Contacts of the helix formed by residues 186 - 200 (chain D) in PDB entry 4K9P
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 186 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182C SER* 2.8 42.5 + - - +
183C VAL* 4.4 0.2 - - - +
184C ARG* 4.5 9.6 - - + -
320C ALA* 4.5 13.9 - - + -
184D ARG* 3.5 3.0 + - - +
185D LEU* 1.3 77.4 - - - +
187D ASP* 1.3 67.3 + - - +
188D GLN* 3.2 13.6 + - - +
189D ASP* 2.5 48.2 + - - +
190D LEU* 2.9 20.1 + - - +
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Residues in contact with ASP 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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184C ARG* 3.5 17.0 + - - +
184D ARG* 2.7 38.8 + - - +
185D LEU 3.6 0.2 + - - -
186D ASN* 1.3 72.0 - - - +
188D GLN* 1.3 63.8 + - - +
190D LEU* 3.4 4.0 + - - +
191D ASP* 3.0 34.5 + - - +
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Residues in contact with GLN 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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186D ASN* 3.3 10.4 + - - +
187D ASP* 1.3 81.0 - - - +
189D ASP* 1.3 74.1 + - - +
191D ASP* 3.4 6.5 + - - +
192D ILE* 3.3 28.0 + - + +
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Residues in contact with ASP 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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180C SER* 4.7 4.0 + - - -
182C SER* 4.2 6.8 + - - -
185D LEU* 3.7 20.4 - - + +
186D ASN* 2.5 35.1 + - - +
188D GLN* 1.3 84.9 - - - +
190D LEU* 1.3 66.6 + - - +
192D ILE* 3.1 19.0 + - - +
193D LEU* 3.0 20.8 + - - +
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Residues in contact with LEU 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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184D ARG* 3.9 29.2 - - - +
185D LEU* 3.6 22.1 - - + +
186D ASN 2.9 19.1 + - - +
187D ASP* 3.7 4.7 - - - +
189D ASP* 1.3 77.5 - - - +
191D ASP* 1.3 58.7 + - - +
193D LEU* 3.0 14.4 + - + +
194D VAL* 2.8 27.8 + - + +
321D MET* 4.5 9.9 - - + -
324D ALA* 4.2 11.7 - - + -
325D LEU* 3.9 27.8 - - + -
328D LEU* 3.7 29.2 - - + -
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Residues in contact with ASP 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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187D ASP* 3.0 26.0 + - - +
188D GLN* 3.7 6.9 - - - +
189D ASP 3.3 0.4 - - - -
190D LEU* 1.3 79.0 - - - +
192D ILE* 1.3 62.1 + - + +
194D VAL* 3.3 7.3 + - - +
195D LYS* 2.9 26.5 + - - +
328D LEU* 4.8 13.3 - - - +
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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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188D GLN* 3.3 21.7 + - + +
189D ASP* 3.1 22.7 + - - +
191D ASP* 1.3 77.4 - - + +
193D LEU* 1.3 62.1 + - - +
195D LYS* 3.2 9.1 - - + +
196D ALA* 3.0 23.2 + - + +
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Residues in contact with LEU 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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185D LEU* 4.7 3.6 - - + -
189D ASP 3.0 11.7 + - - +
190D LEU* 3.0 13.9 + - + +
192D ILE* 1.3 77.2 - - - +
194D VAL* 1.3 56.9 + - - +
196D ALA* 3.1 6.4 + - + +
197D LEU* 3.0 35.9 + - + +
271D LEU* 5.0 2.9 - - + -
294D ARG* 5.8 0.7 - - - +
296D ILE* 3.7 39.3 - - + -
298D VAL* 4.9 4.0 - - + -
314D ILE* 3.8 24.2 - - + -
321D MET* 4.3 12.3 - - + -
325D LEU* 3.9 29.4 - - + -
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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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190D LEU* 2.8 23.7 + - + +
191D ASP* 3.8 8.7 - - - +
193D LEU* 1.3 68.9 - - - +
195D LYS* 1.3 55.3 - - - +
197D LEU* 3.1 8.7 + - - +
198D ASN* 2.8 51.6 + - - +
325D LEU* 4.1 21.1 - - + -
328D LEU* 3.8 48.2 - - + +
329D VAL* 4.2 8.5 - - + -
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Residues in contact with LYS 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 ASP 2.9 14.1 + - - +
192D ILE* 3.2 15.9 - - + +
194D VAL* 1.3 75.4 - - - +
196D ALA* 1.3 54.8 + - - +
198D ASN* 3.3 10.7 + - - +
199D SER* 2.7 62.7 + - - +
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Residues in contact with ALA 196 (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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192D ILE* 3.0 11.5 + - + +
193D LEU* 3.1 12.3 + - - +
195D LYS* 1.3 79.7 - - - +
197D LEU* 1.3 61.9 + - - +
199D SER* 3.5 5.9 + - - -
200D ALA* 3.2 22.2 + - - +
269D VAL* 4.5 9.5 - - + +
294D ARG* 4.0 24.9 - - - +
296D ILE* 4.8 9.2 - - + -
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Residues in contact with LEU 197 (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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193D LEU* 3.0 31.9 + - + +
194D VAL* 3.1 6.9 + - - +
196D ALA* 1.3 74.0 - - - +
198D ASN* 1.3 64.2 + - - +
199D SER 3.5 0.3 + - - -
200D ALA* 3.5 17.1 + - - +
203D PRO* 4.8 6.4 - - + +
223D LEU* 5.1 1.1 - - + -
227D LEU* 3.6 31.2 - - + +
269D VAL* 4.4 20.6 - - + -
271D LEU* 4.0 38.4 - - + -
296D ILE* 5.1 0.9 - - + -
325D LEU* 4.2 20.0 - - + -
329D VAL* 4.1 24.7 - - + -
334D ARG* 5.1 0.9 + - - -
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Residues in contact with ASN 198 (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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194D VAL* 2.8 41.9 + - - +
195D LYS* 3.7 11.0 - - - +
197D LEU* 1.3 72.7 - - - +
199D SER* 1.3 61.4 + - - +
200D ALA 3.5 5.4 + - - +
227D LEU* 4.9 3.5 - - - +
328D LEU 4.7 0.8 + - - -
329D VAL* 3.7 8.0 - - - +
330D GLU* 2.8 64.6 + - - +
334D ARG* 5.2 3.1 + - - -
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Residues in contact with SER 199 (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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195D LYS* 2.7 44.2 + - - +
196D ALA* 4.0 5.8 - - - -
197D LEU 3.3 0.2 - - - -
198D ASN* 1.3 75.1 - - - +
200D ALA* 1.3 64.7 + - - +
201D SER* 3.6 2.9 + - - -
268D ASP* 4.9 0.3 - - - +
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Residues in contact with ALA 200 (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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196D ALA 3.2 12.5 + - - +
197D LEU* 3.7 13.4 - - + +
198D ASN 3.3 6.1 - - - +
199D SER* 1.3 79.1 - - - +
201D SER* 1.3 59.4 + - - +
203D PRO* 4.1 14.6 - - + -
268D ASP* 3.6 12.1 - - - +
269D VAL* 3.7 27.8 - - + -
334D ARG* 3.0 22.7 + - - -
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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