Contacts of the strand formed by residues 1153 - 1166 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008A ILE* 3.0 47.7 + - + +
1085A ASP* 2.7 27.5 + - - -
1151A PHE* 3.8 2.8 - - - +
1152A HIS* 1.3 100.4 + + + +
1154A PHE* 1.4 86.7 + - - +
1250A ASN* 3.8 20.6 - - - +
1252A LYS* 4.5 9.9 - - + -
1253A ALA* 3.7 20.6 - - + +
1258A LYS* 3.8 21.0 - - + -
1259A ALA* 3.0 32.6 + - - +
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Residues in contact with PHE1154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885A HIS* 5.4 0.2 - - - -
954A THR* 4.7 3.1 - - + -
956A PHE* 4.3 10.8 - + - -
958A GLN* 3.1 39.5 - - + -
959A LYS 4.9 4.3 - - - -
960A LEU* 4.0 18.8 - - + -
1005A LYS* 4.0 31.4 - - + -
1006A PHE 3.3 7.6 - - - +
1007A GLY* 3.5 29.4 - - - -
1008A ILE 4.5 0.2 - - - +
1151A PHE* 4.3 8.7 - + + -
1153A TYR* 1.4 88.6 - - - +
1155A SER* 1.4 62.3 + - - +
1156A TYR* 3.4 41.6 - + + +
1258A LYS* 3.2 24.5 - - - +
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Residues in contact with SER1155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004A THR* 4.5 0.6 - - - -
1005A LYS* 3.3 6.1 - - - +
1006A PHE* 2.9 31.0 + - - +
1008A ILE* 3.7 14.8 - - - +
1154A PHE* 1.4 72.7 - - - +
1156A TYR* 1.3 60.0 + - - +
1181A MET* 3.5 14.6 - - - +
1182A ASP 3.2 21.0 + - - -
1258A LYS* 4.5 7.6 - - - +
1259A ALA 3.9 12.4 + - - -
1263A PRO* 3.5 27.8 - - - +
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Residues in contact with TYR1156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960A LEU* 3.8 6.9 - - - +
961A GLU 4.6 6.6 + - - -
962A GLY 4.4 9.9 - - - -
963A PHE* 3.8 37.3 - + - +
964A THR* 3.2 34.5 - - - +
965A LEU* 3.7 25.6 - - + +
968A CYS* 4.7 1.1 - - - -
1004A THR* 3.3 7.2 - - - -
1005A LYS* 3.7 30.1 - - + -
1154A PHE* 3.4 47.7 + - + +
1155A SER* 1.3 72.2 + - - +
1157A GLY* 1.3 59.1 + - - +
1181A MET* 3.3 15.1 - - - +
1182A ASP* 3.2 33.2 + - + +
1258A LYS* 4.9 2.2 - - - -
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Residues in contact with GLY1157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A LEU* 3.8 3.4 - - - +
968A CYS* 4.3 7.4 - - - -
1004A THR* 3.0 35.0 + - - +
1156A TYR* 1.3 77.0 - - - +
1158A VAL* 1.3 70.8 + - - +
1180A VAL 3.5 14.6 - - - -
1181A MET* 4.4 10.1 - - - -
1267A LEU* 4.2 1.1 - - - -
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Residues in contact with VAL1158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A LEU* 4.2 12.8 - - + -
968A CYS* 4.4 16.4 - - + +
969A TRP* 4.1 24.7 - - + +
972A CYS* 3.8 28.8 - - + -
1001A ILE* 4.1 13.5 - - + -
1002A ILE 3.3 14.6 - - - +
1003A PRO* 3.8 9.9 - - + -
1157A GLY* 1.3 81.1 - - - +
1159A ALA* 1.3 64.4 + - - +
1178A ASP 3.8 1.4 - - - +
1179A ILE* 3.5 2.6 - - - -
1180A VAL* 3.1 33.5 + - - +
1267A LEU* 3.6 8.7 - - - +
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Residues in contact with ALA1159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000A CYS 3.5 1.4 - - - +
1001A ILE* 3.3 7.3 - - - +
1002A ILE* 2.9 32.3 + - + +
1158A VAL* 1.3 77.0 - - - +
1160A CYS* 1.3 62.6 + - - +
1161A SER* 5.3 0.2 - - - +
1177A THR* 5.5 0.9 - - + -
1178A ASP 3.4 5.2 - - - +
1179A ILE* 4.4 8.7 - - + -
1200A PHE* 5.0 3.1 - - + -
1267A LEU* 3.7 34.3 - - + +
1270A SER* 3.8 18.0 - - - +
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Residues in contact with CYS1160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972A CYS* 4.3 7.9 - - - -
976A SER* 4.2 21.3 - - - +
978A TYR* 4.2 13.7 - - - -
981A ARG* 4.9 5.4 + - - -
999A LEU* 4.0 22.0 - - - -
1000A CYS 3.2 16.8 - - - +
1001A ILE* 3.8 13.7 - - + -
1159A ALA* 1.3 78.6 - - - +
1161A SER* 1.4 56.6 + - - +
1176A ARG 3.8 0.5 - - - +
1177A THR* 2.9 9.3 - - - +
1178A ASP* 2.7 44.9 + - - +
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Residues in contact with SER1161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981A ARG* 5.3 0.4 - - - -
999A LEU* 3.5 8.3 - - - +
1000A CYS 3.0 31.7 + - - -
1160A CYS* 1.4 73.6 - - - +
1162A GLU* 1.4 62.9 + - - +
1163A VAL* 5.0 0.7 - - - -
1176A ARG 3.0 4.9 - - - -
1177A THR* 3.3 18.2 + - - +
1200A PHE* 4.7 0.3 - - - -
1270A SER* 2.9 26.7 + - - -
1271A ILE* 3.6 29.3 + - - +
1274A ALA* 3.8 4.8 - - - +
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Residues in contact with GLU1162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981A ARG* 2.7 46.3 + - - +
984A GLU* 3.7 8.5 - - - +
985A VAL* 3.5 25.2 - - + +
997A ARG* 3.3 24.0 + - - -
998A GLY 3.2 14.1 - - - +
999A LEU* 4.3 7.9 - - + -
1161A SER* 1.4 71.6 - - - +
1163A VAL* 1.3 71.0 + - - +
1174A ASN* 3.8 2.1 - - - +
1175A LEU* 3.3 36.5 + - + +
1176A ARG* 2.8 23.4 + - - +
1271A ILE* 6.0 0.3 - - - +
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Residues in contact with VAL1163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997A ARG* 3.3 5.2 - - - +
998A GLY 2.8 31.7 + - - +
1161A SER* 5.0 1.6 - - - -
1162A GLU* 1.3 81.1 - - - +
1164A GLU* 1.3 64.9 + - - +
1165A ILE* 5.1 5.4 - - + -
1172A HIS* 4.5 3.1 - - + -
1173A LYS 3.8 11.4 - - - +
1174A ASN* 3.8 18.8 - - - +
1175A LEU* 4.2 6.8 - - - +
1271A ILE* 4.0 18.6 - - + +
1274A ALA* 3.7 31.2 - - + +
1275A ILE* 3.7 25.4 - - + -
1278A ALA* 5.3 1.3 - - + -
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Residues in contact with GLU1164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988A PHE* 3.5 15.1 - - + -
995A LYS* 3.4 24.3 + - + +
996A LYS 3.2 12.3 - - - +
997A ARG* 3.2 48.4 + - + +
1163A VAL* 1.3 73.0 - - - +
1165A ILE* 1.3 68.6 + - - +
1172A HIS* 3.3 3.4 - - - +
1173A LYS* 3.0 61.1 + - + +
1175A LEU* 4.0 15.2 - - + +
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Residues in contact with ILE1165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995A LYS* 3.5 8.8 - - - +
996A LYS* 3.0 36.3 + - + +
997A ARG* 4.9 0.2 - - - +
1163A VAL* 5.1 5.2 - - + -
1164A GLU* 1.3 79.9 - - - +
1166A ASP* 1.3 62.7 + - - +
1167A CYS* 4.7 7.9 - - + -
1171A ASP 3.8 6.1 - - - +
1172A HIS* 4.0 13.9 - - + -
1275A ILE* 5.1 10.1 - - + -
1278A ALA* 3.4 37.9 - - + +
1279A ILE* 3.9 11.9 - - + +
1282A ALA* 5.4 0.7 - - + -
1306A ILE* 4.9 20.9 - - + -
1310A CYS* 4.8 13.9 - - - -
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Residues in contact with ASP1166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A LYS* 3.4 25.2 + - - -
994A TRP 3.7 8.2 - - - +
995A LYS* 4.2 27.1 + - - +
1165A ILE* 1.3 73.1 - - - +
1167A CYS* 1.3 59.0 + - - +
1168A LEU* 3.0 20.6 + - - +
1169A THR* 3.4 19.0 + - - +
1170A GLY* 3.0 25.5 + - - -
1171A ASP* 3.1 20.4 + - + +
1306A ILE* 5.8 0.2 - - - +
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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