Contacts of the helix formed by residues 189 - 211 (chain D) in PDB entry 2QW4
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 GLU 189 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU* 4.5 2.9 - - + +
103D ASP* 3.3 7.3 + - - +
188D GLN* 1.3 89.5 - - + +
190D PRO* 1.4 62.9 - - - +
191D ARG* 3.0 34.0 + - - +
192D ARG* 2.9 59.5 + - - +
193D VAL* 3.4 11.5 - - - +
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Residues in contact with PRO 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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183D ASP* 5.5 6.3 - - - +
187D LEU* 3.8 21.5 - - + +
188D GLN 3.2 12.3 - - - +
189D GLU* 1.4 82.1 - - - +
191D ARG* 1.3 67.7 + - + +
192D ARG 3.1 1.8 - - - -
193D VAL* 2.8 16.4 + - + +
194D GLU* 2.7 34.1 + - - +
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Residues in contact with ARG 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D GLN 4.7 0.4 + - - -
189D GLU* 3.0 74.5 + - - +
190D PRO* 1.3 90.2 - - + +
192D ARG* 1.3 61.3 - - + +
193D VAL 3.3 0.2 - - - -
194D GLU* 3.5 22.4 - - - +
195D GLU* 2.7 36.6 + - - +
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Residues in contact with ARG 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D GLU* 3.3 29.0 + - - +
99D LEU* 3.7 28.3 - - + +
100D SER* 4.8 6.3 - - - +
189D GLU* 2.9 54.3 + - - +
190D PRO 3.1 0.4 - - - -
191D ARG* 1.3 86.0 - - + +
193D VAL* 1.3 62.7 + - + +
195D GLU* 3.4 22.2 - - - +
196D LEU* 3.3 21.5 + - - +
199D ARG* 5.0 0.5 + - - -
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Residues in contact with VAL 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LEU* 3.6 25.6 - - + -
107D LEU* 4.2 13.5 - - + -
181D ILE* 3.6 7.6 - - + +
182D THR* 4.0 27.1 - - - +
183D ASP* 4.9 0.4 - - - +
187D LEU* 3.7 36.8 - - + -
189D GLU 3.4 13.9 - - - +
190D PRO* 2.8 14.9 + - + +
192D ARG* 1.3 74.1 - - - +
194D GLU* 1.3 56.8 + - - +
196D LEU* 3.2 5.5 + - - +
197D GLN* 2.9 27.8 + - - +
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Residues in contact with GLU 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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56B PHE* 4.3 4.2 - - - +
57B GLN* 3.1 53.0 - - + +
58B GLU* 3.5 10.4 + - - +
183D ASP* 6.1 1.1 - - - +
190D PRO 2.7 16.3 + - - +
191D ARG* 3.5 22.5 - - - +
193D VAL* 1.3 70.7 - - - +
195D GLU* 1.3 66.6 + - - +
197D GLN* 3.4 14.0 + - - +
198D ASN* 3.0 39.5 + - - +
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Residues in contact with GLU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D ARG* 2.7 26.3 + - - +
192D ARG* 3.4 24.0 - - - +
194D GLU* 1.3 76.9 - - - +
196D LEU* 1.3 60.5 + - - +
198D ASN* 3.3 19.6 + - - +
199D ARG* 2.8 42.4 + - - +
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Residues in contact with LEU 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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33D LEU* 4.5 8.7 - - + -
93D ILE* 5.3 2.7 - - + -
94D PRO 3.8 25.6 - - - +
95D GLY* 4.0 22.4 - - - +
96D PHE* 4.3 2.9 - - - +
99D LEU* 4.7 9.9 - - + -
181D ILE* 4.3 18.4 - - + -
192D ARG 3.3 9.6 + - - +
193D VAL* 3.2 9.7 + - - +
195D GLU* 1.3 76.1 - - - +
197D GLN* 1.3 69.9 + - - +
198D ASN 3.2 0.2 + - - -
199D ARG* 3.3 28.5 + - + +
200D ILE* 3.1 48.6 + - + +
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Residues in contact with GLN 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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57B GLN* 4.8 8.3 + - - -
59B LEU* 5.4 9.4 - - + +
178D LEU* 3.7 15.7 - - + +
181D ILE* 3.4 31.4 - - + +
182D THR* 3.4 13.2 + - - +
183D ASP* 4.1 25.7 + - - +
193D VAL* 2.9 14.2 + - - +
194D GLU* 3.4 18.9 - - - +
196D LEU* 1.3 76.5 - - - +
198D ASN* 1.3 66.0 + - - +
200D ILE* 3.3 7.0 + - - +
201D ALA* 2.8 28.6 + - + +
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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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58B GLU* 2.8 39.1 + - - +
59B LEU* 5.0 6.2 - - - +
60B VAL* 3.6 15.9 + - + +
194D GLU* 3.0 27.4 + - - +
195D GLU* 3.4 10.5 + - - +
196D LEU 3.2 0.2 - - - -
197D GLN* 1.3 85.4 + - - +
199D ARG* 1.3 59.2 + - + +
201D ALA* 3.0 11.3 - - - +
202D SER* 2.8 28.4 + - - -
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Residues in contact with ARG 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 4.9 19.8 - - + +
94D PRO 5.7 0.4 + - - -
95D GLY* 6.2 1.4 - - - -
192D ARG 5.0 0.6 + - - -
195D GLU* 2.8 47.6 + - - +
196D LEU* 3.3 36.8 + - - +
198D ASN* 1.3 74.1 - - + +
200D ILE* 1.3 67.7 + - - +
202D SER* 2.9 11.1 + - - +
203D CYS* 2.8 28.9 + - - -
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Residues in contact with ILE 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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33D LEU* 4.7 6.9 - - + +
37D LEU* 4.0 12.6 - - + -
93D ILE* 5.0 6.1 - - + -
174D CYS* 3.8 27.3 - - + +
177D ALA* 3.9 22.0 - - + -
178D LEU* 3.5 18.6 - - + -
181D ILE* 4.2 19.3 - - + -
196D LEU* 3.1 42.8 + - + +
197D GLN* 3.4 7.2 - - - +
199D ARG* 1.3 74.1 - - - +
201D ALA* 1.3 61.9 + - - +
203D CYS* 3.0 21.7 + - - +
204D LEU* 3.1 12.6 + - - +
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Residues in contact with ALA 201 (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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60B VAL* 3.6 25.4 - - + +
61B LEU* 4.2 19.6 - - + +
178D LEU* 4.1 7.8 - - + +
197D GLN* 2.8 16.8 + - + +
198D ASN* 3.0 15.5 - - - +
200D ILE* 1.3 75.9 - - - +
202D SER* 1.3 49.2 + - - +
204D LEU* 3.4 7.6 + - - +
205D LYS* 2.8 35.2 + - - +
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Residues in contact with SER 202 (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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60B VAL* 4.2 12.8 - - - +
198D ASN 2.8 17.6 + - - -
199D ARG* 2.9 12.7 + - - -
201D ALA* 1.3 69.8 - - - +
203D CYS* 1.3 67.4 + - - +
205D LYS* 4.1 6.5 - - - +
206D GLU* 2.9 27.6 + - - +
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Residues in contact with CYS 203 (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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32D ASN* 5.9 1.6 - - - -
33D LEU* 3.6 32.5 - - - -
34D LEU* 3.9 22.8 - - + +
37D LEU* 4.8 3.1 - - - -
174D CYS* 4.0 13.2 - - - -
199D ARG* 2.8 22.0 + - - -
200D ILE* 3.2 13.9 - - - +
202D SER* 1.3 74.7 - - - +
204D LEU* 1.3 54.2 + - - +
206D GLU* 3.6 1.9 - - - +
207D HIS* 2.7 38.2 + - - +
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Residues in contact with LEU 204 (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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61B LEU* 4.1 10.5 - - + -
171D ALA* 4.0 33.0 - - + +
174D CYS* 3.9 15.8 - - + -
175D LEU* 4.8 6.1 - - + +
178D LEU* 4.1 22.9 - - + -
200D ILE 3.1 8.9 + - - +
201D ALA* 3.6 9.6 - - - +
203D CYS* 1.3 79.3 - - - +
205D LYS* 1.3 62.3 + - - +
207D HIS* 3.2 4.2 + - + +
208D VAL* 3.0 40.9 + - + +
221D LEU* 3.6 23.3 - - + -
224D LEU* 4.8 6.3 - - + -
225D LEU* 4.5 7.0 - - + -
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Residues in contact with LYS 205 (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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60B VAL* 3.5 38.4 - - + -
61B LEU* 3.8 15.9 - - + -
62B PRO* 5.6 2.9 - - - -
201D ALA 2.8 20.7 + - - +
202D SER* 4.1 7.0 - - - +
204D LEU* 1.3 73.6 - - - +
206D GLU* 1.3 60.7 + - - +
208D VAL* 3.3 10.1 - - + +
209D ALA* 3.2 22.0 + - - +
221D LEU* 4.4 11.2 - - + +
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Residues in contact with GLU 206 (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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202D SER* 2.9 19.0 + - - +
203D CYS* 4.0 1.6 - - - +
205D LYS* 1.3 74.3 - - - +
207D HIS* 1.3 63.9 + - - +
209D ALA* 3.4 9.5 - - + +
210D ALA* 3.3 18.9 + - - +
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Residues in contact with HIS 207 (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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34D LEU* 3.4 25.8 - - + +
168D ASP* 2.9 30.2 + - - -
170D PRO* 3.3 22.3 - - + +
171D ALA* 3.3 32.6 + - + -
203D CYS 2.7 22.3 + - - +
204D LEU* 3.6 5.2 - - + +
206D GLU* 1.3 74.9 - - - +
208D VAL* 1.3 64.3 + - + +
210D ALA* 3.4 8.7 - - - +
211D VAL* 3.4 35.7 + - + +
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Residues in contact with VAL 208 (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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171D ALA* 5.0 5.6 - - + -
204D LEU* 3.0 37.1 + - + +
205D LYS* 3.3 16.6 - - + +
207D HIS* 1.3 77.7 - - + +
209D ALA* 1.3 64.6 + - - +
210D ALA 3.2 1.0 + - - -
211D VAL* 3.6 24.7 - - + -
220D CYS* 5.6 10.5 - - + -
221D LEU* 3.7 34.8 - - + +
224D LEU* 5.1 4.5 - - + -
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Residues in contact with ALA 209 (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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205D LYS 3.2 15.9 + - - +
206D GLU* 3.4 19.3 - - + +
208D VAL* 1.3 79.1 - - - +
210D ALA* 1.3 62.9 + - - +
211D VAL 4.8 0.2 - - - -
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Residues in contact with ALA 210 (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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206D GLU 3.3 9.4 + - - +
207D HIS* 3.4 13.2 - - + +
208D VAL 3.2 0.2 - - - -
209D ALA* 1.3 80.3 - - - +
211D VAL* 1.3 74.7 + - + +
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Residues in contact with VAL 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ASP* 4.0 15.7 - - - +
207D HIS* 3.4 41.9 + - + +
208D VAL* 3.6 18.8 + - + +
209D ALA 4.8 0.2 - - - -
210D ALA* 1.3 80.4 - - + +
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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