Contacts of the strand formed by residues 1153 - 1166 (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 TYR1153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008B ILE* 3.0 50.5 + - + +
1085B ASP* 2.4 27.7 + - - -
1151B PHE* 3.7 1.6 - - - +
1152B HIS* 1.3 101.6 + + + +
1154B PHE* 1.4 80.7 + - - +
1250B ASN* 3.7 21.3 - - - +
1252B LYS* 4.1 11.0 - - + -
1253B ALA* 3.5 22.2 - - + +
1258B LYS* 3.8 25.9 - - + -
1259B ALA* 3.0 28.6 + - - +
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Residues in contact with PHE1154 (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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885B HIS* 5.5 0.4 - - - -
954B THR* 4.8 2.7 - - + -
956B PHE* 4.5 9.9 - + - -
958B GLN* 3.3 36.1 - - + -
959B LYS 4.9 4.0 - - - -
960B LEU* 4.1 22.2 - - + -
961B GLU 6.1 1.3 - - - -
1005B LYS* 4.2 26.7 - - + -
1006B PHE 3.4 6.3 - - - +
1007B GLY* 3.5 32.8 - - - -
1008B ILE 4.5 0.2 - - - +
1151B PHE* 4.2 9.9 - + + -
1152B HIS 6.0 0.4 - - - -
1153B TYR* 1.4 88.1 - - - +
1155B SER* 1.4 61.0 + - - +
1156B TYR* 3.3 38.0 + - + +
1258B LYS* 3.3 22.3 - - - -
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Residues in contact with SER1155 (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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1004B THR 3.9 0.3 - - - +
1005B LYS* 3.2 6.8 - - - +
1006B PHE* 3.0 34.1 + - - +
1008B ILE* 3.6 13.8 - - - +
1154B PHE* 1.4 72.1 - - - +
1156B TYR* 1.3 63.1 + - - +
1181B MET* 3.6 16.5 - - - +
1182B ASP 3.3 16.9 + - - -
1258B LYS* 4.5 7.9 - - - -
1259B ALA 4.0 11.1 + - - -
1260B VAL* 5.5 0.5 - - - +
1263B PRO* 3.6 27.8 - - - +
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Residues in contact with TYR1156 (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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960B LEU* 4.2 6.2 - - - +
961B GLU 4.6 5.5 + - - -
962B GLY 4.4 10.1 - - - -
963B PHE* 3.7 37.2 - + - -
964B THR* 3.3 33.0 - - - +
965B LEU* 3.9 28.9 - - + +
968B CYS* 4.7 2.0 - - - -
1004B THR 3.3 6.7 - - - -
1005B LYS* 3.8 30.5 - - + -
1154B PHE* 3.3 45.8 + - + +
1155B SER* 1.3 73.4 + - - +
1157B GLY* 1.3 59.4 - - - +
1181B MET* 3.7 11.4 - - - +
1182B ASP* 3.0 35.1 + - + +
1258B LYS* 5.2 1.1 - - - -
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Residues in contact with GLY1157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965B LEU* 3.9 3.7 - - - +
968B CYS* 4.4 5.4 - - - -
1003B PRO 3.6 0.2 - - - -
1004B THR* 3.1 28.5 + - - +
1156B TYR* 1.3 79.4 - - - +
1158B VAL* 1.3 74.8 - - - +
1180B VAL 3.5 11.2 - - - -
1181B MET* 3.8 12.3 - - - -
1267B LEU* 4.0 6.3 - - - -
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Residues in contact with VAL1158 (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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965B LEU* 4.3 9.0 - - + -
968B CYS* 4.5 11.9 - - + +
969B TRP* 4.1 24.5 - - + +
972B CYS* 4.1 15.2 - - + -
1001B ILE* 4.1 22.9 - - + -
1002B ILE 3.3 9.4 - - - +
1003B PRO* 3.4 24.9 - - + -
1157B GLY* 1.3 83.4 - - - +
1159B ALA* 1.3 67.2 + - - +
1178B ASP 3.7 0.7 - - - +
1179B ILE* 3.3 5.4 - - - +
1180B VAL* 3.1 32.5 + - - +
1267B LEU* 3.6 8.1 - - - +
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Residues in contact with ALA1159 (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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972B CYS* 4.9 0.2 - - - -
1000B CYS 3.6 0.9 - - - +
1001B ILE* 3.2 5.2 - - - +
1002B ILE* 3.1 28.7 + - + +
1158B VAL* 1.3 83.9 - - - +
1160B CYS* 1.3 62.7 + - - +
1177B THR* 5.5 0.9 - - + -
1178B ASP 3.2 6.5 - - - +
1179B ILE* 4.4 9.2 - - + -
1200B PHE* 4.8 3.1 - - + -
1267B LEU* 3.6 42.8 - - + +
1270B SER* 4.0 7.9 - - - +
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Residues in contact with CYS1160 (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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972B CYS* 4.3 9.0 - - - -
976B SER* 3.8 21.5 - - - -
978B TYR* 4.0 22.0 - - - -
981B ARG* 4.3 8.4 + - - -
999B LEU* 4.1 15.3 - - - -
1000B CYS 3.0 11.4 - - - +
1001B ILE* 4.1 12.1 - - + -
1159B ALA* 1.3 78.3 - - - +
1161B SER* 1.4 60.6 + - - +
1176B ARG 4.0 0.5 - - - +
1177B THR* 3.3 3.6 - - - +
1178B ASP* 2.8 41.6 + - + +
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Residues in contact with SER1161 (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* 5.3 0.2 - - - -
999B LEU* 4.2 5.2 - - - -
1000B CYS 3.1 27.1 + - - +
1160B CYS* 1.4 71.8 - - - +
1162B GLU* 1.3 62.1 + - - +
1163B VAL* 5.2 0.2 - - - -
1176B ARG 3.2 6.7 - - - -
1177B THR* 3.2 20.0 + - - +
1270B SER* 2.9 31.6 + - - -
1271B ILE* 3.3 22.6 - - - +
1274B ALA* 3.5 10.7 - - - +
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Residues in contact with GLU1162 (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 44.4 + - - +
984B GLU* 3.5 12.3 - - - +
985B VAL* 3.7 23.0 - - + +
997B ARG* 3.1 27.3 + - - -
998B GLY 3.1 11.7 - - - +
999B LEU* 4.2 8.2 - - + +
1161B SER* 1.3 73.6 - - - +
1163B VAL* 1.3 64.8 + - - +
1174B ASN* 4.0 1.2 - - - +
1175B LEU* 3.4 38.5 + - + +
1176B ARG* 3.1 21.4 + - - +
1271B ILE* 5.9 0.2 - - - +
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Residues in contact with VAL1163 (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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997B ARG* 3.5 2.4 - - - +
998B GLY 2.9 25.8 + - - +
1162B GLU* 1.3 74.0 - - - +
1164B GLU* 1.3 60.1 + - - +
1165B ILE* 5.4 2.2 - - + -
1172B HIS* 4.4 3.6 - - + -
1173B LYS 3.8 11.0 - - - +
1174B ASN* 3.5 24.5 - - - +
1175B LEU* 4.2 5.4 - - - +
1271B ILE* 4.0 20.2 - - + +
1274B ALA* 3.5 35.9 - - + +
1275B ILE* 3.8 18.4 - - + -
1278B ALA* 5.1 4.0 - - + +
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Residues in contact with GLU1164 (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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988B PHE* 3.7 14.5 - - + -
995B LYS* 3.4 27.3 + - - +
996B LYS 3.4 10.3 - - - +
997B ARG* 3.3 43.9 + - + -
1163B VAL* 1.3 72.6 - - - +
1165B ILE* 1.4 68.0 + - - +
1172B HIS* 3.4 2.2 - - - +
1173B LYS* 3.1 56.3 + - + +
1175B LEU* 4.1 17.2 - - + +
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Residues in contact with ILE1165 (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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995B LYS* 3.3 24.7 - - - +
996B LYS* 2.9 28.8 + - + +
1163B VAL* 4.5 2.0 + - + -
1164B GLU* 1.4 75.4 - - - +
1166B ASP* 1.3 64.0 + - - +
1167B CYS* 4.5 18.2 - - + -
1171B ASP 3.7 5.8 - - - +
1172B HIS* 4.1 14.6 - - + -
1275B ILE* 5.0 11.4 - - + +
1278B ALA* 3.7 34.0 - - + +
1279B ILE* 4.3 7.6 - - + +
1282B ALA* 5.3 0.2 - - + -
1306B ILE* 4.5 22.2 - - + -
1310B CYS* 4.6 11.2 - - - -
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Residues in contact with ASP1166 (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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518B LYS* 3.2 27.2 + - - -
994B TRP 3.9 7.7 - - - +
995B LYS* 4.3 25.0 + - - +
1165B ILE* 1.3 76.5 - - - +
1167B CYS* 1.3 57.8 + - - +
1168B LEU* 3.2 21.7 + - - +
1169B THR* 3.0 23.5 + - - +
1170B GLY* 2.9 30.1 + - - -
1171B ASP* 3.0 20.8 + - + +
1306B ILE* 5.6 0.3 - - - +
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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