Contacts of the helix formed by residues 189 - 201 (chain D) in PDB entry 3Q2K
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 189 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160D VAL* 3.9 20.0 - - + -
184D ALA 2.9 19.4 + - - +
185D PHE* 3.6 7.4 - - - +
188D GLN* 1.3 70.7 - - - +
190D SER* 1.3 59.1 + - - +
191D HIS 3.1 3.4 - - - -
192D TYR* 2.7 27.4 + - + -
193D VAL* 2.8 15.8 + - + +
237D ILE* 5.2 0.4 - - + -
239D VAL* 3.8 31.2 - - + -
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Residues in contact with SER 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D LYS* 3.3 22.2 - - - +
104D PRO* 4.9 3.1 - - - -
130D LYS* 4.3 12.1 + - - -
185D PHE 3.1 12.3 + - - -
186D MET 3.7 18.6 + - - -
187D ASN 3.2 12.9 + - - -
188D GLN 3.3 2.0 - - - -
189D ALA* 1.3 78.5 - - - +
191D HIS* 1.3 59.0 + - - +
193D VAL* 3.8 6.9 - - - +
194D ASP* 3.0 27.5 + - - +
328D SER* 4.9 2.9 - - - -
332D LEU* 4.4 12.8 - - - -
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Residues in contact with HIS 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D LYS* 3.5 22.0 - - + +
129D VAL 4.6 2.7 - - - -
130D LYS* 4.7 11.2 - - - +
131D GLN* 3.4 31.4 - - - -
132D ASN* 3.4 41.1 + - + +
188D GLN 4.2 6.5 - - - -
189D ALA 3.1 0.6 - - - -
190D SER* 1.3 77.7 + - - +
192D TYR* 1.3 65.4 + - + +
194D ASP* 3.3 21.3 - - - +
195D LEU* 3.4 15.9 - - - +
500D NAI 3.5 13.2 + - - -
550D HP7 3.1 42.3 + - - -
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Residues in contact with TYR 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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132D ASN* 4.3 7.4 + - - -
158D VAL* 4.0 16.9 - - + +
160D VAL* 3.7 29.2 - - + -
162D TRP* 3.5 29.6 - + - -
188D GLN 4.7 0.4 - - - -
189D ALA* 2.7 18.1 + - - +
191D HIS* 1.3 88.2 - - + +
193D VAL* 1.3 65.9 + - - +
195D LEU* 2.9 34.4 + - + +
196D LEU* 3.9 7.1 + - - +
237D ILE* 4.1 6.3 - - + +
250D GLY* 4.1 15.5 - - - -
251D SER 5.0 0.2 - - - -
267D ALA* 3.1 35.5 - - - +
268D VAL* 3.7 29.5 - - + +
550D HP7 4.6 2.0 + - - -
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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
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185D PHE* 4.0 18.8 - - + +
189D ALA* 2.8 17.5 + - + +
190D SER* 3.8 7.6 - - - +
192D TYR* 1.3 73.1 - - - +
194D ASP* 1.3 61.9 + - - +
196D LEU* 3.2 24.8 + - + +
237D ILE* 3.8 22.2 - - + +
328D SER* 4.4 5.6 - - - +
331D LEU* 3.7 35.9 - - + +
332D LEU* 4.0 30.7 - - + +
335D ILE* 4.5 7.6 - - + -
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Residues in contact with ASP 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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130D LYS* 3.1 31.2 - - - +
132D ASN* 6.0 1.0 - - - +
133D ARG* 2.9 49.0 + - - +
190D SER 3.0 14.3 + - - +
191D HIS 3.3 14.6 - - - +
193D VAL* 1.3 74.5 - - - +
195D LEU* 1.3 66.3 + - - +
196D LEU 3.3 0.5 + - - -
197D ASP* 3.6 4.5 + - - +
198D TRP* 3.0 24.2 + - - +
324D GLU 4.9 2.6 - - - +
327D GLN* 5.8 0.9 - - - +
328D SER* 4.1 19.6 + - - +
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Residues in contact with LEU 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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132D ASN* 5.5 5.2 - - + +
133D ARG* 5.8 1.1 - - + -
138D LEU* 3.8 28.3 - - + -
158D VAL* 5.5 1.6 - - + -
191D HIS 3.4 14.6 - - - +
192D TYR* 2.9 36.6 + - + +
194D ASP* 1.3 78.2 - - - +
196D LEU* 1.3 66.6 + - + +
198D TRP* 4.0 21.3 - - + +
199D LEU* 2.8 35.0 + - + +
200D VAL* 3.7 1.2 + - - +
252D ILE* 4.2 30.5 - - + -
268D VAL* 4.4 15.0 - - + -
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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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156D VAL* 5.0 2.9 - - + -
158D VAL* 3.9 29.4 - - + -
192D TYR 4.1 4.7 - - - +
193D VAL* 3.2 25.7 + - + +
195D LEU* 1.3 76.3 - - - +
197D ASP* 1.3 61.3 + - - +
200D VAL* 3.3 14.7 + - - +
201D GLY 3.4 0.5 + - - -
203D VAL* 4.3 3.4 - - + -
227D LEU* 4.1 34.3 - - + -
229D TRP* 3.2 45.8 + - + -
237D ILE* 4.4 13.2 - - + -
252D ILE* 5.6 0.9 - - + -
331D LEU* 3.9 19.7 - - + -
335D ILE* 5.4 1.1 - - + -
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Residues in contact with ASP 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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133D ARG* 5.5 1.1 + - - +
193D VAL 4.1 0.8 + - - -
194D ASP* 3.6 6.1 + - - +
196D LEU* 1.3 81.0 - - - +
198D TRP* 1.3 66.5 + - - +
201D GLY* 3.0 39.6 + - - +
202D PRO* 3.4 17.0 - - - +
203D VAL* 4.2 5.0 + - + +
324D GLU* 5.0 5.0 - - - +
327D GLN* 2.6 43.7 - - + +
328D SER* 5.8 0.9 - - - +
331D LEU* 4.3 15.2 - - + +
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Residues in contact with TRP 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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133D ARG* 3.4 83.1 - - + +
138D LEU* 4.2 15.5 - - + -
139D GLN* 3.7 19.5 - - - -
142D LYS* 3.1 49.6 + - + +
194D ASP 3.0 20.3 + - - +
195D LEU* 4.0 14.8 - - + -
197D ASP* 1.3 81.3 - - - +
199D LEU* 1.3 92.5 + - + +
201D GLY 4.7 0.2 + - - -
324D GLU* 3.7 9.4 - - - -
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Residues in contact with LEU 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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138D LEU* 4.0 19.5 - - + +
141D VAL* 4.1 18.4 - - + -
142D LYS* 3.6 36.4 + - + +
145D ILE* 3.2 31.7 - - + +
195D LEU* 2.8 22.6 + - + +
198D TRP* 1.3 105.7 - - + +
200D VAL* 1.3 67.3 + - + +
252D ILE* 3.8 26.9 - - + -
254D ILE* 4.3 2.2 - - + -
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Residues in contact with VAL 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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145D ILE* 4.8 5.7 - - + +
153D ILE* 4.1 22.8 - - + +
156D VAL* 4.2 20.2 - - + -
195D LEU 4.6 2.0 - - - +
196D LEU* 3.3 16.3 + - - +
199D LEU* 1.3 84.5 - - + +
201D GLY* 1.3 58.7 + - - +
229D TRP* 3.7 22.2 - - + +
231D HIS* 2.8 43.1 + - + +
252D ILE* 5.0 3.1 - - + -
254D ILE* 4.0 26.9 - - + -
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Residues in contact with GLY 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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196D LEU 3.4 0.2 + - - -
197D ASP* 3.0 29.4 + - - +
199D LEU 3.6 0.8 - - - -
200D VAL* 1.3 80.7 - - - +
202D PRO* 1.3 78.2 - - - +
203D VAL 3.4 0.2 + - - -
229D TRP* 3.2 14.2 + - - -
231D HIS* 4.6 1.8 - - - -
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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