Contacts of the helix formed by residues 221 - 230 (chain A) in PDB entry 1KKQ
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 ASN 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A TYR* 3.9 15.6 + - + -
215A LEU* 4.0 21.4 - - - +
218A PHE* 4.4 8.8 + - + +
220A MET* 1.3 75.0 - - - +
222A LYS* 1.3 59.1 + - - +
223A VAL* 3.3 9.2 + - - +
224A LYS* 3.2 42.5 + - - +
225A ALA* 2.8 31.8 + - - +
323A SER* 4.6 5.2 - - - -
372A ASP* 3.2 22.9 - - - +
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Residues in contact with LYS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ASN* 1.3 75.9 - - - +
223A VAL* 1.3 56.2 + - + +
225A ALA* 3.9 4.5 - - - -
226A ARG* 2.6 65.0 + - + +
323A SER* 3.9 24.6 - - - +
365A PHE* 5.5 1.8 + - - -
366A ASN* 3.6 34.1 + - - +
369A GLU* 4.7 1.8 - - - +
370A LEU* 3.0 37.6 + - - +
371A ASP* 4.6 3.4 - - - -
372A ASP* 3.2 18.4 + - - +
375A ILE* 3.9 19.2 - - + +
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Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A TYR* 5.9 1.6 - - - +
215A LEU* 6.2 1.6 - - + -
221A ASN* 3.3 7.8 + - - +
222A LYS* 1.3 73.7 - - + +
224A LYS* 1.3 60.4 + - + +
226A ARG* 3.1 5.7 + - + +
227A VAL* 2.6 41.9 + - + +
371A ASP* 6.6 0.2 - - + -
372A ASP* 3.1 20.0 - - + +
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Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A PHE 4.0 1.6 + - - -
219A ASN* 2.1 40.1 + - - -
220A MET* 3.3 20.8 - - + +
221A ASN* 3.2 27.3 + - - +
223A VAL* 1.3 75.8 - - + +
225A ALA* 1.3 65.3 + - - +
227A VAL* 2.9 20.3 + - - +
228A ILE* 3.1 19.5 + - + +
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A MET* 3.5 20.0 - - - -
221A ASN 2.8 21.6 + - - +
222A LYS* 3.7 6.3 - - - +
224A LYS* 1.3 80.6 - - - +
226A ARG* 1.3 61.8 + - - +
227A VAL 3.3 0.7 + - - -
228A ILE* 3.4 1.9 + - - +
229A LEU* 3.3 28.6 + - - +
323A SER 4.0 9.6 - - - +
324A VAL* 3.9 23.1 - - + -
331A LEU* 3.9 3.3 - - + +
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LYS* 2.6 51.2 + - + +
223A VAL* 3.1 6.7 + - + +
225A ALA* 1.3 74.1 - - - +
227A VAL* 1.3 58.5 + - + +
229A LEU* 4.2 14.4 - - - +
230A SER* 3.2 36.4 + - - -
323A SER 3.1 21.3 + - - -
325A MET 2.5 30.8 + - - -
326A ASN* 4.6 7.7 - - - +
363A MET* 5.6 0.2 - - - +
366A ASN* 3.1 22.1 + - - +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A VAL* 2.6 35.4 - - + +
224A LYS* 2.9 9.0 + - - +
226A ARG* 1.3 75.5 - - + +
228A ILE* 1.3 63.2 + - + +
230A SER* 5.1 0.4 - - - -
231A GLY* 2.4 41.4 + - - +
232A LYS* 3.6 14.2 + - + +
233A ALA* 5.9 1.1 - - + -
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A MET* 3.3 33.7 - - + -
224A LYS* 3.1 14.9 + - + +
225A ALA 3.4 1.1 + - - +
227A VAL* 1.3 81.2 - - + +
229A LEU* 1.3 68.7 + - - +
231A GLY* 3.6 5.2 + - - +
237A PRO* 5.6 1.9 - - - +
238A PRO* 3.6 37.8 - - + +
331A LEU* 3.8 14.1 - - + -
334A TYR 4.5 2.0 - - - +
335A GLY* 3.6 23.1 - - - +
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ALA 3.3 16.3 + - - +
226A ARG* 4.2 17.5 - - - +
228A ILE* 1.3 86.4 - - - +
230A SER* 1.3 62.7 + - - +
231A GLY 3.1 2.8 + - - +
238A PRO* 5.9 1.3 - - + -
323A SER 4.5 1.1 - - - +
324A VAL* 3.7 22.0 - - - +
325A MET 3.8 16.8 - - - +
326A ASN* 4.2 21.5 - - + +
331A LEU* 3.6 26.7 - - + -
338A PHE* 3.8 27.4 - - + -
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ARG* 3.2 18.1 + - - -
227A VAL* 5.1 0.5 - - - -
229A LEU* 1.3 78.8 - - - +
231A GLY* 1.3 66.2 + - - +
232A LYS* 4.5 7.1 - - - +
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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