Contacts of the strand formed by residues 1235 - 1239 (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 PHE1235 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1234E LYS* 1.3 87.1 - - - +
1236E THR* 1.3 61.0 + - - +
1237E LYS* 4.6 5.4 - - - +
1238E CYS* 5.4 1.3 - - - -
1248E CYS* 4.5 2.2 - - + -
1249E HIS 3.2 17.0 - - - +
1250E TRP* 3.6 16.6 - + + -
1266E LEU* 3.4 30.3 - - + -
1309E ILE* 3.1 55.4 - - + -
1310E LYS 4.2 2.2 - - - -
1311E LEU* 3.8 22.4 - - + -
1319E ASP* 2.7 29.7 + - + +
1321E LYS* 3.9 21.8 - - + -
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Residues in contact with THR1236 (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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1234E LYS* 3.6 16.8 + - - +
1235E PHE* 1.3 75.6 - - - +
1237E LYS* 1.3 85.6 + - + +
1249E HIS* 2.9 39.9 + - + -
1250E TRP* 3.2 9.4 - - - +
1251E THR* 5.0 7.4 - - + -
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Residues in contact with LYS1237 (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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1235E PHE* 3.7 2.3 - - - +
1236E THR* 1.3 95.1 + - + +
1238E CYS* 1.3 77.2 + - - +
1239E ARG* 5.1 3.8 - - + -
1247E SER 4.2 0.3 - - - +
1248E CYS* 3.4 0.7 - - - -
1249E HIS* 2.6 39.2 + - + +
1321E LYS* 5.0 9.4 - - - +
1330E GLN* 3.9 28.5 - - - +
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Residues in contact with CYS1238 (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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1235E PHE* 5.4 2.7 - - - -
1237E LYS* 1.3 88.5 - - - +
1239E ARG* 1.3 63.7 + - - +
1247E SER 3.2 5.8 - - - +
1248E CYS* 2.1 47.6 - - - -
1249E HIS* 5.7 0.4 - - - -
1309E ILE* 3.7 14.4 - - - -
1321E LYS* 3.9 24.9 + - - +
1323E PHE* 4.1 4.5 - - + -
1328E ILE* 3.7 30.3 - - + +
1330E GLN* 4.5 2.4 - - - +
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Residues in contact with ARG1239 (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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1237E LYS* 5.1 4.3 - - + -
1238E CYS* 1.3 76.6 - - - +
1240E SER* 1.3 61.5 + - - +
1241E PRO* 3.2 32.2 - - + +
1246E PHE* 4.1 4.5 - - - -
1247E SER* 3.1 30.7 + - - +
1249E HIS* 5.9 1.7 - - + -
1328E ILE* 3.3 6.4 - - - +
1330E GLN* 2.9 48.1 + - + +
1331E PRO 3.9 1.4 + - - -
1332E ASP* 2.7 36.4 + - - +
1333E PRO* 5.5 0.2 - - - +
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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