Contacts of the strand formed by residues 1235 - 1249 (chain B) in PDB entry 5J67
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 ILE1235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142B VAL* 4.7 11.2 - - + +
1144B ASP* 2.8 40.8 + - + +
1184B ARG* 3.4 34.3 - - - +
1229B LEU 3.7 7.2 - - - +
1230B LEU* 3.7 37.2 - - + -
1232B SER* 4.1 6.5 - - - -
1234B TYR* 1.3 76.3 - - - +
1236B GLN* 1.3 67.7 + - - +
1280B ASN* 3.7 36.8 - - + +
1281B THR 3.4 4.3 - - - +
1282B TYR* 4.0 6.7 - - + -
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Residues in contact with GLN1236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142B VAL 5.6 0.9 - - - -
1234B TYR* 4.9 6.7 - - + -
1235B ILE* 1.3 83.9 - - - +
1237B SER* 1.3 62.4 + - - +
1280B ASN* 3.4 4.2 - - - -
1281B THR* 2.6 55.5 + - + +
1286B LYS* 4.0 49.8 + - - +
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Residues in contact with SER1237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A ASN* 2.8 45.2 + - - +
752A PHE* 5.4 1.7 - - - -
1141B LEU* 4.3 13.8 - - - +
1142B VAL 3.8 14.6 + - - -
1143B ASP* 5.4 1.0 - - - -
1236B GLN* 1.3 75.4 - - - +
1238B ARG* 1.3 61.2 + - - +
1239B VAL* 5.9 2.0 - - - -
1279B ARG 3.3 7.6 + - - -
1280B ASN* 3.7 15.1 + - - -
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Residues in contact with ARG1238 (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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750A ASN* 4.5 0.7 - - - -
752A PHE* 3.8 44.0 - - + +
753A ILE 5.1 3.8 + - - -
754A LYS 5.8 2.0 + - - -
1026B GLU* 6.0 0.2 + - - -
1237B SER* 1.3 74.5 - - - +
1239B VAL* 1.3 64.9 + - - +
1240B GLU* 3.6 37.7 + - - +
1277B MET 4.1 0.5 - - - +
1278B ALA* 3.8 0.3 - - - +
1279B ARG* 3.0 64.5 + - + +
1280B ASN 5.6 0.4 + - - -
1281B THR* 3.8 24.8 + - - +
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Residues in contact with VAL1239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A ASN* 2.9 35.8 + - + +
751A ASN* 4.3 8.8 - - - +
752A PHE* 3.1 30.7 + - - +
1237B SER* 5.2 2.0 - - - +
1238B ARG* 1.3 76.5 - - - +
1240B GLU* 1.3 69.8 + - - +
1241B THR* 3.9 5.4 + - - +
1276B SER* 4.2 19.5 - - - +
1277B MET 3.8 8.5 - - - +
1278B ALA* 4.4 15.5 - - + +
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Residues in contact with GLU1240 (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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752A PHE 4.3 5.6 - - - -
753A ILE 3.9 17.6 - - - +
754A LYS* 5.8 1.2 - - - +
1024B THR 5.8 0.2 - - - +
1238B ARG* 3.6 32.0 + - - +
1239B VAL* 1.3 76.7 - - - +
1241B THR* 1.3 61.7 + - - +
1242B VAL* 3.9 24.4 - - + +
1276B SER* 3.5 0.5 - - - -
1277B MET* 2.7 45.8 + - + +
1279B ARG* 3.1 33.4 + - - +
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Residues in contact with THR1241 (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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751A ASN* 5.4 2.9 + - - -
752A PHE 4.3 8.7 + - - -
753A ILE* 5.2 12.7 + - - +
764A LEU* 5.3 12.1 - - + +
765A VAL 4.5 15.4 - - - +
767A PRO* 5.0 8.3 - - - +
1239B VAL* 3.9 7.4 + - - +
1240B GLU* 1.3 77.3 + - - +
1242B VAL* 1.3 65.9 + - - +
1243B PRO* 4.8 0.5 - - - +
1274B MET* 4.1 27.9 - - + +
1275B VAL 3.4 11.7 - - - +
1276B SER* 4.0 12.9 - - - -
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Residues in contact with VAL1242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024B THR 6.0 0.9 - - - +
1025B VAL* 4.6 16.6 - - + -
1104B ILE* 6.3 0.2 - - + -
1240B GLU* 3.9 28.9 - - + +
1241B THR* 1.3 79.5 - - - +
1243B PRO* 1.3 75.9 - - + +
1274B MET* 3.4 6.6 - - - -
1275B VAL* 2.9 39.3 + - + +
1277B MET* 3.6 37.2 - - + -
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Residues in contact with PRO1243 (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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767A PRO* 4.8 10.5 - - + -
1025B VAL* 5.3 6.8 - - - +
1241B THR 4.8 0.4 - - - +
1242B VAL* 1.3 96.7 - - + +
1244B TYR* 1.3 62.4 + - - +
1272B GLU* 3.7 31.9 - - - +
1273B LYS 3.2 8.3 - - - +
1274B MET* 3.5 15.9 - - + -
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Residues in contact with TYR1244 (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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1087B ALA* 3.4 24.2 - - + +
1104B ILE* 3.6 31.2 - - + -
1106B LYS* 2.3 29.0 + - + -
1243B PRO* 1.3 75.1 - - - +
1245B LEU* 1.3 71.6 + - - +
1246B PHE* 3.6 11.0 + - + -
1272B GLU* 3.8 4.9 - - - -
1273B LYS* 3.0 67.6 + - + +
1274B MET 3.8 9.7 + - - -
1275B VAL* 3.2 33.7 - - + -
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Residues in contact with LEU1245 (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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771A GLU* 5.6 5.6 - - - +
1087B ALA* 5.0 0.3 - - - +
1088B ALA 3.0 18.9 + - - +
1089B GLY* 4.0 5.5 - - - -
1090B ARG 3.2 33.7 - - - +
1091B SER* 4.4 11.0 - - - +
1102B SER* 5.3 5.1 + - - +
1104B ILE* 5.7 0.3 - - - +
1244B TYR* 1.3 82.0 - - - +
1246B PHE* 1.3 58.6 + - - +
1247B CYS* 3.8 18.4 - - - -
1270B CYS* 4.3 13.7 - - + -
1271B GLU 3.9 11.0 - - - +
1272B GLU* 4.8 11.9 - - + +
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Residues in contact with PHE1246 (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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1077B LEU 5.3 5.6 - - - -
1081B LEU* 4.0 3.8 - - + -
1083B THR* 3.4 30.7 - - + -
1087B ALA* 3.7 23.1 - - + -
1088B ALA 3.5 2.9 - - - -
1244B TYR* 3.6 8.9 + + + -
1245B LEU* 1.3 71.8 - - - +
1247B CYS* 1.3 67.5 + - - +
1248B ARG* 3.3 51.6 - - + -
1269B THR 3.8 1.9 - - - +
1270B CYS* 3.8 0.2 - - - -
1271B GLU* 2.8 47.8 + - + +
1273B LYS* 3.8 39.5 - - + -
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Residues in contact with CYS1247 (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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1077B LEU 4.1 5.0 - - - +
1078B LEU* 3.4 29.5 - - + +
1088B ALA 3.0 14.1 + - - +
1089B GLY* 3.8 11.7 - - - -
1090B ARG 3.9 2.5 - - - -
1245B LEU* 3.8 19.7 - - - -
1246B PHE* 1.3 80.3 - - - +
1248B ARG* 1.3 65.2 + - - +
1268B ILE* 4.3 9.2 - - + -
1269B THR 3.6 4.0 - - - -
1270B CYS* 2.0 48.9 - - - -
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Residues in contact with ARG1248 (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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1077B LEU 5.6 0.4 - - - +
1078B LEU* 3.3 17.0 - - - +
1079B SER 6.1 0.4 - - - +
1081B LEU* 3.5 41.8 - - + +
1083B THR* 5.0 1.4 + - - -
1246B PHE* 3.3 36.3 + - + -
1247B CYS* 1.3 76.8 - - - +
1249B SER* 1.3 64.1 + - - +
1268B ILE* 3.3 8.2 - - - -
1269B THR* 3.0 44.7 + - + +
1273B LYS* 5.2 3.8 - - - +
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Residues in contact with SER1249 (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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1074B ALA 5.4 0.4 - - - -
1078B LEU* 3.3 18.7 + - - +
1079B SER* 4.1 20.5 - - - -
1248B ARG* 1.3 73.9 - - - +
1250B GLU* 1.3 63.0 + - - +
1251B GLU 3.1 23.9 + - - -
1252B VAL* 4.8 1.9 - - - -
1266B THR* 3.4 18.3 - - - +
1267B LYS 3.9 4.5 - - - -
1268B ILE* 4.2 3.1 - - - -
1269B THR* 5.1 1.1 - - - -
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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