Contacts of the helix formed by residues 1082 - 1093 (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 LYS1082 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1219A THR* 3.9 11.0 - - - +
1221A GLU* 2.5 33.9 + - - +
753B ASP* 2.8 37.0 + - - +
1076B LEU* 4.1 4.7 - - + -
1078B LYS* 3.8 29.4 - - + +
1079B GLY 2.9 14.8 + - - +
1080B MET 2.9 1.4 - - - -
1081B GLY* 1.3 77.9 - - - +
1083B SER* 1.3 64.1 + - - +
1084B GLN 3.4 2.2 - - - -
1085B ASP* 3.1 23.2 + - + +
1086B VAL* 2.9 31.6 + - + +
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Residues in contact with SER1083 (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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750B ASN* 3.2 11.0 - - - +
814B GLY 3.2 12.3 + - - -
816B GLY* 5.3 0.7 - - - -
1070B THR* 2.8 36.3 + - - -
1076B LEU* 4.0 3.6 - - - +
1080B MET* 2.8 28.5 + - - +
1082B LYS* 1.3 76.5 - - - +
1084B GLN* 1.4 59.4 + - - +
1086B VAL* 3.1 2.8 + - - +
1087B MET* 2.8 40.3 + - - +
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Residues in contact with GLN1084 (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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698B VAL* 3.2 42.2 - - + +
750B ASN* 3.2 16.8 - - + +
754B ILE* 3.3 26.9 - - + -
819B PRO* 4.7 3.5 - - - +
1042B MET* 3.4 25.4 + - - +
1043B GLY* 3.0 42.5 - - - +
1046B LYS* 4.7 3.2 - - - +
1083B SER* 1.4 74.8 - - - +
1085B ASP* 1.3 57.7 + - - +
1087B MET* 3.3 17.2 + - - +
1088B ASN* 2.9 26.4 + - - +
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Residues in contact with ASP1085 (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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753B ASP* 4.0 17.7 + - - +
754B ILE* 4.2 6.9 - - + +
1082B LYS* 3.1 27.6 + - + +
1084B GLN* 1.3 82.3 - - - +
1086B VAL* 1.3 56.8 + - + +
1088B ASN* 3.3 15.3 + - - +
1089B THR* 2.9 40.3 + - - -
1092B LYS* 5.6 2.1 + - - -
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Residues in contact with VAL1086 (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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1068B TYR* 4.4 9.4 - - + +
1070B THR* 4.2 10.5 - - + -
1074B GLN* 5.7 0.2 - - - +
1076B LEU* 3.7 36.8 - - + -
1082B LYS* 2.9 27.0 + - + +
1083B SER 3.7 3.4 - - - +
1085B ASP* 1.3 72.8 - - + +
1087B MET* 1.3 55.9 + - - +
1089B THR* 3.3 5.5 + - - -
1090B ALA* 2.8 32.4 + - - +
1127B PHE* 3.6 22.3 - - + -
1130B ALA* 5.8 7.9 - - + +
1131B GLN* 4.7 6.5 - - + +
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Residues in contact with MET1087 (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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816B GLY* 4.0 19.1 - - - +
819B PRO* 5.6 3.8 - - + -
820B TYR* 4.0 12.3 - - + +
1041B SER* 2.8 28.4 + - - +
1042B MET* 4.1 2.9 - - + -
1043B GLY 3.6 19.5 - - - +
1044B TYR 4.2 0.9 - - - -
1068B TYR* 3.7 35.2 - - + +
1070B THR* 3.8 24.9 - - + +
1083B SER* 2.8 20.3 + - - +
1084B GLN* 3.5 27.1 - - - +
1086B VAL* 1.3 75.4 - - - +
1088B ASN* 1.3 63.7 + - - +
1090B ALA* 3.4 11.7 + - - +
1091B VAL* 3.5 9.0 + - - +
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Residues in contact with ASN1088 (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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1043B GLY 3.3 23.4 + - - +
1044B TYR* 3.3 29.9 + - - +
1084B GLN 2.9 10.0 + - - +
1085B ASP* 3.4 19.0 - - - +
1086B VAL 3.2 0.2 - - - -
1087B MET* 1.3 76.0 - - - +
1089B THR* 1.3 59.2 + - - +
1091B VAL* 3.1 6.1 + - - +
1092B LYS* 3.0 51.8 + - - +
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Residues in contact with THR1089 (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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1085B ASP* 2.9 25.0 + - - -
1086B VAL* 3.8 5.2 - - - -
1088B ASN* 1.3 74.2 - - - +
1090B ALA* 1.4 62.1 - - - +
1092B LYS* 4.3 17.9 + - + +
1093B SER* 2.7 32.9 + - - -
1123B SER* 3.9 21.3 - - - +
1126B GLU* 5.8 1.8 - - + -
1127B PHE* 3.8 29.4 - - + +
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Residues in contact with ALA1090 (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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1041B SER* 5.0 0.7 - - - +
1068B TYR* 4.1 17.7 - - + -
1086B VAL 2.8 20.9 + - - +
1087B MET 3.7 6.7 - - - +
1088B ASN 3.2 0.6 - - - -
1089B THR* 1.4 72.9 - - - +
1091B VAL* 1.3 58.5 + - - +
1093B SER* 3.0 14.8 + - - -
1095B TYR* 3.1 5.9 + - + +
1096B TRP* 2.8 38.4 + - + -
1127B PHE* 3.6 26.7 - - + -
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Residues in contact with VAL1091 (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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1041B SER* 3.3 32.8 - - - -
1044B TYR* 3.5 36.1 - - + -
1087B MET 3.5 1.8 + - - +
1088B ASN 3.1 1.9 + - - +
1089B THR 3.1 0.2 - - - -
1090B ALA* 1.3 75.4 - - - +
1092B LYS* 1.3 60.3 + - - +
1093B SER 3.1 1.8 - - - -
1094B GLY* 2.8 22.3 + - - -
1096B TRP* 3.3 24.1 - - + +
1097B PRO* 5.2 0.2 - - - +
1098B LEU* 3.8 7.2 - - + -
1117B SER* 3.3 34.0 + - - +
1118B LYS 4.7 5.7 - - - +
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Residues in contact with LYS1092 (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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1044B TYR* 3.9 13.2 - - + -
1085B ASP* 5.6 2.2 + - - -
1088B ASN* 3.0 50.6 + - - +
1089B THR* 4.3 13.5 + - - +
1091B VAL* 1.3 76.8 - - - +
1093B SER* 1.4 58.8 + - - +
1094B GLY 3.3 0.9 + - - -
1118B LYS* 4.1 17.3 - - - +
1119B ALA 4.0 3.8 - - - +
1120B PRO* 3.8 1.9 - - - +
1121B ASP* 3.0 46.8 + - + +
1123B SER* 5.1 0.9 - - - +
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Residues in contact with SER1093 (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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1089B THR 2.7 24.4 + - - -
1090B ALA* 3.0 12.0 + - - -
1092B LYS* 1.4 76.2 - - - +
1094B GLY* 1.3 56.5 + - - +
1095B TYR* 3.3 14.9 + - - +
1120B PRO* 3.3 18.4 - - - +
1121B ASP* 3.5 10.4 + - - -
1122B GLY 5.0 0.9 + - - -
1123B SER* 3.5 14.5 + - - +
1124B VAL* 3.7 28.5 + - - +
1127B PHE* 4.3 5.7 - - - -
1156B LEU* 3.6 9.9 - - - +
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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