Contacts of the helix formed by residues 181 - 195 (chain D) 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 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D TRP* 3.8 12.6 - - + -
179D SER* 3.4 3.9 + - - +
180D PRO* 1.3 79.8 - - + +
182D VAL* 1.3 67.6 + - - +
183D ASN* 3.0 2.0 - - - +
184D SER* 3.0 18.5 + - - -
185D ALA 3.2 9.5 + - - -
242D VAL* 3.5 16.8 - - + +
246D GLU* 3.6 38.4 - - + -
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Residues in contact with VAL 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D LYS* 5.3 8.5 - - + +
58D TRP* 4.8 13.9 - - + -
112D ILE* 4.3 12.7 - - + +
115D ALA* 3.7 27.4 - - + -
116D CYS* 3.6 26.7 - - - -
179D SER* 3.5 24.8 + - - +
181D ALA* 1.3 75.9 - - - +
183D ASN* 1.3 56.1 + - - +
185D ALA* 3.9 6.6 - - - +
186D TYR* 3.0 27.4 + - - +
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Residues in contact with ASN 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D CYS* 5.7 1.6 - - - -
179D SER 2.9 24.3 + - - +
180D PRO* 2.4 34.2 + - - +
182D VAL* 1.3 76.5 - - - +
184D SER* 1.3 78.2 + - - +
186D TYR* 3.2 7.9 - - - +
187D ASN* 3.0 38.5 + - - +
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Residues in contact with SER 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D PRO 3.6 6.1 + - - -
181D ALA* 3.0 9.2 + - - -
183D ASN* 1.3 90.6 + - - +
185D ALA* 1.3 57.2 + - - +
187D ASN* 3.4 11.7 + - - +
188D ALA* 2.8 29.0 + - - +
238D ILE* 5.4 0.2 - - - +
242D VAL* 3.7 20.7 - - - +
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Residues in contact with ALA 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D TRP* 4.6 8.3 - - + -
112D ILE* 3.9 29.2 - - + +
181D ALA 3.2 12.0 + - - +
182D VAL* 3.9 7.2 - - - +
184D SER* 1.3 74.9 - - - +
186D TYR* 1.3 66.5 + - - +
188D ALA* 3.3 9.5 - - - +
189D MET* 3.0 23.9 + - - +
239D ILE* 4.2 12.0 - - + +
242D VAL* 4.3 13.9 - - + -
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Residues in contact with TYR 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ILE* 4.1 3.5 - - + +
113D LEU* 3.6 18.2 - - + -
116D CYS* 3.6 28.3 - - + -
117D THR* 5.7 0.2 - - + -
166D LEU 4.1 2.4 + - - -
171D GLY 2.8 26.0 + - - -
173D ALA 4.1 8.8 + - - -
174D ALA 4.5 4.7 - - - -
182D VAL 3.0 16.7 + - - +
183D ASN* 3.2 11.9 - - - +
185D ALA* 1.3 74.3 - - - +
187D ASN* 1.3 74.5 + - - +
189D MET* 3.0 23.6 + - + +
190D MET* 2.9 59.0 + - + +
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Residues in contact with ASN 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D ASN* 3.0 23.7 + - - +
184D SER* 3.6 9.7 - - - +
186D TYR* 1.3 83.7 - - - +
188D ALA* 1.3 55.6 + - - +
190D MET* 3.1 8.3 + - - +
191D MET* 2.7 46.1 + - + +
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Residues in contact with ALA 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D SER 2.8 21.4 + - - +
185D ALA* 3.3 11.7 - - - +
187D ASN* 1.3 71.0 - - - +
189D MET* 1.3 56.6 + - - +
191D MET* 3.6 17.1 + - - +
192D ILE* 3.0 32.4 + - - +
235D PHE* 3.9 9.6 - - + -
238D ILE* 3.5 33.0 - - + +
239D ILE* 4.6 1.8 - - + -
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Residues in contact with MET 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D PHE* 3.3 55.0 - - + +
112D ILE* 4.3 12.6 - - + -
113D LEU* 3.9 18.8 - - + -
166D LEU* 4.3 11.4 - - + -
185D ALA 3.0 11.1 + - - +
186D TYR* 3.0 35.7 + - + +
188D ALA* 1.3 71.5 - - - +
190D MET* 1.3 94.1 - - + +
191D MET 3.1 1.3 - - - -
192D ILE* 3.1 11.3 + - - +
193D ILE* 3.1 26.3 + - - +
235D PHE* 4.1 2.8 - - + -
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Residues in contact with MET 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU* 4.8 1.6 - - + -
166D LEU* 3.6 49.1 - - + +
167D TYR* 3.3 38.2 + - + +
171D GLY 5.1 0.4 - - - +
186D TYR* 2.9 63.1 + - + +
187D ASN* 3.6 7.2 - - - +
189D MET* 1.3 96.0 - - + +
191D MET* 1.3 62.5 + - - +
193D ILE* 3.4 9.2 - - - +
194D VAL* 3.3 18.9 - - - +
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Residues in contact with MET 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D TYR* 4.5 3.6 - - - -
187D ASN* 2.7 30.4 + - + +
188D ALA* 3.6 15.9 - - - +
190D MET* 1.3 74.8 - - - +
192D ILE* 1.3 56.7 + - + +
194D VAL* 4.0 1.5 - - - +
195D VAL* 2.5 52.9 + - + +
238D ILE* 4.7 16.2 - - - -
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Residues in contact with ILE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LEU* 5.9 0.7 - - + -
109D PHE* 4.1 12.1 - - + -
188D ALA 3.0 17.1 + - - +
189D MET* 3.1 12.0 + - - +
191D MET* 1.3 75.6 - - + +
193D ILE* 1.3 62.8 + - - +
194D VAL 3.1 2.2 - - - -
195D VAL* 4.2 3.1 - - + -
196D GLY* 2.8 16.4 + - - +
197D TRP* 2.8 39.6 + - + +
230D VAL* 4.8 12.1 - - + +
231D ASN* 3.7 19.3 - - + +
234D LEU* 5.6 1.1 - - + -
235D PHE* 3.7 47.6 - - + +
238D ILE* 5.3 9.0 - - + -
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Residues in contact with ILE 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D PHE* 3.9 17.9 - - + -
127D LEU* 4.7 0.7 - - + -
159D TRP* 2.8 32.0 + - - +
162D MET* 3.8 41.5 - - + -
163D ILE* 3.7 6.5 - - + +
166D LEU* 3.9 31.9 - - + -
167D TYR* 5.2 1.6 - - + -
189D MET 3.3 15.7 - - - +
190D MET* 3.4 8.7 - - - +
192D ILE* 1.3 81.2 - - - +
194D VAL* 1.3 66.3 - - + +
197D TRP* 3.3 34.3 - - + +
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Residues in contact with VAL 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D TRP* 3.3 21.3 - - + -
163D ILE* 3.5 41.3 - - + -
167D TYR* 3.7 15.9 - - + +
190D MET 3.3 17.7 - - - +
191D MET* 3.4 3.0 + - - +
192D ILE 3.1 0.2 - - - -
193D ILE* 1.3 79.9 - - + +
195D VAL* 1.3 68.6 + - + +
198D ALA* 3.5 9.7 + - - +
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Residues in contact with VAL 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D MET* 2.5 57.7 + - + +
192D ILE* 4.2 3.4 - - + +
194D VAL* 1.3 78.2 - - + +
196D GLY* 1.3 65.8 + - - +
198D ALA* 3.5 15.8 - - - +
199D ILE* 4.5 4.9 + - - +
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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