Contacts of the strand formed by residues 1268 - 1283 (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 ILE1268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1078A LEU* 4.1 28.3 - - + -
1090A ARG* 3.4 49.8 - - + +
1247A CYS* 4.3 7.2 - - + -
1248A ARG 3.2 16.2 - - - +
1249A SER* 4.1 2.2 - - - -
1250A GLU* 4.3 4.7 - - - +
1266A THR* 3.4 14.6 + - + +
1267A LYS* 1.3 78.3 - - - +
1269A THR* 1.3 59.2 + - - +
1270A CYS* 3.7 25.9 + - - -
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Residues in contact with THR1269 (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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1246A PHE 3.9 2.1 - - - +
1247A CYS* 3.5 1.0 - - - -
1248A ARG* 2.9 39.8 + - + +
1249A SER 5.2 0.4 - - - -
1250A GLU* 3.2 33.3 + - + +
1268A ILE* 1.3 72.1 - - - +
1270A CYS* 1.3 63.6 + - - +
1271A GLU* 5.3 1.4 - - - +
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Residues in contact with CYS1270 (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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1090A ARG 3.9 10.1 - - - -
1245A LEU* 4.3 13.2 - - + -
1246A PHE 3.6 3.6 - - - -
1247A CYS* 2.0 46.2 - - - -
1268A ILE* 3.7 22.8 + - - -
1269A THR* 1.3 75.5 + - - +
1271A GLU* 1.3 59.2 + - - +
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Residues in contact with GLU1271 (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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1245A LEU* 3.8 4.3 - - - -
1246A PHE* 2.8 49.7 + - + +
1269A THR* 4.1 2.2 + - - +
1270A CYS* 1.3 74.1 - - - +
1272A GLU* 1.3 70.3 + - - +
1273A LYS* 3.7 29.7 - - + +
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Residues in contact with GLU1272 (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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1243A PRO* 3.7 25.3 - - + +
1244A TYR 3.8 7.4 - - - +
1245A LEU* 4.8 11.7 - - + +
1271A GLU* 1.3 82.3 - - - +
1273A LYS* 1.3 75.0 + - - +
1274A MET* 4.0 12.0 - - + +
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Residues in contact with LYS1273 (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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1083A THR* 6.0 0.8 - - - +
1243A PRO* 3.1 9.4 - - - +
1244A TYR* 3.0 63.4 + - + +
1246A PHE* 4.0 40.5 - - + -
1271A GLU* 3.7 23.6 - - - +
1272A GLU* 1.3 78.9 - - - +
1274A MET* 1.3 67.3 + - - +
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Residues in contact with MET1274 (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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1241A THR* 4.2 23.1 - - + +
1242A VAL* 3.4 27.4 - - - +
1243A PRO* 3.6 21.8 - - + -
1244A TYR* 3.8 5.4 + - - -
1272A GLU* 4.0 13.7 - - + +
1273A LYS* 1.3 79.1 - - - +
1275A VAL* 1.3 63.5 + - - +
1276A SER 4.3 0.2 + - - -
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Residues in contact with VAL1275 (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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1031A VAL* 4.8 11.9 - - + -
1104A ILE* 3.9 18.8 - - + -
1106A LYS* 4.0 15.5 - - + +
1241A THR* 3.3 6.3 - - - +
1242A VAL* 2.9 35.8 + - + +
1244A TYR* 3.4 30.5 - - + -
1274A MET* 1.3 72.8 - - - +
1276A SER* 1.3 74.5 + - - +
1277A MET* 3.8 25.8 - - + -
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Residues in contact with SER1276 (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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1031A VAL* 5.6 2.1 - - - +
1239A VAL* 4.4 11.8 - - - +
1240A GLU 3.4 5.4 - - - -
1241A THR* 4.1 12.8 - - - -
1274A MET 4.3 0.4 + - - -
1275A VAL* 1.3 83.5 - - - +
1277A MET* 1.3 60.8 + - - +
1278A ALA 4.0 1.9 + - - -
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Residues in contact with MET1277 (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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1025A VAL* 3.5 28.5 - - + -
1026A GLU 4.1 2.9 - - - +
1028A SER* 3.9 26.0 - - - +
1031A VAL* 3.5 26.2 - - + -
1104A ILE* 4.5 5.6 - - + -
1239A VAL* 4.5 1.8 - - - +
1240A GLU* 2.6 41.5 + - + +
1242A VAL* 3.7 22.7 - - + -
1275A VAL* 3.8 20.4 - - + -
1276A SER* 1.3 77.1 - - - +
1278A ALA* 1.3 63.4 + - - +
1279A ARG* 3.6 31.2 + - - +
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Residues in contact with ALA1278 (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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1028A SER* 4.1 11.2 + - - -
1029A SER* 4.9 4.2 + - - +
1141A LEU* 3.5 40.2 - - + +
1238A ARG 3.8 4.9 - - - -
1239A VAL* 4.4 17.7 - - + +
1276A SER* 4.0 2.6 + - - -
1277A MET* 1.3 72.9 - - - +
1279A ARG* 1.3 62.2 + - - +
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Residues in contact with ARG1279 (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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796A GLU* 5.9 1.1 - - - +
1025A VAL* 4.7 1.2 - - - +
1026A GLU* 2.4 50.1 + - - +
1027A PRO 3.3 19.8 + - - -
1028A SER* 3.5 13.9 - - - +
1141A LEU* 4.2 3.4 - - - -
1237A SER* 3.3 8.0 - - - -
1238A ARG* 3.0 63.6 + - + +
1240A GLU* 3.1 31.6 + - + +
1242A VAL* 6.1 0.2 - - - +
1277A MET* 3.8 22.8 + - - +
1278A ALA* 1.3 79.4 - - - +
1280A ASN* 1.3 69.2 + - - +
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Residues in contact with ASN1280 (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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796A GLU* 4.5 9.3 + - - +
797A ALA* 5.8 0.9 - - - -
1139A CYS* 4.4 4.3 + - - +
1140A PRO 2.8 29.8 + - - -
1141A LEU* 3.5 10.3 - - - +
1142A VAL* 3.4 22.5 + - - +
1230A LEU* 5.0 1.0 - - - +
1235A ILE* 3.6 19.9 - - + +
1236A GLN 3.3 2.2 - - - -
1237A SER* 3.7 12.8 + - - -
1238A ARG* 5.7 0.3 + - - -
1279A ARG* 1.3 80.6 - - - +
1281A THR* 1.3 62.1 + - - +
1282A TYR* 3.3 42.7 + - + +
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Residues in contact with THR1281 (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 3.5 2.1 - - - +
1235A ILE* 3.4 5.1 - - - -
1236A GLN* 2.5 59.9 + - + +
1237A SER 4.7 0.2 - - - -
1238A ARG* 3.8 31.2 + - - +
1280A ASN* 1.3 75.7 + - - +
1282A TYR* 1.3 67.0 + - - +
1288A ARG* 4.6 13.0 - - - +
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Residues in contact with TYR1282 (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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796A GLU* 2.9 37.8 + - + -
797A ALA* 3.7 33.2 - - + +
873A LYS* 5.5 2.4 + - - -
1139A CYS* 3.5 14.9 - - - +
1229A LEU* 3.5 46.2 - - + -
1230A LEU* 4.8 3.4 - - + -
1232A SER* 3.8 11.2 - - - +
1234A TYR 3.5 4.0 - - - -
1235A ILE* 4.0 23.3 - - + -
1280A ASN* 3.3 41.2 + - + +
1281A THR* 1.3 77.6 - - - +
1283A GLY* 1.3 59.7 + - - +
1288A ARG 4.4 9.2 - - - +
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Residues in contact with GLY1283 (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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1232A SER* 4.3 3.1 - - - -
1233A ALA 3.5 4.9 + - - -
1234A TYR* 3.1 33.0 + - - +
1282A TYR* 1.3 77.4 - - - +
1284A GLU* 1.3 68.4 + - - -
1285A SER 3.3 10.0 + - - -
1288A ARG 5.0 4.5 - - - -
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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