Contacts of the helix formed by residues 298 - 309 (chain B) in PDB entry 4KIK
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 GLY 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B GLY 3.3 1.2 + - - -
291B ASP* 3.6 12.3 - - - +
294B TYR* 3.7 24.0 - - - -
295B GLY 3.2 12.6 + - - -
296B PRO 3.2 4.9 - - - -
297B ASN* 1.3 75.1 - - - +
299B CYS* 1.3 56.4 + - - +
300B PHE 3.3 2.7 - - - -
301B LYS* 3.4 9.3 + - - -
302B ALA* 3.1 27.4 + - - +
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Residues in contact with CYS 299 (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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205B TYR* 3.8 35.9 - - - -
276B TRP* 2.8 24.5 + - - +
279B LEU* 4.0 15.9 - - + -
280B MET* 3.5 34.5 - - - -
289B GLY* 3.1 19.3 + - - +
297B ASN 4.4 1.6 - - - -
298B GLY* 1.3 75.6 - - - +
300B PHE* 1.3 76.6 + - - +
302B ALA* 3.5 0.8 - - - +
303B LEU* 3.2 9.4 + - - +
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Residues in contact with PHE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA* 3.8 34.8 - - + -
133B LEU* 3.8 27.6 - - + -
134B ARG* 3.3 50.5 + - + +
137B HIS* 4.1 11.2 - - + -
205B TYR* 3.7 35.4 - + - -
208B PHE* 4.3 15.5 - + - -
276B TRP* 5.9 1.1 - + - -
280B MET* 5.2 1.6 - - + -
297B ASN 4.3 10.8 - - - +
298B GLY 3.3 0.8 - - - -
299B CYS* 1.3 83.5 - - - +
301B LYS* 1.4 60.6 + - + +
303B LEU* 3.5 7.1 + - + +
304B ASP* 3.1 21.8 + - - -
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Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ARG* 6.1 1.3 - - - +
294B TYR* 3.7 38.7 - - + -
297B ASN 5.9 0.7 - - - +
298B GLY* 3.4 8.7 + - - +
300B PHE* 1.4 75.6 - - + +
302B ALA* 1.4 64.2 + - - +
304B ASP* 3.3 16.4 + - + +
305B ASP* 3.2 25.8 + - - +
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Residues in contact with ALA 302 (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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272B ARG* 3.9 4.3 + - - +
276B TRP* 3.9 13.7 - - + -
279B LEU* 4.3 2.2 - - + -
291B ASP* 3.1 26.9 - - - +
294B TYR* 3.7 10.0 - - - -
298B GLY 3.1 13.6 + - - +
299B CYS* 3.5 10.1 - - - +
301B LYS* 1.4 75.9 - - - +
303B LEU* 1.4 59.6 + - - +
305B ASP* 3.3 21.5 + - - +
306B ILE* 3.4 12.3 + - + +
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Residues in contact with LEU 303 (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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126B LEU* 3.9 28.0 - - + +
130B ALA* 3.6 31.0 - - + -
208B PHE* 4.5 0.9 - - + -
273B LEU* 3.9 27.1 - - + -
276B TRP* 3.6 41.9 - - + +
299B CYS 3.2 7.3 + - - +
300B PHE* 3.7 4.7 - - + +
301B LYS 3.4 0.2 - - - -
302B ALA* 1.4 74.6 - - - +
304B ASP* 1.4 55.4 + - - +
306B ILE* 3.1 10.4 + - + +
307B LEU* 2.8 48.6 + - + +
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Residues in contact with ASP 304 (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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134B ARG* 3.2 30.2 + - - -
300B PHE 3.1 14.6 + - - +
301B LYS* 3.3 20.4 + - - +
303B LEU* 1.4 74.1 - - - +
305B ASP* 1.4 57.5 + - - +
307B LEU* 3.4 12.1 + - - +
308B ASN* 2.9 46.4 + - - +
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Residues in contact with ASP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ARG* 4.0 18.9 + - - +
294B TYR* 2.7 38.9 + - - -
301B LYS 3.2 8.8 + - - +
302B ALA* 3.4 9.2 - - - +
303B LEU 3.2 0.4 - - - -
304B ASP* 1.4 76.2 - - - +
306B ILE* 1.4 61.9 + - - +
308B ASN* 3.2 14.5 + - - +
309B LEU* 3.2 15.8 + - - +
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Residues in contact with ILE 306 (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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123B LEU* 5.7 0.8 - - + +
269B LEU* 3.8 29.4 - - + +
272B ARG* 3.3 61.9 - - + +
273B LEU* 4.1 14.6 - - + -
275B LYS* 5.7 0.7 - - + -
276B TRP* 3.6 25.8 - - + -
302B ALA* 3.4 10.3 + - + +
303B LEU* 3.1 10.7 + - + +
305B ASP* 1.4 74.2 - - - +
307B LEU* 1.3 63.7 - - + +
309B LEU* 3.2 31.2 - - + +
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Residues in contact with LEU 307 (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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123B LEU* 3.4 53.4 - - + +
126B LEU* 4.4 2.7 - - + -
127B SER* 3.7 33.4 - - - +
130B ALA* 5.7 0.7 - - + -
303B LEU* 2.8 44.9 + - + +
304B ASP* 3.7 13.7 - - - +
306B ILE* 1.3 75.3 - - + +
308B ASN* 1.3 65.0 + - - +
309B LEU 3.3 6.3 + - - +
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Residues in contact with ASN 308 (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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304B ASP* 2.9 33.1 + - - +
305B ASP* 3.2 6.8 + - - +
307B LEU* 1.3 79.2 + - - +
309B LEU* 1.4 63.4 + - - +
310B LYS* 3.6 12.5 + - - +
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Residues in contact with LEU 309 (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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268B VAL* 4.5 14.4 - - + -
269B LEU* 5.9 2.2 - - + -
272B ARG* 4.0 31.2 - - + +
305B ASP 3.2 11.6 + - - +
306B ILE* 3.2 33.2 - - + +
307B LEU 3.3 7.0 - - - +
308B ASN* 1.4 78.1 - - - +
310B LYS* 1.3 62.5 + - - +
311B LEU* 3.9 16.1 + - + +
326B PRO* 3.8 28.3 - - + -
327B VAL 5.9 1.1 - - - +
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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