Contacts of the helix formed by residues 216 - 232 (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 TYR 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A ALA 3.4 27.1 - - - +
207A GLY* 2.8 14.6 + - - +
210A MET* 4.6 18.1 + - + -
211A GLY* 4.1 28.2 - - - -
212A GLY 4.9 2.4 + - - -
214A GLY* 4.6 10.3 - - - -
215A VAL* 1.3 73.9 - - - +
217A ALA* 1.3 64.6 + - - +
218A SER* 3.4 2.7 - - - -
219A ASN* 3.3 21.7 + - - +
220A LEU* 3.1 21.1 + - - +
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Residues in contact with ALA 217 (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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83A TRP* 4.3 14.4 - - + -
87A GLY 5.3 1.6 - - - +
89A THR* 4.2 28.0 - - + +
215A VAL* 3.0 15.3 + - + +
216A TYR* 1.3 70.9 - - - +
218A SER* 1.3 64.1 + - - +
220A LEU* 3.2 11.0 + - - +
221A ASN* 2.9 29.9 + - - +
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Residues in contact with SER 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.6 25.2 - - - +
83A TRP* 4.4 8.9 - - - -
216A TYR 3.4 0.4 - - - -
217A ALA* 1.3 78.3 - - - +
219A ASN* 1.3 69.9 + - - +
222A LEU* 3.1 32.2 + - - +
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Residues in contact with ASN 219 (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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206A ALA* 4.4 19.1 + - + +
210A MET* 6.1 2.8 - - - +
216A TYR* 3.3 29.7 + - + +
218A SER* 1.3 82.2 - - - +
220A LEU* 1.3 58.1 + - - +
222A LEU* 3.3 11.1 + - - +
223A ILE* 2.9 40.0 + - + +
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Residues in contact with LEU 220 (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* 3.6 30.3 - - + +
142A GLU* 3.8 2.2 - - - +
203A GLY 3.8 20.0 - - - +
204A TYR* 4.2 0.7 - - - -
207A GLY* 4.0 8.5 - - - -
208A TYR* 3.7 36.6 - - + +
215A VAL* 4.8 3.4 - - + -
216A TYR 3.1 15.5 + - - +
217A ALA* 3.5 11.7 - - - +
219A ASN* 1.3 78.1 - - - +
221A ASN* 1.3 63.4 + - - +
223A ILE* 3.4 1.0 + - - +
224A TYR* 3.1 72.0 + - + +
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Residues in contact with ASN 221 (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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29A VAL* 4.0 19.5 - - + -
33A PHE* 4.3 6.3 - - + -
83A TRP* 3.7 12.5 - - - -
89A THR* 3.3 36.8 + - - +
90A PRO* 3.7 14.8 - - - +
94A ARG* 2.8 29.5 + - - +
217A ALA 2.9 21.3 + - - +
218A SER 4.3 0.4 - - - +
220A LEU* 1.3 81.1 - - - +
222A LEU* 1.3 56.5 + - - +
224A TYR* 3.4 3.3 + - - +
225A ASN* 2.8 39.0 + - - +
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 4.2 19.3 - - + -
29A VAL* 3.6 39.3 - - + +
32A SER* 3.8 17.3 + - - -
218A SER* 3.1 26.0 + - - +
219A ASN* 3.5 8.5 - - - +
221A ASN* 1.3 74.9 - - - +
223A ILE* 1.3 59.8 + - + +
225A ASN* 3.6 5.7 + - - +
226A LEU* 3.0 26.7 + - - +
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Residues in contact with ILE 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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199A ILE* 3.4 36.7 - - + +
202A ALA* 4.4 5.4 - - + +
203A GLY* 3.5 25.1 - - - +
206A ALA* 3.8 20.9 - - + -
219A ASN* 2.9 20.2 + - + +
220A LEU 4.0 0.7 - - - +
222A LEU* 1.3 78.0 - - + +
224A TYR* 1.3 61.5 + - - +
226A LEU* 3.3 10.1 + - + +
227A ALA* 2.9 25.8 + - - +
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Residues in contact with TYR 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.5 41.5 - - + +
98A TRP* 3.6 28.7 - + + -
142A GLU* 2.8 28.1 + - - -
200A TYR* 3.4 35.2 - + - -
203A GLY* 4.2 2.7 - - - -
204A TYR* 3.4 24.9 - - - +
220A LEU* 3.1 43.0 + - + +
221A ASN* 3.8 2.5 - - - +
223A ILE* 1.3 74.4 - - - +
225A ASN* 1.3 67.7 + - - +
227A ALA* 2.9 5.9 + - - +
228A ASP* 2.8 27.0 + - - -
301A RET 3.6 5.2 - - + +
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Residues in contact with ASN 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 4.3 1.2 + - - +
32A SER* 2.6 35.7 + - - +
33A PHE* 3.3 32.0 - - - +
36A VAL* 4.0 16.1 - - + +
76A TYR* 3.3 17.4 + - - -
94A ARG* 3.0 28.1 + - - -
221A ASN* 2.8 26.0 + - - +
222A LEU 3.7 3.1 - - - +
224A TYR* 1.3 71.7 - - - +
226A LEU* 1.3 61.7 + - - +
228A ASP 3.6 0.2 + - - -
229A PHE* 3.1 22.9 + - - +
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Residues in contact with LEU 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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36A VAL* 5.7 0.4 - - - -
199A ILE* 4.5 20.2 - - + -
222A LEU 3.0 15.9 + - - +
223A ILE* 3.5 11.4 - - + +
224A TYR 3.2 0.2 - - - -
225A ASN* 1.3 74.9 - - - +
227A ALA* 1.3 58.2 + - - +
229A PHE* 3.3 14.9 + - + +
230A VAL* 2.9 43.8 + - + +
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Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ILE* 3.6 26.7 - - + +
200A TYR* 3.1 38.3 + - + +
223A ILE 2.9 16.4 + - - +
224A TYR 2.9 2.8 + - - +
226A LEU* 1.3 75.2 - - - +
228A ASP* 1.3 59.9 + - - +
231A ASN* 2.6 38.8 + - - +
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Residues in contact with ASP 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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36A VAL* 5.1 0.9 - - + -
40A MET* 5.1 3.4 - - - -
76A TYR* 2.6 42.7 + - + +
94A ARG* 3.3 15.9 + - - -
97A ASN* 4.6 3.1 + - - -
98A TRP* 2.9 25.6 + - - -
200A TYR* 2.7 27.1 + - - -
224A TYR 2.8 13.0 + - - +
227A ALA* 1.3 68.5 - - - +
229A PHE* 1.3 59.7 + - - +
232A LYS* 2.8 57.7 + - + +
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Residues in contact with PHE 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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35A LEU 5.9 0.9 - - - -
36A VAL* 4.8 22.0 - - + +
39A GLY* 5.1 6.5 - - - -
40A MET* 5.6 0.2 - - - -
225A ASN 3.1 13.2 + - - +
226A LEU* 3.4 19.1 - - + +
228A ASP* 1.3 79.4 - - - +
230A VAL* 1.3 65.7 + - + +
233A ILE* 3.3 46.4 + - + +
234A LEU* 3.1 49.8 + - + -
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Residues in contact with VAL 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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192A ILE* 4.4 7.6 - - + +
196A GLY* 4.3 13.2 - - - -
199A ILE* 4.1 18.6 - - + -
226A LEU* 2.9 31.9 + - + +
227A ALA 3.3 3.6 + - - +
229A PHE* 1.3 76.2 - - + +
231A ASN* 1.3 72.8 + - - +
234A LEU* 3.1 30.4 + - + +
235A PHE* 3.0 27.2 + - - +
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Residues in contact with ASN 231 (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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105A LEU* 4.0 10.0 - - + +
192A ILE* 3.2 20.3 - - + +
196A GLY* 3.0 40.1 + - - -
197A TRP* 3.3 16.4 - - + +
200A TYR* 3.4 24.2 - - + +
227A ALA* 2.6 30.3 + - - +
230A VAL* 1.3 82.2 - - - +
232A LYS* 1.3 59.3 + - + +
235A PHE* 3.2 30.3 - - - +
301A RET 4.7 6.1 - - + -
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Residues in contact with LYS 232 (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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40A MET* 4.2 13.9 - - + -
47A PHE* 4.3 1.0 - - - -
65A SER* 5.5 0.3 - - - +
68A ILE* 3.5 28.0 - - + -
69A THR* 4.2 9.7 - - + +
72A ALA* 3.9 21.5 - - + -
97A ASN* 4.5 3.6 - - - +
98A TRP* 4.0 3.4 - - - -
101A THR* 3.1 21.4 + - - -
105A LEU* 5.4 2.2 - - + -
228A ASP* 2.8 39.7 + - + +
231A ASN* 1.3 72.7 - - - +
233A ILE* 1.3 67.6 + - - +
235A PHE* 5.5 0.2 - - - -
236A GLY* 3.2 17.3 + - - -
301A RET 1.3 73.6 - - + +
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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