Contacts of the helix formed by residues 189 - 199 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160E VAL* 4.0 29.4 - - + -
184E ALA 2.7 21.7 + - - +
185E PHE* 3.6 6.3 - - - +
188E GLN* 1.3 73.0 - - - +
190E SER* 1.3 60.1 + - - +
191E HIS 3.1 3.1 - - - -
192E TYR* 2.8 28.1 + - + +
193E VAL* 3.0 13.7 + - + +
237E ILE* 5.3 0.2 - - + -
239E VAL* 4.0 19.5 - - + -
241E MET* 4.9 0.4 - - + -
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Residues in contact with SER 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E LYS* 3.2 27.2 + - - +
104E PRO* 5.4 2.5 - - - -
130E LYS* 3.5 16.6 + - - -
185E PHE 3.1 8.8 + - - -
186E MET* 3.2 27.1 - - - -
187E ASN 3.1 5.9 + - - -
188E GLN 3.2 0.6 - - - -
189E ALA* 1.3 78.9 - - - +
191E HIS* 1.3 60.3 + - - +
193E VAL* 3.3 7.3 + - - +
194E ASP* 3.0 27.7 + - - +
328E SER* 5.4 1.4 - - - -
332E LEU* 4.7 9.1 - - - +
550E HP7 4.4 0.2 + - - -
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Residues in contact with HIS 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E LYS* 4.2 13.7 - - + -
129E VAL 4.8 1.6 - - - -
130E LYS* 4.4 10.5 + - - +
131E GLN* 3.5 31.4 + - - -
132E ASN* 4.6 18.8 + - + +
188E GLN 4.9 2.2 - - - -
189E ALA 3.1 0.8 - - - -
190E SER* 1.3 77.3 + - - +
192E TYR* 1.3 74.2 + - + +
194E ASP* 3.5 16.7 + - - +
195E LEU* 3.4 19.1 - - - +
500E NAI 3.2 15.9 + - - -
550E HP7 3.0 59.7 + - + +
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Residues in contact with TYR 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ASN* 6.3 0.7 - - - -
158E VAL* 3.8 22.4 - - + +
160E VAL* 3.2 29.2 - - + -
162E TRP* 3.8 32.0 - + - -
188E GLN 4.9 0.7 - - - -
189E ALA* 2.8 16.5 + - - +
191E HIS* 1.3 87.5 - - + +
193E VAL* 1.3 69.4 + - - +
194E ASP 3.0 1.3 - - - -
195E LEU* 3.0 29.9 + - + +
196E LEU* 3.7 8.5 + - - +
237E ILE* 4.0 5.6 - - + +
250E GLY* 3.9 15.7 - - - -
251E SER 4.5 0.7 - - - -
267E ALA* 3.4 30.8 - - - +
268E VAL* 3.8 29.1 - - + +
550E HP7 4.7 2.6 + - - -
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Residues in contact with VAL 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185E PHE* 4.2 18.4 - - + +
189E ALA* 3.0 13.8 + - + +
190E SER 3.3 6.0 + - - +
192E TYR* 1.3 75.8 - - - +
194E ASP* 1.3 65.4 + - - +
196E LEU* 3.0 30.7 + - + +
197E ASP* 4.2 0.7 + - - +
237E ILE* 4.1 14.6 - - + -
328E SER* 4.5 5.8 - - - +
331E LEU* 3.8 33.9 - - + +
332E LEU* 3.8 35.2 - - + +
335E ILE* 4.8 7.0 - - + -
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Residues in contact with ASP 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E LYS* 4.0 26.7 - - - +
133E ARG* 2.8 50.0 + - - +
190E SER 3.0 14.2 + - - +
191E HIS* 3.5 16.3 - - - +
193E VAL* 1.3 78.5 - - - +
195E LEU* 1.3 62.1 + - - +
196E LEU 3.4 0.3 + - - -
197E ASP* 3.8 3.9 + - - +
198E TRP* 3.4 21.7 + - - +
324E GLU 5.4 0.2 - - - +
328E SER* 4.2 18.2 - - - -
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Residues in contact with LEU 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ASN* 6.2 1.3 - - + -
133E ARG* 6.0 0.7 - - - -
138E LEU* 4.3 27.4 - - + -
158E VAL* 5.5 0.7 - - + -
191E HIS 3.4 14.1 + - - +
192E TYR* 3.0 32.4 + - + +
194E ASP* 1.3 79.2 - - - +
196E LEU* 1.3 61.4 + - + +
198E TRP* 3.7 31.0 - - + +
199E LEU* 2.8 41.4 + - + +
200E VAL 3.6 0.2 + - - -
252E ILE* 3.9 31.0 - - + -
268E VAL* 4.7 8.1 - - + -
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Residues in contact with LEU 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E VAL* 5.0 3.6 - - + -
158E VAL* 3.9 28.5 - - + -
192E TYR 3.8 4.9 - - - +
193E VAL* 3.0 28.6 + - + +
195E LEU* 1.3 75.5 - - - +
197E ASP* 1.3 60.7 + - - +
200E VAL* 3.3 13.5 - - - +
201E GLY 3.1 1.9 - - - +
203E VAL* 4.6 2.5 - - + -
227E LEU* 4.1 25.4 - - + -
229E TRP* 2.9 51.8 + - + -
236E SER 5.3 0.4 - - - +
237E ILE* 4.5 14.4 - - + -
252E ILE* 5.6 0.4 - - + -
331E LEU* 3.6 23.6 - - + -
335E ILE* 5.6 1.3 - - + -
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Residues in contact with ASP 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ARG* 5.6 0.3 + - - -
193E VAL 4.2 1.6 + - - +
194E ASP* 3.8 5.4 + - - +
196E LEU* 1.3 77.9 - - - +
198E TRP* 1.3 65.9 + - - +
201E GLY* 3.0 29.0 + - - +
202E PRO* 3.3 26.5 - - - +
203E VAL* 4.4 4.3 + - + -
324E GLU* 4.4 6.1 - - - +
327E GLN* 3.7 42.9 + - + +
328E SER* 6.2 0.9 - - - -
331E LEU* 4.6 12.3 - - + +
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Residues in contact with TRP 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E ARG* 3.1 89.5 - - + +
138E LEU* 4.1 14.6 - - + -
139E GLN* 3.8 11.7 - - - -
142E LYS* 3.3 45.6 + - + +
194E ASP* 3.4 16.1 + - - +
195E LEU* 3.0 32.9 + - + -
197E ASP* 1.3 85.4 - - - +
199E LEU* 1.3 87.7 + - + +
201E GLY* 4.6 0.5 + - - -
324E GLU* 4.5 4.7 - - - +
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Residues in contact with LEU 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E LEU* 4.1 13.9 - - + +
141E VAL* 4.1 18.2 - - + -
142E LYS* 3.6 40.2 - - + +
145E ILE* 3.5 30.8 - - + +
195E LEU* 2.8 28.3 + - + +
198E TRP* 1.3 102.8 - - + +
200E VAL* 1.3 69.2 + - + +
252E ILE* 3.9 26.7 - - + -
254E ILE* 4.7 2.0 - - + -
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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