Contacts of the helix formed by residues 951 - 970 (chain D) in PDB entry 3KKA
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 LEU 951 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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921D TYR* 3.9 7.3 + - - +
949D VAL 3.7 0.4 - - - -
950D ARG* 1.3 78.0 - - + +
952D PRO* 1.4 73.1 - - + +
953D GLY 3.5 0.9 - - - +
954D HIS* 3.1 46.0 + - + +
955D GLN* 2.9 27.9 + - - +
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Residues in contact with PRO 952 (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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950D ARG 3.4 5.5 - - - +
951D LEU* 1.4 91.2 - - + +
953D GLY* 1.3 63.7 + - - +
955D GLN* 3.4 16.1 + - - +
956D LYS* 3.3 37.7 + - - +
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Residues in contact with GLY 953 (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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951D LEU* 3.5 0.6 - - - +
952D PRO* 1.3 80.6 - - - +
954D HIS* 1.3 62.2 + - - +
956D LYS* 3.5 9.8 + - - +
957D ARG* 3.1 35.3 + - - +
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Residues in contact with HIS 954 (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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918D MET* 4.0 25.5 - - + +
920D GLN* 3.8 16.2 + - - -
921D TYR* 2.8 40.6 - + - +
949D VAL* 3.9 8.7 - - + -
951D LEU* 3.1 34.8 + - + +
953D GLY* 1.3 77.7 - - - +
955D GLN* 1.3 64.7 + - - +
957D ARG* 3.5 4.0 + - - +
958D ILE* 3.1 30.8 + - - +
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Residues in contact with GLN 955 (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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944D ILE* 4.4 14.2 - - + +
945D LYS* 4.0 19.3 - - - +
949D VAL* 2.9 36.8 + - + +
950D ARG* 3.4 21.2 + - - +
951D LEU 2.9 11.2 + - - +
952D PRO* 3.4 15.9 + - - +
954D HIS* 1.3 73.0 - - - +
956D LYS* 1.3 61.6 + - + +
958D ILE* 3.2 1.7 + - - +
959D ALA* 2.8 33.9 + - - +
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Residues in contact with LYS 956 (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 PRO* 3.3 29.0 + - - +
953D GLY* 3.9 8.7 - - - +
955D GLN* 1.3 76.9 - - + +
957D ARG* 1.3 65.0 + - - +
959D ALA* 4.5 4.3 - - - -
960D TYR* 2.9 28.9 + - - +
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Residues in contact with ARG 957 (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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916D ILE* 3.2 40.7 + - + +
917D LYS* 4.4 20.4 - - - +
918D MET* 3.9 26.1 - - + +
953D GLY* 3.1 25.1 + - - +
954D HIS* 3.7 8.3 + - - +
955D GLN 3.3 0.2 - - - -
956D LYS* 1.3 75.0 - - - +
958D ILE* 1.3 64.1 + - - +
960D TYR* 3.8 4.8 - - - +
961D SER* 3.2 22.9 + - - -
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Residues in contact with ILE 958 (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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912D TRP* 3.9 23.9 - - + -
913D LEU* 4.7 1.1 - - + -
916D ILE* 4.2 9.2 - - + -
918D MET* 3.9 23.6 - - + -
921D TYR* 4.1 19.3 - - + -
925D PHE* 4.3 15.3 - - + -
944D ILE* 4.0 24.0 - - + -
949D VAL* 4.1 28.5 - - + -
954D HIS 3.1 18.6 + - - +
955D GLN 3.9 2.2 - - - +
957D ARG* 1.3 74.8 - - - +
959D ALA* 1.3 59.0 + - - +
961D SER* 3.3 3.1 + - - -
962D LEU* 2.8 27.9 + - - +
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Residues in contact with ALA 959 (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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941D ASN* 3.2 28.8 - - + +
944D ILE* 3.8 14.1 - - + +
955D GLN* 2.8 21.9 + - + +
956D LYS* 4.0 4.5 - - - +
958D ILE* 1.3 73.2 - - - +
960D TYR* 1.3 58.2 + - - +
962D LEU* 3.4 4.0 + - - +
963D LEU* 2.9 30.4 + - - +
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Residues in contact with TYR 960 (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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956D LYS 2.9 18.5 + - - +
957D ARG* 3.8 4.5 - - - +
959D ALA* 1.3 78.4 - - - +
961D SER* 1.3 63.6 + - - +
963D LEU* 3.2 26.4 + - + +
964D GLY* 3.3 9.2 + - - -
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Residues in contact with SER 961 (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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912D TRP* 2.6 33.1 + - - -
916D ILE* 3.8 26.3 - - - +
957D ARG 3.2 15.4 + - - -
958D ILE 3.7 2.9 - - - -
960D TYR* 1.3 81.6 - - - +
962D LEU* 1.3 61.4 + - - +
964D GLY* 3.1 5.9 + - - +
965D LEU* 3.1 22.2 + - - +
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Residues in contact with LEU 962 (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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912D TRP* 4.1 14.0 - - + -
936D VAL* 3.4 37.5 - - + +
937D VAL* 4.2 2.0 - - - -
939D MET* 3.5 37.2 - - + +
940D THR 4.7 3.4 - - - +
941D ASN* 5.3 2.5 - - - +
944D ILE* 4.2 17.3 - - + -
958D ILE* 2.8 21.0 + - + +
959D ALA* 3.5 7.2 - - - +
961D SER* 1.3 69.7 + - - +
963D LEU* 1.3 66.7 + - - +
965D LEU* 3.1 8.4 + - + +
966D LYS* 3.0 48.6 + - + +
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Residues in contact with LEU 963 (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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959D ALA 2.9 13.8 + - - +
960D TYR* 3.2 21.7 + - + +
962D LEU* 1.3 76.1 - - - +
964D GLY* 1.3 61.8 + - - +
966D LYS* 3.4 12.0 + - + +
967D ASP* 3.1 27.2 + - + +
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Residues in contact with GLY 964 (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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960D TYR 3.3 5.9 + - - -
961D SER* 3.1 8.9 + - - -
963D LEU* 1.3 76.4 - - - +
965D LEU* 1.3 64.2 + - - +
967D ASP* 3.4 8.1 + - - +
968D GLN* 3.0 32.8 + - - +
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Residues in contact with LEU 965 (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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904D VAL* 4.0 19.3 - - + +
906D PHE* 3.9 28.0 - - + -
912D TRP* 3.5 40.2 - - + +
933D ILE* 4.7 7.4 - - + -
936D VAL* 4.1 17.5 - - + -
937D VAL* 4.3 13.0 - - + -
961D SER* 3.1 17.5 + - - +
962D LEU* 3.1 9.6 + - + +
964D GLY* 1.3 74.9 - - - +
966D LYS* 1.3 64.1 - - - +
968D GLN* 3.2 14.6 + - - +
969D VAL* 3.2 26.0 + - - +
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Residues in contact with LYS 966 (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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937D VAL* 3.1 26.5 + - - +
938D GLN 4.6 1.6 + - - -
939D MET 2.3 33.7 + - - +
940D THR* 4.4 5.5 - - - +
962D LEU* 3.0 39.5 + - + +
963D LEU* 3.7 11.0 - - + +
965D LEU* 1.3 76.2 - - - +
967D ASP* 1.3 56.0 + - - +
969D VAL* 4.1 3.1 - - - -
970D ASN* 2.7 52.5 + - - +
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Residues in contact with ASP 967 (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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963D LEU* 3.1 23.3 + - + +
964D GLY* 3.6 9.0 - - - +
965D LEU 3.2 0.2 - - - -
966D LYS* 1.3 77.9 - - - +
968D GLN* 1.3 58.1 + - + +
970D ASN 3.4 15.7 - - - +
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Residues in contact with GLN 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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903D GLY 4.2 11.9 + - - +
904D VAL* 3.7 16.7 - - + +
905D PRO* 3.9 23.9 - - - +
964D GLY* 3.0 25.1 + - - +
965D LEU* 3.6 13.9 + - - +
967D ASP* 1.3 78.6 - - - +
969D VAL* 1.3 58.5 + - - +
970D ASN 4.8 0.9 - - - -
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Residues in contact with VAL 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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960A LEU* 3.7 14.9 - - + +
961A PRO* 4.2 11.8 - - - +
903D GLY* 4.4 20.0 - - - +
904D VAL* 4.4 15.3 - - + -
933D ILE* 6.3 1.6 - - + -
937D VAL* 3.4 38.4 - - + -
965D LEU 3.2 17.5 + - - +
966D LYS* 4.1 0.2 - - - -
968D GLN* 1.3 81.3 - - - +
970D ASN* 1.3 72.8 + - - +
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Residues in contact with ASN 970 (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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959A THR* 4.1 8.0 + - - +
960A LEU* 3.9 7.1 - - - +
961A PRO* 3.4 34.2 - - + +
937D VAL* 4.4 5.7 + - - +
966D LYS* 2.7 47.4 + - - +
967D ASP* 3.4 22.3 - - - +
968D GLN 5.1 0.4 - - - -
969D VAL* 1.3 88.8 - - - +
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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