Contacts of the helix formed by residues 198 - 209 (chain A) in PDB entry 4KNF
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 ALA 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A TRP* 3.5 22.7 - - + -
194A VAL* 3.1 20.2 + - + +
195A VAL* 3.6 9.4 - - - +
196A GLY 3.2 0.8 - - - -
197A TRP* 1.3 75.9 - - - +
199A ILE* 1.3 61.7 + - - +
201A PRO* 3.2 6.2 - - - +
202A ALA* 3.1 23.3 + - - +
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Residues in contact with ILE 199 (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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195A VAL 4.0 8.3 - - - +
196A GLY* 3.2 17.3 - - - +
197A TRP 3.0 1.0 + - - -
198A ALA* 1.3 78.5 - - - +
200A TYR* 1.3 56.2 + - - +
202A ALA* 3.4 6.5 + - + +
203A GLY 2.8 24.3 + - - -
223A ILE* 3.4 36.0 - - + +
226A LEU* 4.5 17.3 - - + -
227A ALA* 3.6 15.3 - - + +
230A VAL* 4.1 33.2 - - + -
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Residues in contact with TYR 200 (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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98A TRP* 3.4 36.1 - + - -
197A TRP* 3.1 21.1 + + - -
199A ILE* 1.3 73.6 - - - +
201A PRO* 1.3 71.5 - - + +
203A GLY* 2.9 4.2 + - - -
204A TYR* 2.9 20.1 + - - +
224A TYR* 3.4 15.2 - + - -
227A ALA* 3.1 27.4 + - + -
228A ASP* 2.7 34.5 + - - -
231A ASN* 3.4 23.3 + - - +
301A RET 3.3 63.9 - - + +
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Residues in contact with PRO 201 (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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152A PHE* 3.7 12.3 - - + -
156A MET* 3.7 24.0 - - - -
159A TRP* 3.6 27.8 - - + -
197A TRP 3.2 12.3 - - - +
198A ALA* 3.2 13.9 - - + +
200A TYR* 1.3 92.8 - - + +
202A ALA* 1.3 54.3 + - - +
204A TYR* 3.3 9.0 + - + +
205A ALA* 2.9 30.9 + - - +
301A RET 4.0 21.2 - - + -
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Residues in contact with ALA 202 (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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198A ALA 3.1 15.3 + - - +
199A ILE* 3.4 14.1 - - + +
200A TYR 3.1 0.4 - - - -
201A PRO* 1.3 77.0 - - - +
203A GLY* 1.3 56.3 + - - +
205A ALA* 3.4 6.7 + - - +
206A ALA* 3.0 29.2 + - - +
223A ILE* 4.4 8.0 - - + +
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Residues in contact with GLY 203 (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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199A ILE 2.8 14.1 + - - -
200A TYR 2.9 4.4 + - - -
202A ALA* 1.3 73.1 - - - +
204A TYR* 1.3 56.7 + - - +
206A ALA* 3.4 4.2 + - - +
207A GLY* 3.1 22.3 + - - -
220A LEU* 3.8 13.3 - - - +
223A ILE* 3.5 31.8 - - - +
224A TYR* 4.2 9.6 - - - -
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Residues in contact with TYR 204 (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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138A GLY* 3.6 9.9 - - - -
141A GLY* 3.6 19.9 - - - -
142A GLU* 3.5 40.6 - - + -
148A VAL* 2.9 30.1 + - - +
151A ALA* 4.2 0.3 - - - +
152A PHE* 3.4 37.0 + + + -
200A TYR 2.9 9.7 + - - +
201A PRO* 3.6 11.4 - - + +
203A GLY* 1.3 73.9 - - - +
205A ALA* 1.3 58.8 + - - +
207A GLY 3.3 0.3 + - - -
208A TYR* 3.0 39.2 + + - +
209A LEU* 4.2 12.3 - - + -
220A LEU* 4.2 4.5 - - - -
224A TYR* 3.4 12.8 + - - +
301A RET 3.6 20.2 - - + -
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Residues in contact with ALA 205 (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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152A PHE* 4.8 5.6 - - + -
201A PRO 2.9 19.5 + - - +
202A ALA* 3.6 7.2 - - - +
204A TYR* 1.3 73.5 - - - +
206A ALA* 1.3 60.2 + - - +
209A LEU* 2.8 57.4 + - + +
210A MET* 3.7 9.2 + - + +
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Residues in contact with ALA 206 (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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202A ALA 3.0 18.3 + - - +
203A GLY 3.5 7.0 - - - +
205A ALA* 1.3 76.5 - - - +
207A GLY* 1.3 57.0 + - - +
210A MET* 3.9 25.2 - - + +
216A TYR* 3.4 28.3 - - - +
219A ASN* 4.4 15.0 - - + +
223A ILE* 3.8 20.2 - - + -
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Residues in contact with GLY 207 (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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203A GLY 3.1 13.2 + - - -
204A TYR 3.8 1.6 - - - -
206A ALA* 1.3 78.6 - - - +
208A TYR* 1.3 65.7 + - - +
210A MET 5.4 0.4 - - - -
214A GLY 4.6 1.2 - - - +
215A VAL* 3.6 10.4 - - - +
216A TYR* 2.8 44.5 + - - +
220A LEU* 4.0 10.3 - - - -
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Residues in contact with TYR 208 (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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89A THR* 4.7 4.9 + - + +
91A THR* 4.5 5.7 + - - -
141A GLY 5.3 0.2 - - - -
142A GLU* 2.6 63.5 + - + +
148A VAL* 4.1 32.3 - - + +
204A TYR* 3.0 31.8 + + + +
207A GLY* 1.3 78.8 - - - +
209A LEU* 1.3 73.3 + - + +
210A MET 3.6 2.8 + - - -
211A GLY 5.0 2.6 + - - -
214A GLY 5.8 0.7 - - - -
215A VAL* 3.6 34.6 - - + +
220A LEU* 3.7 27.1 - - + +
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Residues in contact with LEU 209 (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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148A VAL* 3.8 35.0 - - + +
149A LEU* 4.3 16.2 - - + +
152A PHE* 3.9 37.9 - - + -
204A TYR* 4.2 3.4 - - + -
205A ALA* 2.8 38.8 + - + +
208A TYR* 1.3 84.0 - - + +
210A MET* 1.3 64.3 + - + +
211A GLY 4.0 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