Contacts of the helix formed by residues 981 - 992 (chain B) 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 ARG 981 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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976B SER* 3.2 26.2 + - - +
977B GLN* 3.5 13.2 + - + +
978B TYR* 3.4 11.2 - - - +
980B ALA* 1.3 79.0 - - - +
982B LYS* 1.3 64.6 + - - +
984B GLU* 2.8 39.2 + - - +
985B VAL* 2.9 15.4 + - + +
999B LEU* 3.6 26.7 - - + +
1160B CYS* 4.3 15.0 + - - -
1162B GLU* 2.9 37.9 + - - +
1176B ARG* 3.3 39.0 - - - +
1178B ASP* 3.5 11.1 + - - -
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Residues in contact with LYS 982 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978B TYR* 2.8 43.9 + - + +
979B HIS* 4.5 9.0 - - + -
980B ALA 2.2 12.6 + - - +
981B ARG* 1.3 71.0 - - - +
983B SER* 1.3 64.9 + - - +
985B VAL* 2.8 22.7 + - - +
986B ASP* 3.0 36.0 + - - +
999B LEU* 3.8 25.8 - - + +
1277B ASP* 4.4 18.6 + - - -
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Residues in contact with SER 983 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979B HIS* 5.2 1.3 - - - +
980B ALA* 2.6 18.5 + - - -
982B LYS* 1.3 77.0 - - - +
984B GLU* 1.3 58.5 + - - -
985B VAL 2.8 0.7 + - - -
986B ASP* 2.4 36.9 + - - +
987B LYS* 3.8 2.1 - - - +
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Residues in contact with GLU 984 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B PHE* 4.8 12.2 - - + -
545B SER* 3.8 25.5 - - - +
546B ALA* 3.6 32.9 + - - +
980B ALA* 3.6 3.0 + - + -
981B ARG* 2.8 41.4 + - - +
983B SER* 1.3 76.1 + - - +
985B VAL* 1.4 61.6 + - - +
987B LYS* 3.4 26.1 - - + +
988B PHE* 3.6 5.7 + - - +
997B ARG* 4.3 8.3 + - - +
1162B GLU* 3.5 20.8 - - - +
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Residues in contact with VAL 985 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981B ARG 2.9 16.2 + - - +
982B LYS* 2.8 23.4 + - - +
984B GLU* 1.4 66.8 - - - +
986B ASP* 1.3 62.8 + - - +
988B PHE* 2.7 31.8 + - - +
989B ASN* 3.0 25.5 + - - +
997B ARG* 3.9 26.7 - - + +
998B GLY* 4.6 2.7 - - - +
999B LEU* 4.8 11.2 - - + +
1162B GLU* 3.7 33.2 - - + +
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Residues in contact with ASP 986 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982B LYS* 3.0 40.2 + - - +
983B SER* 2.4 30.5 - - - +
985B VAL* 1.3 70.1 - - - +
987B LYS* 1.3 60.4 + - - +
989B ASN* 4.0 20.3 + - + +
990B LYS* 4.9 1.3 - - + +
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Residues in contact with LYS 987 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545B SER* 4.4 17.8 + - - -
983B SER 3.8 3.4 - - - +
984B GLU* 3.4 21.5 - - + +
986B ASP* 1.3 77.0 - - - +
988B PHE* 1.3 63.8 + - - +
989B ASN 3.6 2.8 - - - +
990B LYS* 3.7 20.6 - - - +
991B GLU* 3.2 50.2 + - - +
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Residues in contact with PHE 988 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540B ASP 5.9 0.7 - - - -
541B PRO* 4.9 14.4 - - + -
543B PHE* 4.8 12.1 - + + -
984B GLU 3.6 4.9 + - - +
985B VAL* 2.7 19.4 + - - +
987B LYS* 1.3 77.3 - - + +
989B ASN* 1.3 63.4 + - - -
990B LYS 3.3 0.2 + - - -
991B GLU* 5.0 1.6 - - - -
992B ASN* 3.0 64.4 + - - +
995B LYS* 4.0 20.2 - - + -
996B LYS* 4.1 6.3 - - - -
997B ARG* 3.5 58.6 - - + +
1164B GLU* 3.7 19.5 - - - -
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Residues in contact with ASN 989 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985B VAL* 3.0 23.3 + - - +
986B ASP* 4.0 19.6 + - + +
987B LYS 3.4 0.2 - - - -
988B PHE* 1.3 77.8 - - - +
990B LYS* 1.3 56.9 + - - +
992B ASN* 3.1 10.4 - - - +
996B LYS* 2.8 39.4 + - - +
997B ARG* 2.7 43.7 + - - +
1281B ALA* 4.0 21.9 - - + +
1285B GLN* 5.2 1.7 + - - -
378C GLY* 5.5 2.8 - - - +
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Residues in contact with LYS 990 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986B ASP* 4.9 0.6 - - - +
987B LYS* 3.7 20.5 + - - +
988B PHE 3.4 0.6 - - - -
989B ASN* 1.3 77.6 - - - +
991B GLU* 1.3 64.6 + - + +
992B ASN 3.6 2.1 + - - +
1285B GLN* 5.0 7.8 + - - -
377C ARG 5.4 2.4 - - - +
378C GLY 5.6 5.4 - - - -
399C SER* 4.2 12.7 + - - -
401C GLU* 3.1 36.9 + - - +
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Residues in contact with GLU 991 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536B CYS* 6.0 1.2 - - - +
541B PRO* 5.0 20.9 - - + +
987B LYS* 3.2 41.1 + - - +
988B PHE* 5.0 0.7 - - - -
990B LYS* 1.3 81.5 - - + +
992B ASN* 1.3 68.6 + - - +
993B CYS 4.3 0.3 + - - -
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Residues in contact with ASN 992 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539B LEU 5.8 0.3 - - - -
540B ASP 4.4 5.0 + - - +
541B PRO* 4.1 26.5 - - - +
988B PHE* 3.0 61.8 + - + +
989B ASN 3.1 2.6 - - - +
990B LYS 3.5 2.0 - - - +
991B GLU* 1.3 88.0 + - - +
993B CYS* 1.3 60.8 + - - +
994B TRP 3.7 0.2 - - - -
995B LYS* 3.4 25.1 - - - +
996B LYS* 2.9 26.2 + - - -
1285B GLN* 3.7 2.1 - - - +
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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