Contacts of the helix formed by residues 1045 - 1059 (chain B) in PDB entry 1KEK
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 SER1045 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041B SER 3.1 9.9 + - - +
1042B MET 3.4 6.0 + - - +
1044B TYR* 1.3 99.9 - - - +
1046B LYS* 1.3 62.1 + - - +
1047B GLN* 3.0 24.2 + - - +
1048B GLN* 2.8 37.1 + - - +
1049B PHE* 3.3 18.4 + - - +
1098B LEU* 5.0 0.2 - - - -
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Residues in contact with LYS1046 (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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694B GLN* 2.5 52.7 + - + +
697B PHE* 3.6 36.0 - - + -
698B VAL* 3.7 30.8 - - - +
754B ILE* 4.9 10.1 - - - +
796B LEU* 4.0 15.0 - - + -
1042B MET* 3.7 15.8 + - + +
1043B GLY* 5.6 3.2 + - - -
1045B SER* 1.3 70.8 - - - +
1047B GLN* 1.3 69.2 + - - +
1049B PHE* 3.3 8.0 + - - +
1050B LEU* 2.8 40.9 + - - +
1084B GLN* 4.7 2.6 - - - +
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Residues in contact with GLN1047 (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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694B GLN* 6.1 0.3 - - - -
796B LEU* 4.5 20.0 - - + +
1044B TYR 5.0 1.3 + - - +
1045B SER* 3.0 23.1 + - - +
1046B LYS* 1.3 97.6 + - - +
1048B GLN* 1.3 58.7 + - - +
1050B LEU* 3.4 9.8 + - - +
1051B LYS* 3.1 24.3 + - - +
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Residues in contact with GLN1048 (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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1039B THR 3.1 18.5 + - - +
1040B VAL* 3.4 21.4 - - - +
1041B SER 4.7 0.2 - - - +
1044B TYR* 5.7 0.4 - - + -
1045B SER* 2.8 31.1 + - - +
1047B GLN* 1.3 69.9 - - - +
1049B PHE* 1.3 65.5 + - - +
1051B LYS* 3.2 9.8 + - + +
1052B VAL* 2.9 37.1 + - + +
1098B LEU* 3.8 23.7 - - + +
1099B PHE 4.1 2.6 - - - +
1100B ARG* 5.0 2.0 - - - +
1116B ASP* 2.9 41.2 - - + +
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Residues in contact with PHE1049 (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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697B PHE* 3.9 22.7 - + - -
820B TYR* 3.6 38.4 - + + -
823B VAL* 3.5 23.1 - - + -
824B ILE* 4.4 1.3 - - + -
987B PHE* 4.3 11.0 - + - -
1040B VAL* 4.0 24.5 - - + -
1041B SER 5.6 0.2 - - - -
1042B MET* 3.8 26.0 - - + +
1045B SER 3.3 11.5 + - - +
1046B LYS* 3.3 8.7 - - - +
1048B GLN* 1.3 81.9 - - - +
1050B LEU* 1.3 62.3 + - - +
1052B VAL* 3.1 3.8 + - - +
1053B LEU* 3.0 51.9 + - + +
1065B VAL* 5.5 0.2 - - + -
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Residues in contact with LEU1050 (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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697B PHE* 3.7 14.8 - - + -
794B ASP* 3.7 16.3 - - + +
795B SER 3.6 6.5 - - - -
796B LEU* 3.5 37.9 - - + +
799B SER* 4.3 4.0 - - - -
823B VAL* 3.7 29.2 - - + -
827B LEU* 3.8 28.6 - - + +
1046B LYS 2.8 26.3 + - - +
1047B GLN* 3.4 7.4 + - - +
1049B PHE* 1.3 73.0 - - + +
1051B LYS* 1.3 61.4 + - - +
1053B LEU* 3.5 6.5 + - + +
1054B LYS* 3.1 23.7 + - - +
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Residues in contact with LYS1051 (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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1047B GLN 3.1 17.5 + - - +
1048B GLN* 3.6 9.4 - - + +
1050B LEU* 1.3 72.8 - - - +
1052B VAL* 1.3 61.4 + - - +
1054B LYS* 3.3 8.6 + - + +
1055B GLU* 2.9 60.6 + - + +
1100B ARG* 3.4 35.0 - - - +
1114B GLN* 5.4 0.2 + - - -
1116B ASP* 6.2 0.2 - - - -
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Residues in contact with VAL1052 (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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1036B TYR* 4.0 7.1 + - + +
1038B ALA* 3.6 22.9 - - + -
1040B VAL* 3.8 11.2 - - + -
1048B GLN* 2.9 36.8 + - - +
1049B PHE 3.1 8.0 + - - +
1051B LYS* 1.3 78.7 - - - +
1053B LEU* 1.3 58.6 + - + +
1055B GLU* 3.3 0.7 + - - +
1056B ALA* 2.7 30.0 + - - +
1065B VAL* 3.6 31.2 - - + -
1100B ARG* 3.7 23.8 - - + -
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Residues in contact with LEU1053 (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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823B VAL* 4.3 9.4 - - + -
824B ILE* 3.8 34.1 - - + -
827B LEU* 4.1 17.9 - - + -
828B PHE* 3.6 12.2 - - + -
958B TRP* 4.0 19.9 - - + -
987B PHE* 5.0 5.2 - - + -
1049B PHE* 3.0 53.0 + - + +
1050B LEU* 3.8 7.9 - - + +
1052B VAL* 1.3 74.8 - - + +
1054B LYS* 1.3 58.7 + - - +
1056B ALA* 4.0 2.8 - - - +
1057B GLU* 2.9 34.7 + - - +
1065B VAL* 5.2 7.2 - - + -
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Residues in contact with LYS1054 (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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794B ASP* 3.6 31.3 + - + +
827B LEU* 4.8 1.9 - - + +
828B PHE* 4.5 10.0 - - - -
1050B LEU 3.1 15.7 + - - +
1051B LYS* 3.6 9.6 - - + +
1053B LEU* 1.3 79.6 - - - +
1055B GLU* 1.3 59.4 + - + +
1057B GLU* 4.3 0.3 - - - +
1058B SER* 2.7 43.9 + - - -
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Residues in contact with GLU1055 (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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1036B TYR* 2.7 41.7 + - + +
1051B LYS* 2.9 41.8 + - + +
1054B LYS* 1.3 80.2 - - + +
1056B ALA* 1.4 64.3 + - - +
1058B SER* 3.3 5.6 + - - -
1059B PHE* 3.1 11.6 + - - +
1100B ARG* 3.0 31.6 + - - +
1102B ASP* 4.2 8.0 - - - +
1104B ARG* 2.7 26.1 + - - +
1114B GLN* 4.9 1.0 + - - -
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Residues in contact with ALA1056 (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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958B TRP* 5.1 5.6 - - + -
985B ASN* 3.7 2.9 - - + +
1036B TYR* 3.9 12.5 - - + -
1052B VAL 2.7 22.7 + - - +
1053B LEU* 4.0 3.6 - - - +
1055B GLU* 1.4 73.9 - - - +
1057B GLU* 1.3 62.2 + - - +
1059B PHE 3.4 2.6 + - - -
1063B SER* 2.6 35.1 + - - +
1065B VAL* 3.8 26.5 - - + -
3238B CA 2.9 11.6 - - - -
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Residues in contact with GLU1057 (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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828B PHE* 3.4 26.8 - - + -
831B ARG* 3.2 31.1 + - - -
920B PRO* 4.7 5.4 - - - +
954B LYS* 4.9 5.5 + - - -
955B LYS 4.7 1.0 - - - +
956B SER* 2.6 33.5 + - - +
958B TRP* 3.9 12.1 - - + -
983B ASP* 4.2 7.3 - - - +
985B ASN* 3.4 12.4 + - - +
1053B LEU 2.9 19.5 + - - +
1054B LYS 4.3 0.7 - - - +
1056B ALA* 1.3 80.0 - - - +
1058B SER* 1.3 65.6 + - - +
1059B PHE 3.4 1.9 + - - +
3238B CA 3.5 9.2 - - - -
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Residues in contact with SER1058 (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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1054B LYS* 2.7 31.9 + - - +
1055B GLU* 3.3 5.4 + - - -
1057B GLU* 1.3 83.3 - - - +
1059B PHE* 1.3 61.9 + - - +
1060B PRO* 3.2 9.9 - - - +
1104B ARG* 3.0 19.5 + - - -
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Residues in contact with PHE1059 (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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983B ASP* 3.6 4.9 - - - +
1034B TYR 3.4 23.6 - - - -
1036B TYR* 3.7 13.5 - - + -
1055B GLU 3.1 18.5 + - - +
1056B ALA 3.5 7.9 - - - +
1057B GLU 3.3 1.1 - - - +
1058B SER* 1.3 76.5 - - - +
1060B PRO* 1.3 69.1 - - + +
1061B GLY* 3.0 28.1 + - - -
1062B PRO 3.2 28.7 - - - -
1063B SER* 3.8 2.9 - - - +
1102B ASP* 4.1 3.1 - - - -
1103B PRO* 3.8 23.1 - - + -
1104B ARG* 3.4 27.6 - - - +
1175B PHE* 3.7 34.1 - + - -
3238B CA 2.7 23.6 - - - -
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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