Contacts of the strand formed by residues 1234 - 1249 (chain A) in PDB entry 5J68
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 TYR1234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144A ASP* 3.9 9.4 - - - +
1184A ARG* 4.0 0.2 - - - +
1232A SER* 3.5 1.9 - - - -
1233A ALA* 1.3 99.7 - - + +
1235A ILE* 1.3 65.5 + - - +
1236A GLN* 4.8 11.9 - - + -
1281A THR 3.5 4.9 - - - +
1282A TYR* 3.5 2.9 - - - -
1283A GLY 3.1 28.6 + - - +
1284A GLU 3.9 9.0 - - - -
1285A SER* 4.0 24.2 - - - -
1286A LYS* 4.4 32.1 - - + -
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Residues in contact with ILE1235 (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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1142A VAL* 4.1 17.0 - - + +
1144A ASP* 3.3 31.4 + - + +
1184A ARG* 3.7 34.8 - - - +
1229A LEU 4.7 1.1 - - - +
1230A LEU* 3.6 36.1 - - + -
1232A SER* 4.8 1.3 - - - -
1234A TYR* 1.3 77.9 - - - +
1236A GLN* 1.3 64.1 + - - +
1280A ASN* 3.6 39.0 - - + +
1281A THR 3.4 3.1 - - - +
1282A TYR* 4.0 15.7 - - + -
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Residues in contact with GLN1236 (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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1234A TYR* 4.8 7.2 - - + +
1235A ILE* 1.3 81.9 - - - +
1237A SER* 1.3 63.6 + - - +
1280A ASN* 3.3 3.8 - - - -
1281A THR* 2.5 56.5 + - - +
1286A LYS* 4.0 51.0 + - - +
1288A ARG 5.9 0.8 + - - -
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Residues in contact with SER1237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141A LEU* 3.8 15.2 - - - +
1142A VAL 4.4 9.7 + - - -
1143A ASP* 5.9 0.2 - - - -
1236A GLN* 1.3 76.8 - - - +
1238A ARG* 1.3 60.5 + - - +
1239A VAL* 4.4 5.9 + - - +
1279A ARG 3.3 8.7 - - - -
1280A ASN* 3.7 14.7 + - - -
1281A THR* 4.7 0.2 - - - -
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Residues in contact with ARG1238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A GLU* 5.0 8.9 + - - -
1237A SER* 1.3 75.0 - - - +
1239A VAL* 1.3 64.1 + - - +
1240A GLU* 3.8 35.7 + - - +
1277A MET 4.0 0.9 - - - +
1278A ALA* 3.8 0.2 - - - -
1279A ARG* 3.0 65.5 + - + +
1280A ASN 5.7 0.2 + - - -
1281A THR* 3.8 22.6 + - - +
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Residues in contact with VAL1239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1237A SER* 5.1 6.7 - - - +
1238A ARG* 1.3 79.5 - - - +
1240A GLU* 1.3 69.8 + - - +
1241A THR* 4.0 6.1 + - - +
1276A SER* 4.4 17.9 - - - -
1277A MET 3.7 7.0 - - - +
1278A ALA* 4.4 15.9 - - + +
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Residues in contact with GLU1240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024A THR 5.2 4.7 - - - +
1025A VAL* 6.0 0.6 - - - -
1026A GLU* 5.4 1.4 + - - +
1238A ARG* 3.8 29.8 + - - +
1239A VAL* 1.3 75.3 - - - +
1241A THR* 1.3 60.8 + - - +
1242A VAL* 3.9 23.0 - - + +
1276A SER* 3.4 2.8 - - - -
1277A MET* 2.6 47.9 + - + +
1279A ARG* 3.1 33.5 + - - +
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Residues in contact with THR1241 (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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1239A VAL* 4.0 8.0 + - - +
1240A GLU* 1.3 79.3 + - - +
1242A VAL* 1.3 65.5 + - - +
1243A PRO* 4.7 1.2 - - - +
1274A MET* 4.2 27.0 - - + +
1275A VAL 3.3 11.7 - - - +
1276A SER* 4.1 12.2 - - - +
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Residues in contact with VAL1242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024A THR 4.9 6.5 - - - +
1025A VAL* 4.2 24.0 - - + -
1240A GLU* 3.9 28.7 - - + +
1241A THR* 1.3 79.7 - - - +
1243A PRO* 1.3 72.4 - - + +
1274A MET* 3.4 6.4 - - - -
1275A VAL* 2.9 33.8 + - + +
1277A MET* 3.7 37.2 - - + -
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Residues in contact with PRO1243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025A VAL* 4.6 11.4 - - - +
1241A THR 4.7 0.7 - - - +
1242A VAL* 1.3 95.4 - - + +
1244A TYR* 1.3 63.8 + - - +
1272A GLU* 3.7 28.7 - - - +
1273A LYS 3.1 12.6 - - - +
1274A MET* 3.6 14.4 - - + -
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Residues in contact with TYR1244 (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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1087A ALA* 3.8 22.6 - - + +
1104A ILE* 3.6 35.7 - - + -
1106A LYS* 2.7 26.4 + - - -
1243A PRO* 1.3 78.2 - - - +
1245A LEU* 1.3 69.9 + - - +
1246A PHE* 3.6 10.4 + + + -
1272A GLU* 3.8 3.6 - - - -
1273A LYS* 3.0 72.2 + - + +
1274A MET 3.6 8.9 + - - -
1275A VAL* 3.4 30.7 - - + -
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Residues in contact with LEU1245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087A ALA 5.0 0.5 - - - -
1088A ALA 3.0 18.6 + - - +
1089A GLY* 4.0 5.0 - - - -
1090A ARG 3.2 35.7 - - - +
1091A SER* 4.0 13.9 - - - +
1102A SER* 4.9 8.4 + - - +
1104A ILE* 5.5 0.3 - - - +
1244A TYR* 1.3 80.7 - - - +
1246A PHE* 1.3 58.6 + - - +
1247A CYS* 3.7 18.4 - - - -
1270A CYS* 4.3 13.5 - - + -
1271A GLU 3.9 11.7 - - - +
1272A GLU* 4.9 11.2 - - + +
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Residues in contact with PHE1246 (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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1077A LEU 6.0 0.4 - - - -
1081A LEU* 4.5 4.5 - - + -
1083A THR* 3.5 31.2 - - + -
1087A ALA* 3.5 22.4 - - + -
1088A ALA 3.5 2.2 - - - -
1244A TYR* 3.6 9.2 + + + -
1245A LEU* 1.3 72.3 - - - +
1247A CYS* 1.3 61.6 + - - +
1248A ARG* 3.7 37.2 - - + -
1269A THR 3.9 1.7 - - - +
1270A CYS* 3.6 0.3 - - - -
1271A GLU* 2.8 50.5 + - + +
1273A LYS* 4.0 43.1 - - + -
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Residues in contact with CYS1247 (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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1077A LEU 4.3 4.3 - - - +
1078A LEU* 3.6 18.0 - - + +
1088A ALA 3.0 15.4 + - - +
1089A GLY* 3.5 24.5 - - - -
1090A ARG 3.6 6.3 - - - +
1245A LEU* 3.7 10.1 - - - -
1246A PHE* 1.3 76.8 - - - +
1248A ARG* 1.3 71.7 + - - +
1268A ILE* 4.3 10.8 - - + -
1269A THR 3.5 4.3 - - - -
1270A CYS* 2.0 48.2 - - - -
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Residues in contact with ARG1248 (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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1077A LEU 3.1 23.2 + - - -
1078A LEU* 3.3 14.9 + - - -
1079A SER 2.9 28.3 + - - -
1080A GLY 3.4 10.9 + - - +
1081A LEU* 3.4 39.8 - - - +
1082A GLY* 5.7 0.4 - - - -
1083A THR* 5.4 1.0 - - - +
1246A PHE* 3.7 35.8 - - + -
1247A CYS* 1.3 82.1 - - - +
1249A SER* 1.3 63.6 + - - +
1268A ILE* 3.2 8.3 - - - -
1269A THR* 2.9 41.7 + - + +
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Residues in contact with SER1249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074A ALA 5.4 0.4 - - - -
1078A LEU* 3.0 32.7 + - - +
1079A SER* 4.0 13.5 + - - -
1248A ARG* 1.3 73.1 - - - +
1250A GLU* 1.3 63.3 + - - +
1251A GLU 3.2 23.2 + - - -
1252A VAL* 4.9 1.7 - - - -
1266A THR* 3.5 16.5 - - - +
1267A LYS 3.9 4.0 - - - -
1268A ILE* 4.1 3.4 - - - -
1269A THR* 5.2 0.9 - - - -
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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
------------------------------------------------------------
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