Contacts of the helix formed by residues 964 - 976 (chain D) in PDB entry 2CKJ
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 THR 964 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962D GLY 3.7 13.1 + - - +
963D PHE* 1.3 76.7 - - - +
965D LEU* 1.3 55.9 + - - +
966D PRO* 3.3 2.0 - - - -
967D ARG* 2.8 38.8 + - - +
968D CYS* 3.3 9.0 + - - -
1156D TYR* 3.3 19.0 - - - +
1182D ASP* 3.0 35.6 + - - +
1245D LEU* 4.4 16.6 - - + -
1248D CYS* 4.7 13.2 - - + +
1258D LYS* 4.3 5.8 - - - +
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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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889D CYS* 3.9 31.6 - - + -
947D LEU* 4.1 17.5 - - + -
963D PHE* 3.3 18.8 - - + -
964D THR* 1.3 76.4 + - - +
966D PRO* 1.4 71.9 - - + +
968D CYS* 3.5 7.4 + - + +
969D TRP* 3.0 22.1 + - + +
1003D PRO* 4.5 3.6 - - + -
1004D THR 3.7 24.9 - - - +
1005D LYS* 5.7 0.2 - - + -
1156D TYR* 4.0 13.6 - - + -
1157D GLY* 3.9 23.3 - - - +
1158D VAL* 4.1 9.9 - - + -
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Residues in contact with PRO 966 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944D ARG* 4.6 16.2 - - - +
947D LEU* 6.0 4.3 - - + -
949D LYS* 6.4 0.7 - - - -
950D GLU* 6.2 0.7 - - + +
963D PHE* 3.0 40.8 - - + +
964D THR 3.3 0.4 - - - -
965D LEU* 1.4 87.8 - - + +
967D ARG* 1.4 53.0 + - - +
969D TRP* 2.9 12.5 + - + +
970D GLU* 2.7 37.9 + - - +
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Residues in contact with ARG 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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964D THR* 2.8 23.5 + - - +
966D PRO* 1.4 75.0 - - + +
968D CYS* 1.3 55.7 + - - +
970D GLU* 4.5 6.3 - - + +
971D GLU* 3.0 47.6 + - + +
1245D LEU* 3.5 24.9 - - + +
1246D ARG 2.8 28.5 + - - -
1247D ASP* 3.2 14.5 + - - +
1248D CYS* 3.6 6.9 - - - +
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Residues in contact with CYS 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 THR* 3.3 17.4 + - - -
965D LEU* 3.7 11.9 - - - +
966D PRO 3.3 0.8 - - - -
967D ARG* 1.3 71.6 - - - +
969D TRP* 1.3 70.2 + - - +
971D GLU 3.8 0.5 - - - -
972D CYS* 3.0 24.3 + - - +
1156D TYR 4.2 8.7 - - - -
1157D GLY* 4.1 18.2 - - - -
1158D VAL* 4.3 15.7 - - + -
1180D VAL* 4.3 26.9 - - + +
1182D ASP* 4.3 16.8 - - - -
1245D LEU* 4.5 10.4 - - - +
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Residues in contact with TRP 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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940D GLU* 3.5 37.1 + - + -
943D ARG* 4.3 17.0 - - + -
944D ARG* 3.8 42.3 - - + +
947D LEU* 5.0 13.2 - - + -
965D LEU* 3.0 14.6 + - + +
966D PRO* 2.9 16.7 + - + +
968D CYS* 1.3 69.9 - - - +
970D GLU* 1.3 68.5 + - - +
972D CYS* 2.9 14.2 + - - +
973D LEU* 3.2 33.5 + - + +
1001D ILE* 3.9 32.5 - - + -
1002D ILE 4.6 0.7 - - - -
1003D PRO* 4.0 39.7 - - + -
1158D VAL* 4.2 18.0 - - + +
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Residues in contact with GLU 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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944D ARG* 3.3 40.8 + - - -
966D PRO* 2.7 19.7 + - - +
967D ARG* 4.3 6.7 - - + +
969D TRP* 1.3 78.1 + - - +
971D GLU* 1.3 57.8 + - - +
972D CYS 3.6 0.2 + - - -
973D LEU* 4.1 10.3 + - + +
974D ALA* 3.7 16.6 + - - +
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Residues in contact with GLU 971 (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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967D ARG* 3.0 34.7 + - + +
968D CYS* 3.8 2.0 - - - +
969D TRP 2.9 1.2 + - - -
970D GLU* 1.3 73.1 - - - +
972D CYS* 1.3 62.3 + - - +
974D ALA* 3.7 13.2 - - + +
975D SER* 3.4 15.0 + - - -
1180D VAL* 4.3 13.4 - - + +
1243D SER* 5.5 5.7 - - - -
1244D LEU 5.3 1.2 - - - +
1245D LEU* 3.7 30.2 - - - +
1246D ARG* 4.4 17.2 - - - +
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Residues in contact with CYS 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 CYS 3.0 15.6 + - - +
969D TRP 2.9 4.4 + - - +
971D GLU* 1.3 77.0 - - - +
973D LEU* 1.3 60.7 + - - +
974D ALA 2.6 11.2 + - - -
975D SER* 3.2 2.7 + - - -
976D SER* 3.0 31.0 + - - -
1001D ILE* 4.3 4.3 - - + -
1158D VAL* 4.0 24.5 - - + -
1160D CYS* 4.2 15.7 - - - -
1178D ASP* 3.8 24.0 - - - -
1180D VAL* 3.4 21.1 - - + -
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Residues in contact with LEU 973 (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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940D GLU* 4.2 29.6 - - + +
969D TRP* 3.2 54.0 + - + +
970D GLU* 4.3 11.7 - - + +
971D GLU 3.7 0.2 - - - -
972D CYS* 1.3 77.3 - - - +
974D ALA* 1.3 60.4 + - - +
976D SER* 3.5 9.9 - - - -
977D GLN* 3.3 18.5 + - - -
978D TYR* 3.4 24.8 + - + -
979D HIS* 4.4 17.1 + - + +
1001D ILE* 4.3 15.9 - - + -
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Residues in contact with ALA 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 GLU 3.7 14.5 + - - +
971D GLU* 3.7 15.7 - - + +
972D CYS 2.6 2.6 + - - -
973D LEU* 1.3 76.5 - - - +
975D SER* 1.4 64.8 + - - +
977D GLN* 3.3 18.7 + - - +
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Residues in contact with SER 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 GLU 3.4 11.4 + - - -
972D CYS* 3.2 10.9 + - - -
974D ALA* 1.4 72.4 - - - +
976D SER* 1.3 74.5 + - - -
977D GLN* 2.8 15.5 + - - +
1176D ARG* 4.1 7.7 + - - -
1178D ASP* 4.8 6.1 + - - +
1180D VAL* 5.2 3.5 - - - +
1241D ARG* 6.3 2.5 - - - -
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Residues in contact with SER 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 CYS* 3.0 26.6 + - - -
973D LEU* 3.5 7.4 - - - -
975D SER* 1.3 79.9 + - - +
977D GLN* 1.3 72.2 + - - +
978D TYR* 3.4 17.7 + - - +
981D ARG* 3.4 22.4 + - - -
1001D ILE* 5.3 0.2 - - - +
1160D CYS* 4.3 10.8 - - - +
1176D ARG* 3.8 3.8 + - - +
1178D ASP* 3.8 31.8 + - - -
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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