Contacts of the strand formed by residues 1293 - 1296 (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 SER1293 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1248E CYS 3.2 9.0 - - - -
1249E HIS* 3.3 19.7 - - - -
1250E TRP* 3.5 15.0 - - - -
1286E TYR* 3.4 22.7 + - - +
1289E ALA* 2.8 37.8 + - - +
1290E GLY 2.8 18.4 + - - -
1291E GLU 3.1 1.7 - - - -
1292E ASN* 1.3 80.3 - - - +
1294E CYS* 1.3 59.7 + - - +
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Residues in contact with CYS1294 (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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1247E SER* 2.9 23.3 - - - -
1248E CYS 2.8 14.8 + - - +
1250E TRP* 4.0 2.0 - - + -
1266E LEU* 3.5 28.3 - - + -
1283E CYS* 2.0 54.7 - - - -
1284E PRO* 4.1 2.0 - - - -
1285E ASP 3.5 1.3 - - - -
1289E ALA* 3.7 2.0 - - - +
1293E SER* 1.3 76.2 + - - +
1295E TYR* 1.3 60.9 + - - +
1296E PHE* 3.4 25.4 - - + -
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Residues in contact with TYR1295 (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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1245E THR* 4.0 24.9 + - - +
1246E PHE 4.0 2.7 - - - -
1247E SER* 4.4 8.5 - - - -
1284E PRO* 3.6 12.5 - - - +
1285E ASP* 2.8 45.6 + - + +
1288E SER* 3.9 14.4 - - - -
1289E ALA* 3.6 30.3 - - + +
1294E CYS* 1.3 75.2 - - - +
1296E PHE* 1.3 67.2 + - - +
1297E ASN* 3.8 30.3 + - + +
1300E PHE* 5.3 0.2 - - - -
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Residues in contact with PHE1296 (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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1245E THR* 3.3 4.0 - - - -
1246E PHE* 2.8 88.5 + + + +
1248E CYS* 4.6 5.8 - - - -
1266E LEU* 4.1 14.4 - - + -
1268E TYR* 3.8 36.6 - + + -
1284E PRO* 4.0 11.7 - - + -
1294E CYS* 3.4 35.0 - - + -
1295E TYR* 1.3 80.0 - - - +
1297E ASN* 1.3 64.8 + - - +
1300E PHE* 3.9 23.6 - + + -
1301E THR* 3.2 2.8 + - - +
1307E TYR* 4.7 4.0 - + - -
1309E ILE* 5.1 4.0 - - + -
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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