Contacts of the helix formed by residues 960 - 973 (chain A) 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 960 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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930A TYR* 4.7 5.3 + - - +
959A THR* 1.3 81.1 + - - +
961A PRO* 1.4 74.0 - - + +
962A GLY 3.4 1.8 - - - +
963A HIS* 3.0 44.7 + - + +
964A GLN* 3.0 22.1 + - - +
934D GLU* 4.0 32.3 - - + +
937D VAL* 3.5 27.1 - - + -
938D GLN* 6.4 0.7 - - + -
969D VAL* 3.7 25.1 - - + +
970D ASN* 3.9 8.1 - - - +
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Residues in contact with PRO 961 (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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959A THR 3.3 9.8 - - - +
960A LEU* 1.4 82.7 - - + +
962A GLY* 1.3 54.4 + - - +
964A GLN* 3.1 11.9 + - + +
965A LYS* 2.8 36.1 + - - +
969D VAL 4.2 10.8 - - - +
970D ASN* 3.4 35.0 - - + +
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Residues in contact with GLY 962 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927A MET* 4.9 0.2 - - - +
960A LEU* 3.4 1.8 - - - +
961A PRO* 1.3 77.3 - - - +
963A HIS* 1.3 65.6 + - - +
965A LYS* 3.6 18.5 + - - +
966A ARG* 3.0 28.4 + - - +
973B GLY 4.7 0.7 - - - +
974B PHE* 5.6 1.2 - - - +
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Residues in contact with HIS 963 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927A MET* 3.6 27.6 - - + +
929A ARG* 3.1 31.3 + - - -
930A TYR* 2.9 33.6 + - + +
958A ILE* 4.3 6.5 - - + -
960A LEU* 3.0 31.1 + - + +
962A GLY* 1.3 79.9 - - - +
964A GLN* 1.3 66.6 + - - +
966A ARG* 3.5 2.1 + - - +
967A ILE* 3.1 30.9 + - - +
934D GLU* 3.4 12.8 - - - -
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Residues in contact with GLN 964 (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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950A ALA* 3.4 30.4 + - + +
953A LEU* 3.9 18.4 - - + -
954A THR* 3.2 24.2 + - - +
958A ILE* 2.7 30.0 + - + +
959A THR* 3.6 15.6 + - - +
960A LEU 3.0 12.2 + - - +
961A PRO* 3.4 10.5 - - - +
963A HIS* 1.3 76.7 - - - +
965A LYS* 1.3 53.2 + - - +
967A ILE* 3.1 4.1 + - - +
968A LEU* 2.8 46.1 + - + +
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Residues in contact with LYS 965 (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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961A PRO 2.8 18.7 + - - +
962A GLY* 3.6 16.7 + - - +
964A GLN* 1.3 70.8 - - - +
966A ARG* 1.3 57.6 - - - +
968A LEU* 4.6 4.9 - - - +
969A CYS* 2.8 46.2 + - - +
972B GLN* 3.2 25.8 + - + +
973B GLY 4.1 3.0 + - - -
974B PHE 3.2 28.1 + - - -
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Residues in contact with ARG 966 (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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925A ILE* 2.7 47.4 + - + +
926A ARG* 4.1 4.6 + - - +
927A MET* 3.4 38.0 - - + +
929A ARG* 5.4 1.0 - - - +
962A GLY 3.0 17.1 + - - +
963A HIS 3.5 4.9 - - - +
965A LYS* 1.3 80.9 - - - +
967A ILE* 1.3 61.6 + - - +
969A CYS* 4.5 1.2 - - - +
970A SER* 3.3 21.7 + - - -
912B GLY 5.0 1.4 + - - -
914B PRO* 3.3 35.8 - - - +
915B TYR* 5.6 1.8 - - - -
973B GLY* 3.1 24.8 + - - +
974B PHE* 3.0 23.7 + - - -
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Residues in contact with ILE 967 (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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921A TRP* 3.7 23.7 - - + -
922A LEU* 4.9 2.0 - - + -
925A ILE* 4.1 19.5 - - + -
927A MET* 4.4 17.3 - - + -
930A TYR* 4.8 3.6 - - + -
934A PHE* 4.5 8.7 - - + -
948A LEU* 4.6 1.8 - - + -
953A LEU* 4.2 23.1 - - + -
958A ILE* 4.1 33.9 - - + -
963A HIS 3.1 17.1 + - - +
964A GLN 3.7 4.3 - - - +
966A ARG* 1.3 73.5 - - - +
968A LEU* 1.3 62.2 + - + +
970A SER* 3.4 3.6 + - - -
971A ILE* 3.1 37.1 + - + +
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Residues in contact with LEU 968 (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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948A LEU* 3.4 37.0 - - + +
949A THR* 4.2 4.3 - - - -
950A ALA* 3.8 31.2 - - + +
953A LEU* 4.0 13.0 - - + -
964A GLN* 2.8 28.2 + - + +
965A LYS* 4.1 4.0 - - - +
967A ILE* 1.3 69.3 - - - +
969A CYS* 1.3 65.8 + - - +
971A ILE* 3.2 12.6 + - + +
972A GLN* 3.0 28.5 + - + +
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Residues in contact with CYS 969 (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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965A LYS* 2.8 35.4 + - - +
966A ARG 4.5 0.2 - - - +
968A LEU* 1.3 69.5 - - - +
970A SER* 1.3 59.6 + - - +
972A GLN* 3.3 9.3 + - - +
973A GLY 2.8 24.9 + - - -
969B CYS* 3.3 34.6 - - + +
972B GLN* 4.0 29.6 - - - -
973B GLY* 3.9 12.1 - - - -
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Residues in contact with SER 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A TYR* 4.8 2.4 + - - -
921A TRP* 2.9 27.6 + - - -
925A ILE* 3.6 22.0 - - - +
966A ARG 3.3 18.8 + - - -
967A ILE 3.4 5.4 - - - -
968A LEU 3.2 0.4 - - - -
969A CYS* 1.3 78.1 - - - +
971A ILE* 1.3 63.9 + - - +
973A GLY* 3.1 11.9 + - - -
974A PHE* 3.3 21.2 + - - -
966B ARG* 6.0 0.3 - - - -
969B CYS* 5.5 2.0 - - - -
970B SER* 6.0 2.5 - - - +
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Residues in contact with ILE 971 (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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921A TRP* 3.9 17.0 - - + -
945A VAL* 3.4 22.0 - - + +
946A LEU* 3.8 31.0 - - + +
948A LEU* 4.1 15.9 - - + +
967A ILE* 3.1 34.1 + - + +
968A LEU* 3.2 12.3 + - + +
970A SER* 1.3 73.0 - - - +
972A GLN* 1.3 69.0 + - - +
974A PHE* 3.0 40.9 + - + +
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Residues in contact with GLN 972 (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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968A LEU* 3.0 21.0 + - + +
969A CYS* 3.6 9.0 - - - +
971A ILE* 1.3 76.6 - - - +
973A GLY* 1.3 61.2 + - - +
974A PHE 3.2 7.2 + - - +
965B LYS* 3.5 23.8 - - - +
969B CYS* 4.0 15.3 - - - -
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Residues in contact with GLY 973 (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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969A CYS 2.8 14.2 + - - -
970A SER* 3.1 7.8 + - - -
971A ILE 3.0 0.6 - - - -
972A GLN* 1.3 75.8 - - - +
974A PHE* 1.3 62.0 + - - +
962B GLY 4.8 1.4 - - - +
965B LYS* 4.3 9.4 - - - +
966B ARG* 2.9 36.4 + - - +
969B CYS* 3.8 18.4 - - - -
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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
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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