Contacts of the helix formed by residues 189 - 199 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160P VAL* 4.1 30.5 - - + -
184P ALA 2.9 17.3 + - - +
185P PHE* 3.5 5.8 - - - +
188P GLN* 1.3 76.2 - - - +
190P SER* 1.3 65.2 + - - +
191P HIS 3.1 2.9 - - - -
192P TYR* 2.9 19.6 + - + +
193P VAL* 3.0 13.6 + - + +
237P ILE* 5.8 0.2 - - + -
239P VAL* 4.1 17.7 - - + -
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Residues in contact with SER 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P LYS* 2.9 35.0 - - - +
104P PRO* 5.4 3.8 - - - -
185P PHE 3.2 11.5 + - - -
186P MET* 3.3 22.4 - - - -
187P ASN 3.3 5.3 + - - -
188P GLN 3.7 0.2 - - - -
189P ALA* 1.3 76.3 - - - +
191P HIS* 1.3 56.0 + - - +
193P VAL* 3.1 7.4 + - - +
194P ASP* 2.7 35.0 + - - +
328P SER* 5.5 1.4 - - - -
332P LEU* 4.5 11.6 - - - +
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Residues in contact with HIS 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P LYS* 3.8 22.9 - - + +
130P LYS* 3.9 25.8 - - + +
131P GLN* 3.4 22.5 + - - -
132P ASN* 3.7 35.8 - - + +
188P GLN 5.3 1.1 + - - +
189P ALA* 3.1 1.0 - - - -
190P SER* 1.3 81.5 + - - +
192P TYR* 1.3 68.1 + - + +
194P ASP* 3.1 22.6 + - - +
195P LEU* 3.5 14.7 + - - +
500P NAI 3.3 19.3 + - - -
550P HP7 3.7 36.3 + - - +
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Residues in contact with TYR 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P ASN* 5.1 5.2 + - - -
158P VAL* 3.9 19.8 - - + +
159P ASN 4.7 0.7 - - - -
160P VAL* 3.4 28.7 - - + -
162P TRP* 3.4 34.0 - + - -
188P GLN 4.9 0.2 - - - -
189P ALA* 2.9 19.0 + - + +
191P HIS* 1.3 82.2 - - + +
193P VAL* 1.3 64.5 + - - +
195P LEU* 2.9 30.8 + - + +
196P LEU* 3.8 5.7 + - - +
237P ILE* 4.1 6.3 - - + +
250P GLY* 4.1 12.8 - - - -
251P SER 4.8 0.4 - - - -
266P VAL 4.1 0.7 + - - -
267P ALA* 3.2 32.2 - - - +
268P VAL* 3.8 32.7 - - + +
550P HP7 4.5 7.8 + - - -
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Residues in contact with VAL 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185P PHE* 3.9 32.1 - - + +
189P ALA* 3.0 17.0 + - + +
190P SER* 3.4 8.1 - - - +
192P TYR* 1.3 77.6 - - - +
194P ASP* 1.3 62.0 + - - +
196P LEU* 3.2 28.9 + - + +
197P ASP* 4.2 1.0 + - - +
237P ILE* 4.1 10.1 - - + -
328P SER* 4.7 3.5 - - - +
331P LEU* 3.7 27.7 - - + +
332P LEU* 4.0 31.2 - - + -
335P ILE* 4.6 7.2 - - + -
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Residues in contact with ASP 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130P LYS* 3.3 30.8 + - + +
132P ASN* 5.9 1.6 - - - +
133P ARG* 3.0 49.0 + - - +
190P SER 2.7 15.7 + - - +
191P HIS* 3.1 22.0 + - - +
193P VAL* 1.3 73.5 - - - +
195P LEU* 1.3 64.0 + - - +
196P LEU 3.4 0.2 + - - -
197P ASP* 3.6 5.1 + - - +
198P TRP* 3.1 20.4 + - - +
328P SER* 4.2 13.4 - - - -
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Residues in contact with LEU 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P ASN* 6.0 3.6 - - + +
133P ARG* 6.0 0.7 - - + -
138P LEU* 3.9 35.2 - - + -
158P VAL* 5.3 1.3 - - + -
191P HIS 3.5 13.2 - - - +
192P TYR* 2.9 31.2 + - + +
194P ASP* 1.3 79.0 - - - +
196P LEU* 1.3 65.6 + - + +
198P TRP* 3.9 27.8 - - + -
199P LEU* 2.9 40.0 + - + +
200P VAL* 3.6 0.9 + - - +
252P ILE* 4.0 29.6 - - + -
268P VAL* 4.9 3.8 - - + -
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Residues in contact with LEU 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156P VAL* 4.7 4.3 - - + -
158P VAL* 3.8 27.8 - - + -
192P TYR 4.1 4.7 - - - +
193P VAL* 3.2 20.8 + - + +
195P LEU* 1.3 75.6 - - - +
197P ASP* 1.3 58.5 + - - +
200P VAL* 3.3 15.5 - - - +
201P GLY 3.4 0.3 - - - +
203P VAL* 4.7 4.0 - - + -
227P LEU* 3.9 25.6 - - + -
229P TRP* 3.0 41.5 + - + -
236P SER 5.2 1.1 - - - +
237P ILE* 3.9 34.3 - - + -
252P ILE* 5.6 1.1 - - + -
331P LEU* 4.0 19.7 - - + -
335P ILE* 5.5 1.6 - - + -
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Residues in contact with ASP 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P ARG* 5.1 2.3 + - - -
193P VAL 4.2 1.2 + - - +
194P ASP* 3.6 6.3 + - - +
195P LEU 3.2 0.2 - - - -
196P LEU* 1.3 78.6 - - - +
198P TRP* 1.3 73.5 + - - +
201P GLY* 3.0 35.2 + - - +
202P PRO* 4.0 11.8 - - - +
203P VAL* 4.7 5.5 + - + -
324P GLU* 4.8 6.4 - - - +
327P GLN* 3.3 41.2 - - + +
328P SER* 5.8 2.2 - - - +
331P LEU* 5.0 13.7 - - + -
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Residues in contact with TRP 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P ARG* 3.2 88.0 - - + +
138P LEU* 4.2 13.9 - - + -
139P GLN* 4.0 13.0 - - - -
142P LYS* 3.1 56.0 + - + +
194P ASP 3.1 16.0 + - - +
195P LEU* 3.9 20.6 - - + -
197P ASP* 1.3 88.2 + - - +
199P LEU* 1.3 85.5 + - + +
201P GLY* 4.5 0.7 + - - -
324P GLU* 4.7 3.8 - - - -
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Residues in contact with LEU 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138P LEU* 3.9 17.3 - - + +
141P VAL* 4.0 16.4 - - + -
142P LYS* 3.4 49.8 + - + +
145P ILE* 3.1 31.5 - - + +
195P LEU* 2.9 33.3 + - + +
198P TRP* 1.3 92.9 - - + +
200P VAL* 1.3 66.3 + - + +
252P ILE* 3.8 27.8 - - + -
254P ILE* 4.8 0.7 - - + -
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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