Contacts of the strand formed by residues 1396 - 1403 (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 SER1396 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1354E GLN* 2.5 27.9 + - - +
1355E VAL 3.3 6.7 - - - -
1356E ARG* 3.1 23.4 - - - +
1357E TRP* 4.0 3.7 - - - -
1392E ILE* 4.9 0.7 - - - +
1394E THR* 3.2 21.9 + - - +
1395E THR* 1.3 83.2 - - - +
1397E VAL* 1.3 65.4 + - - +
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Residues in contact with VAL1397 (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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1354E GLN* 2.8 9.8 + - - +
1355E VAL* 2.6 40.8 + - + +
1357E TRP* 3.8 24.7 - - + -
1376E LEU* 3.9 11.0 - - + -
1389E MET* 3.7 27.1 - - + -
1392E ILE* 4.9 20.4 - - + -
1396E SER* 1.3 77.9 - - - +
1398E PRO* 1.3 81.5 - - + +
1399E VAL* 4.8 0.2 - - + -
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Residues in contact with PRO1398 (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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1342E LEU* 4.2 13.9 - - + -
1353E ILE 3.4 8.3 - - - +
1354E GLN* 3.6 18.4 - - - +
1389E MET* 3.3 20.1 - - - +
1397E VAL* 1.3 98.7 - - + +
1399E VAL* 1.3 60.0 + - - +
1400E TYR* 4.0 34.5 - - + +
1692F ILE* 5.7 3.4 - - + -
1694F THR* 6.5 1.6 - - + -
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Residues in contact with VAL1399 (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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1351E ALA 4.3 1.2 - - - +
1352E ASP* 3.5 3.5 - - - +
1353E ILE* 2.7 44.8 + - + +
1355E VAL* 3.8 31.0 - - + -
1376E LEU* 4.6 4.9 - - + -
1378E TYR* 4.0 46.4 - - + -
1389E MET* 4.0 15.3 - - + -
1397E VAL 4.2 2.5 - - - +
1398E PRO* 1.3 78.4 - - - +
1400E TYR* 1.3 63.6 + - - +
1402E LEU* 4.0 12.2 - - + +
1410E VAL* 5.6 2.2 - - + -
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Residues in contact with TYR1400 (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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1342E LEU* 5.4 2.9 - - + -
1352E ASP* 3.1 28.5 - - + -
1378E TYR* 4.6 8.3 + - - -
1398E PRO* 4.0 30.3 - - + +
1399E VAL* 1.3 80.3 - - - +
1401E SER* 1.3 73.5 + - - +
1402E LEU* 3.4 11.0 + - - +
1654F GLN* 5.6 4.0 - - - +
1692F ILE* 3.2 30.7 - - + +
1694F THR* 4.1 14.3 + - + +
1696F SER 4.1 15.0 - - - -
1697F VAL* 3.8 11.1 - - + +
1698F PRO* 3.4 28.7 - - + -
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Residues in contact with SER1401 (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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1350E HIS* 3.6 24.4 + - - -
1351E ALA 3.7 0.9 - - - -
1352E ASP* 3.3 3.4 + - - -
1400E TYR* 1.3 82.2 - - - +
1402E LEU* 1.3 64.7 + - - +
1403E LYS* 3.7 6.6 + - - +
1408E TYR* 4.9 0.7 + - - -
1642F LEU* 4.5 10.2 - - - +
1654F GLN* 4.0 10.6 + - - -
1698F PRO* 3.8 10.6 - - - +
1700F TYR* 3.0 26.5 + - - -
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Residues in contact with LEU1402 (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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1350E HIS* 3.2 6.1 - - - -
1351E ALA* 2.7 40.3 + - - +
1353E ILE* 3.7 44.0 - - + -
1378E TYR* 3.6 33.4 - - + -
1399E VAL* 4.0 13.2 - - + +
1400E TYR 4.2 7.2 - - - +
1401E SER* 1.3 75.1 - - - +
1403E LYS* 1.3 62.0 + - - +
1404E VAL 3.4 0.6 + - - -
1408E TYR* 3.7 37.9 - - + -
1431E VAL* 4.8 2.0 - - + -
1433E LEU* 4.3 12.3 - - + -
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Residues in contact with LYS1403 (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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1349E ILE* 3.4 15.5 - - + +
1350E HIS* 3.6 22.8 - - + +
1401E SER 4.6 4.7 - - - +
1402E LEU* 1.3 68.8 - - - +
1404E VAL* 1.3 57.4 + - - +
1405E ASP* 3.0 11.4 - - - +
1406E LYS* 2.8 51.1 + - + +
1408E TYR* 3.3 23.2 + - - +
1433E LEU* 4.0 1.9 - - - +
1643F ASN* 3.5 26.3 - - - +
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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