Contacts of the strand formed by residues 1335 - 1344 (chain E) in PDB entry 1KF9
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 ILE1335 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1333E PRO 4.0 8.1 - - - +
1334E PRO* 1.3 79.8 - - - +
1336E ALA* 1.3 67.7 + - + +
1337E LEU* 3.2 10.1 + - - +
1358E GLU* 2.9 58.3 + - + +
1359E ALA 4.0 4.9 - - - +
1360E PRO* 5.1 1.6 - - + -
1361E ARG* 3.5 44.2 - - + +
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Residues in contact with ALA1336 (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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1335E ILE* 1.3 79.9 - - + +
1337E LEU* 1.3 67.2 + - - +
1338E ASN* 3.2 8.6 + - - +
1356E ARG 4.4 0.5 - - - -
1357E TRP* 3.7 9.2 - - - -
1358E GLU* 4.0 22.2 - - + +
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Residues in contact with LEU1337 (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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1334E PRO* 4.2 3.4 - - + +
1335E ILE 3.5 9.6 - - - +
1336E ALA* 1.3 75.4 - - - +
1338E ASN* 1.3 60.7 + - - +
1355E VAL* 4.0 22.0 - - + -
1356E ARG 3.6 4.0 - - - +
1357E TRP* 3.2 22.9 - - + -
1410E VAL* 4.1 11.7 - - + +
1412E VAL* 3.5 27.8 - - + -
1426E SER* 3.6 31.0 - - - +
1427E GLU* 4.2 9.6 - - + +
1428E VAL 5.7 0.2 - - - -
1429E LEU* 3.7 27.2 - - + +
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Residues in contact with ASN1338 (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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1336E ALA 3.2 7.1 + - - +
1337E LEU* 1.3 75.6 - - - +
1339E TRP* 1.3 82.2 + - - +
1340E THR* 5.5 1.8 + - - -
1354E GLN 4.0 0.2 - - - +
1355E VAL* 4.8 0.2 - - - -
1356E ARG* 3.0 48.3 + - + +
1429E LEU* 3.8 11.4 - - - +
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Residues in contact with TRP1339 (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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1338E ASN* 1.3 95.7 + - - +
1340E THR* 1.3 78.6 + - - +
1341E LEU* 3.8 21.8 - - + -
1353E ILE* 3.6 34.1 - - + -
1354E GLN 3.4 10.1 - - - +
1355E VAL* 4.4 2.9 - - + +
1429E LEU* 3.7 21.8 - - + +
1430E TYR 3.9 8.5 + - - -
1431E VAL* 3.7 28.1 - - + +
1432E THR* 3.2 30.5 - - - -
1433E LEU* 3.6 24.7 - - + -
1434E PRO* 4.6 3.6 - - + -
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Residues in contact with THR1340 (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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1338E ASN* 5.5 2.1 + - - -
1339E TRP* 1.3 80.9 + - - +
1341E LEU* 1.3 76.0 + - - +
1342E LEU* 4.3 12.1 - - + -
1353E ILE* 3.1 5.7 - - - +
1354E GLN* 2.8 41.0 + - + -
1356E ARG* 4.8 12.9 + - - -
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Residues in contact with LEU1341 (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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1339E TRP* 3.8 20.2 - - + -
1340E THR* 1.3 87.7 - - - +
1342E LEU* 1.3 66.8 + - - +
1343E ASN* 4.7 2.9 - - - +
1344E VAL* 3.9 18.8 - - + -
1351E ALA* 4.4 11.7 - - + -
1352E ASP 3.3 19.7 - - - +
1353E ILE* 3.9 13.2 - - + -
1433E LEU* 4.2 7.2 - - + -
1434E PRO* 3.9 27.1 - - + -
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Residues in contact with LEU1342 (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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1340E THR* 4.3 6.1 - - + -
1341E LEU* 1.3 82.5 - - - +
1343E ASN* 1.3 71.7 + - - +
1352E ASP* 2.8 29.2 + - + +
1353E ILE 3.9 11.9 - - - -
1354E GLN* 3.8 34.8 - - + +
1398E PRO* 4.2 20.6 - - + -
1400E TYR* 5.4 2.7 - - + -
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Residues in contact with ASN1343 (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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1341E LEU* 5.0 2.0 - - - -
1342E LEU* 1.3 93.8 - - - +
1344E VAL* 1.3 67.4 + - - +
1351E ALA* 3.5 3.8 - - - +
1352E ASP* 3.1 34.6 + - - +
1700F TYR* 3.6 24.9 - - - +
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Residues in contact with VAL1344 (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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1341E LEU* 3.9 24.9 - - + -
1343E ASN* 1.3 82.1 - - - +
1345E SER* 1.3 76.7 + - - +
1346E LEU* 3.8 7.3 + - - +
1348E GLY* 4.6 12.1 - - - -
1350E HIS 3.6 13.5 - - - +
1351E ALA* 4.6 7.6 - - + -
1404E VAL* 5.4 9.6 - - + -
1434E PRO* 5.1 9.6 - - + -
1700F TYR* 4.4 2.9 - - - +
1701F SER* 4.3 2.6 + - - -
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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