Contacts of the strand formed by residues 1293 - 1302 (chain E) in PDB entry 3F7P
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 PRO1293 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1259E LEU* 3.7 7.6 - - - +
1260E VAL* 3.2 47.0 + - + +
1261E ASN 4.5 8.5 - - - +
1262E ASP* 4.7 13.0 - - - +
1291E SER 3.9 5.8 - - - +
1292E GLN* 1.3 96.4 - - - +
1294E TYR* 1.3 60.8 + - - +
1313E ILE* 4.5 8.7 - - + -
1314E ILE 3.9 5.8 - - - +
1315E ASN* 3.9 18.2 - - + +
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Residues in contact with TYR1294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257E TYR* 4.4 7.9 - + - -
1258E GLY* 3.4 26.0 - - - -
1259E LEU* 3.1 45.0 - - + +
1260E VAL* 4.4 0.2 - - - -
1287E ASN 5.3 0.2 + - - -
1288E LEU* 3.8 34.1 - - + +
1289E ARG* 3.3 39.7 + - - +
1292E GLN* 3.4 21.8 - - + -
1293E PRO* 1.3 73.8 - - - +
1295E ARG* 1.3 59.7 + - - +
1296E TYR* 3.4 31.7 - - + +
1313E ILE* 3.4 4.9 - - - -
1314E ILE 2.9 33.6 + - - +
1316E LEU* 6.6 0.2 - - + -
1337E ALA* 5.1 4.5 + - + +
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Residues in contact with ARG1295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256E CYS 3.7 0.5 - - - +
1257E TYR* 3.0 26.0 - - - +
1258E GLY 3.0 11.9 + - - +
1260E VAL* 3.6 18.2 - - + +
1266E PRO* 3.6 32.9 - - - +
1270E MET* 4.3 25.3 - - - +
1294E TYR* 1.3 73.4 - - - +
1296E TYR* 1.3 66.2 + - - +
1297E THR* 3.9 15.7 - - + +
1309E GLU* 4.8 7.1 + - - -
1311E GLU* 2.9 36.9 + - + +
1312E ALA 3.6 3.8 - - - -
1313E ILE* 3.4 22.0 - - + -
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Residues in contact with TYR1296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226E LEU* 3.6 16.6 - - + +
1228E PHE* 3.6 28.7 - + + -
1236E THR* 3.9 8.5 - - + +
1238E LEU* 4.0 21.1 - - + -
1256E CYS 3.3 4.9 - - - +
1257E TYR* 3.5 24.7 - + + -
1285E ILE* 3.8 18.8 - - + -
1288E LEU* 3.4 27.4 - - + +
1294E TYR* 3.4 39.2 - + + +
1295E ARG* 1.3 74.4 - - - +
1297E THR* 1.3 65.2 + - - +
1310E ARG 3.6 0.5 - - - +
1311E GLU* 3.3 5.2 - - - +
1312E ALA 2.8 37.8 + - - +
1314E ILE* 4.2 13.9 + - + +
1316E LEU* 5.3 1.9 - - - +
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Residues in contact with THR1297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254E GLU 3.5 1.2 + - - +
1255E VAL* 3.2 6.9 - - - +
1256E CYS* 2.8 53.9 + - - +
1270E MET* 6.5 0.4 - - - -
1295E ARG* 3.9 18.6 - - + +
1296E TYR* 1.3 79.0 - - - +
1298E VAL* 1.3 66.0 + - - +
1309E GLU* 3.8 36.1 + - + +
1310E ARG 3.0 9.4 - - - +
1311E GLU* 3.8 21.5 - - + -
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Residues in contact with VAL1298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223E PRO* 3.3 15.7 - - + +
1226E LEU* 3.5 31.9 - - + -
1238E LEU* 4.3 7.0 - - + -
1240E TRP* 3.6 51.6 - - + +
1253E TYR* 4.0 7.9 - - + -
1254E GLU 3.2 8.1 - - - +
1255E VAL* 4.2 10.1 - - + -
1297E THR* 1.3 80.2 - - - +
1299E LYS* 1.3 63.1 + - - +
1309E GLU* 3.5 2.3 - - - -
1310E ARG 2.9 30.0 + - - -
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Residues in contact with LYS1299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223E PRO* 3.7 7.4 - - - -
1253E TYR* 3.2 7.7 - - - -
1254E GLU* 2.9 74.1 + - + +
1256E CYS* 5.5 1.3 - - - -
1272E LYS* 5.5 2.8 - - - +
1298E VAL* 1.3 75.2 - - - +
1300E ALA* 1.3 60.0 + - - +
1306E TRP* 3.4 30.3 - - + +
1307E GLY 3.6 14.1 - - - +
1308E PRO 3.6 15.7 - - - +
1309E GLU* 3.8 30.7 + - + +
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Residues in contact with ALA1300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220E PRO* 3.9 14.3 - - + +
1221E SER 4.8 1.5 + - - +
1223E PRO* 4.0 4.6 - - + +
1243E PRO* 3.7 23.8 - - + -
1250E ILE* 4.2 6.3 - - + -
1252E ALA 3.6 5.6 - - - +
1253E TYR* 3.5 24.2 - - + -
1299E LYS* 1.3 72.5 - - - +
1301E ARG* 1.3 58.3 + - - +
1306E TRP* 3.3 10.6 - - - -
1307E GLY 2.9 27.5 + - - +
1308E PRO 4.7 1.4 + - - -
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Residues in contact with ARG1301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 3.2 37.6 - - - +
63A ILE* 3.7 31.5 + - - +
66A GLU* 6.4 1.0 - - - +
1220E PRO* 4.2 2.9 - - - -
1250E ILE* 3.3 7.4 - - - +
1251E THR* 2.8 30.6 + - - -
1252E ALA 2.9 14.3 + - - +
1300E ALA* 1.3 74.1 - - - +
1302E ASN* 1.3 71.2 + - - +
1303E GLY 5.3 4.4 + - - -
1305E GLY* 3.3 24.0 - - - +
1306E TRP* 3.5 40.2 - - + +
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Residues in contact with ASN1302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217E GLN* 3.5 5.6 - - - +
1218E GLU 2.7 28.5 + - - +
1220E PRO* 3.6 9.1 - - + +
1246E THR 2.9 21.0 + - - -
1247E ASN 3.5 10.5 + - - -
1248E GLY* 3.7 1.8 - - - -
1249E GLU 3.1 27.6 - - - +
1250E ILE* 4.0 2.2 - - - -
1251E THR* 3.9 7.9 - - - -
1301E ARG* 1.3 86.1 + - - +
1303E GLY* 1.3 67.5 + - - +
1304E ALA* 2.8 14.7 + - - +
1305E GLY* 2.9 26.7 + - - +
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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