - -
982D PHE 4.2 0.3 + - - -
983D LEU* 3.2 37.7 - - + +
984D THR* 3.9 13.5 - - - -
985D ASP* 2.6 36.6 + - - -
988D ARG* 3.6 29.8 - - + -
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Residues in contact with GLU 979 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975D GLU* 2.9 15.0 + - - +
976D GLN* 3.2 28.4 - - - +
978D TYR* 1.3 85.8 - - + +
980D MET* 1.3 79.3 + - - +
981D GLY 3.2 1.8 + - - -
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Residues in contact with MET 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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976D GLN* 3.4 33.2 + - - +
977D ALA* 4.0 2.0 - - - +
978D TYR 3.0 1.4 - - - -
979D GLU* 1.3 100.1 - - - +
981D GLY* 1.3 60.8 + - - +
982D PHE* 3.4 35.4 + - + -
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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
------------------------------------------------------------
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