Contacts of the strand formed by residues 251 - 258 (chain B) in PDB entry 4KPF
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 LYS 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B LYS* 4.0 1.4 - - - +
247B LEU* 2.6 49.1 + - + +
248B LYS 4.3 10.1 - - - +
249B GLY 3.1 4.6 - - - +
250B GLY* 1.3 78.7 - - - +
252B GLU* 1.3 55.7 + - - +
301B GLU* 6.0 1.6 - - - +
302B LEU 4.0 16.8 - - - +
303B LYS 5.0 0.9 - - - -
304B LYS* 4.8 13.2 - - + +
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Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ILE* 3.9 16.5 - - + +
245B GLU 3.5 9.0 - - - +
246B LYS* 5.1 7.2 - - + -
247B LEU* 3.9 5.5 - - - +
250B GLY 4.9 5.4 - - - +
251B LYS* 1.3 78.6 - - - +
253B GLN* 1.3 64.7 + - - +
302B LEU* 3.0 38.7 + - + +
303B LYS 5.2 2.4 + - - -
308B THR* 2.7 39.6 + - + +
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Residues in contact with GLN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ILE* 3.5 6.2 - - - -
245B GLU* 2.8 65.1 + - - +
247B LEU* 3.8 21.8 - - + +
252B GLU* 1.3 77.4 - - - +
254B ILE* 1.3 64.0 + - - +
255B VAL* 3.6 13.7 + - + +
288B ARG* 3.1 29.4 + - - -
297B ARG* 4.0 10.1 - - - +
299B ALA* 4.7 5.8 - - - +
300B ILE 4.3 3.6 - - - +
301B GLU* 3.7 25.3 - - + +
302B LEU* 4.0 2.7 - - - -
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Residues in contact with ILE 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B THR* 4.5 8.3 - - + -
243B GLU 4.3 1.3 - - - +
244B ILE* 3.6 23.8 - - + -
253B GLN* 1.3 71.9 - - - +
255B VAL* 1.3 65.8 + - - +
256B ILE* 4.7 1.8 - - + -
298B ILE 3.4 2.4 - - - +
299B ALA* 3.6 0.9 - - - -
300B ILE* 2.7 58.7 + - + +
302B LEU* 4.1 20.1 - - + +
308B THR* 4.1 10.3 - - - +
311B VAL* 4.3 6.5 - - + -
312B LEU* 3.4 55.2 - - + +
315B LEU* 5.0 4.3 - - + -
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B THR* 3.3 5.7 - - - -
243B GLU* 3.0 42.1 + - + +
245B GLU* 3.4 34.3 - - + +
253B GLN* 3.6 19.5 - - + +
254B ILE* 1.3 78.4 - - - +
256B ILE* 1.3 66.6 + - - +
257B THR* 4.0 12.1 + - + +
297B ARG* 3.6 35.7 - - + +
298B ILE 3.3 6.7 - - - +
299B ALA* 4.7 2.5 - - - -
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Residues in contact with ILE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B SER* 4.0 6.5 - - - -
241B LYS 3.6 7.6 - - - +
242B THR* 3.8 11.7 - - + -
254B ILE* 4.7 3.4 - - + -
255B VAL* 1.3 76.7 - - - +
257B THR* 1.3 62.8 + - - +
258B GLU 3.4 20.9 - - - +
259B ILE* 3.9 16.6 - - + -
268B LEU* 5.6 0.2 - - + -
272B ILE* 4.4 5.6 - - + -
296B LEU* 3.4 3.4 - - + +
297B ARG* 3.3 8.7 - - - -
298B ILE* 2.8 55.6 + - + +
300B ILE* 4.0 21.1 - - + -
321B LEU* 3.1 36.1 - - + -
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Residues in contact with THR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LYS* 3.1 29.7 + - + +
243B GLU* 4.7 13.0 - - + +
255B VAL* 4.1 20.2 - - + +
256B ILE* 1.3 77.0 - - - +
258B GLU* 1.3 76.9 + - - +
296B LEU* 3.3 35.1 + - - +
297B ARG* 5.9 0.4 - - + -
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Residues in contact with GLU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B THR 3.8 11.0 - - - +
216B GLY* 3.3 8.8 - - - -
217B ALA* 2.6 35.8 + - - +
240B SER* 3.3 9.4 - - - -
241B LYS* 2.8 61.4 + - + +
256B ILE* 3.4 2.5 - - - +
257B THR* 1.3 94.0 + - - +
259B ILE* 1.3 66.6 + - - +
296B LEU* 4.3 3.8 - - - -
479B LEU 3.9 7.7 - - - +
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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