Contacts of the strand formed by residues 1341 - 1350 (chain E) in PDB entry 1IV4
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 HIS1341 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1134D SER 4.4 0.4 + - - -
1135D GLU* 2.8 40.1 - - + +
1137D LEU* 3.7 50.6 + - + +
1209E SER* 4.7 3.2 + - - -
1210E HIS 3.2 17.3 + - - +
1211E ARG* 3.0 42.1 + - - -
1212E LEU* 3.4 13.8 - - - +
1299E THR 3.9 2.4 - - - +
1300E LEU* 3.9 11.1 - - - +
1301E ASP 4.9 0.7 + - - -
1338E ALA* 3.4 18.2 + - + +
1339E PRO 3.5 0.7 - - - -
1340E SER* 1.3 84.2 - - - +
1342E VAL* 1.3 64.9 + - - +
1343E GLN* 4.7 3.0 - - + +
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Residues in contact with VAL1342 (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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1209E SER* 3.1 6.4 - - - -
1210E HIS* 2.9 52.1 + - + +
1212E LEU* 3.8 22.3 - - + +
1218E LEU* 4.8 7.2 - - + -
1220E LEU* 4.3 23.1 - - + -
1231E ALA* 5.4 0.4 - - + -
1237E GLY 4.9 4.5 - - - +
1239E ALA* 4.3 12.3 - - + +
1298E LEU* 5.6 1.8 - - + -
1299E THR 3.5 11.0 - - - +
1300E LEU* 3.9 22.4 - - + -
1341E HIS* 1.3 75.2 - - - +
1343E GLN* 1.3 67.1 + - - +
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Residues in contact with GLN1343 (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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1137D LEU* 3.9 22.5 - - + +
1208E ASP 3.5 7.9 - - - +
1209E SER* 4.1 12.2 - - - -
1239E ALA* 4.7 0.4 - - - -
1297E VAL 4.5 0.2 - - - -
1298E LEU* 3.5 3.8 - - - +
1299E THR* 2.8 59.3 + - - +
1334E SER* 4.6 1.2 - - - -
1338E ALA* 3.5 20.4 - - - +
1341E HIS* 4.7 4.0 - - + +
1342E VAL* 1.3 82.7 - - - +
1344E ALA* 1.3 61.0 + - - +
1345E ARG* 3.1 39.2 - - - +
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Residues in contact with ALA1344 (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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1207E GLU* 3.3 4.5 - - - +
1208E ASP 2.8 31.8 + - - +
1239E ALA* 3.4 33.0 - - + +
1240E ALA* 3.9 3.4 - - - +
1243E ALA* 4.0 5.8 - - + -
1296E LEU* 5.2 2.0 - - + -
1297E VAL 3.3 5.2 - - - -
1298E LEU* 3.6 21.5 - - + -
1343E GLN* 1.3 75.5 - - - +
1345E ARG* 1.3 67.1 + - - +
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Residues in contact with ARG1345 (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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1145D ARG* 3.7 26.6 - - - +
1205E TYR* 3.4 22.2 - - - +
1206E GLY 3.5 5.8 - - - +
1207E GLU* 3.6 20.3 + - + +
1296E LEU* 3.2 2.5 - - - +
1297E VAL 2.9 31.3 + - - +
1299E THR* 4.5 9.3 + - - -
1343E GLN* 3.1 36.5 - - - +
1344E ALA* 1.3 81.7 - - - +
1346E ALA* 1.3 59.8 + - - +
1405F TYR* 3.7 19.8 - - + -
1407F GLU* 3.1 43.0 + - - +
1545F ARG* 3.6 17.5 - - - +
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Residues in contact with ALA1346 (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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1204E GLY 3.9 0.3 - - - +
1205E TYR* 3.3 8.8 - - - -
1206E GLY 2.8 34.7 + - - +
1243E ALA* 4.1 22.9 - - + +
1244E LEU* 3.7 23.1 - - + -
1247E ALA* 3.9 3.1 - - + +
1295E SER 3.4 4.5 - - - -
1296E LEU* 3.6 16.8 - - + -
1345E ARG* 1.3 74.4 - - - +
1347E VAL* 1.3 62.3 + - - +
1405F TYR* 5.2 0.4 - - - -
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Residues in contact with VAL1347 (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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1147D VAL* 4.5 9.6 - - + -
1203E ILE* 3.7 22.9 - - + -
1204E GLY 3.3 9.2 - - - +
1205E TYR* 3.5 28.5 - - + -
1293E GLN 4.2 0.2 - - - +
1294E ALA* 3.5 1.9 - - - +
1295E SER* 2.8 38.5 + - - +
1346E ALA* 1.3 74.4 - - - +
1348E VAL* 1.3 67.0 + - - +
1403F ILE* 3.7 25.0 - - + +
1405F TYR* 4.2 24.9 - - + +
1547F VAL* 4.9 4.3 - - + -
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Residues in contact with VAL1348 (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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1203E ILE* 3.3 10.2 - - - +
1204E GLY 2.9 42.9 + - - +
1244E LEU* 4.3 11.0 - - + +
1247E ALA* 3.7 36.3 - - + +
1248E LEU* 4.0 18.6 - - + +
1291E LEU* 4.2 10.1 - - + -
1293E GLN 3.4 11.0 - - - +
1294E ALA* 4.2 13.0 - - + -
1320E MET* 5.5 1.8 - - - -
1347E VAL* 1.3 81.1 - - - +
1349E LEU* 1.3 60.2 + - - +
1350E LEU* 4.1 12.8 - - + -
1403F ILE* 5.2 0.7 - - - -
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Residues in contact with LEU1349 (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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1149D LEU* 5.8 7.2 - - + -
1202E ARG 3.4 18.8 - - - +
1203E ILE* 5.0 7.9 - - + -
1291E LEU* 3.6 1.7 - - - +
1292E LEU* 2.9 48.6 + - + +
1293E GLN* 3.0 32.7 + - + +
1326E ARG* 4.4 1.3 - - - +
1348E VAL* 1.3 74.2 - - - +
1350E LEU* 1.3 69.6 + - - +
1351E ASP 6.0 1.1 - - - -
1402F ARG* 4.4 7.6 - - - +
1403F ILE* 4.2 28.9 - - + +
1549F LEU* 6.1 5.2 - - + -
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Residues in contact with LEU1350 (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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1202E ARG* 2.8 42.8 + - + +
1248E LEU* 4.2 6.7 - - + -
1251E ALA* 3.6 30.5 - - + -
1252E TYR* 4.8 2.0 - - + -
1284E VAL* 4.1 16.8 - - + -
1289E ALA* 3.9 22.7 - - + -
1290E LYS 3.3 8.1 - - - +
1291E LEU* 3.8 29.8 - - + +
1292E LEU* 4.1 1.6 - - - +
1348E VAL* 4.1 14.1 - - + +
1349E LEU* 1.3 85.9 - - - +
1351E ASP* 1.3 77.3 + - - +
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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