Contacts of the helix formed by residues 189 - 201 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160K VAL* 3.9 28.9 - - + -
184K ALA 3.0 21.5 + - - +
185K PHE* 3.4 7.0 - - - +
188K GLN* 1.3 73.0 - - - +
190K SER* 1.3 65.7 + - - +
191K HIS 3.2 2.7 - - - -
192K TYR* 2.8 19.4 + - + +
193K VAL* 2.9 15.2 + - + +
237K ILE* 5.4 0.4 - - + -
239K VAL* 4.0 20.2 - - + -
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Residues in contact with SER 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K LYS* 3.0 24.3 - - - +
104K PRO* 5.0 4.0 - - - -
130K LYS* 3.9 12.3 + - - -
185K PHE 3.0 10.7 + - - -
186K MET 3.5 17.2 + - - -
187K ASN 2.9 15.6 + - - -
188K GLN 3.4 1.0 - - - -
189K ALA* 1.3 76.5 - - - +
191K HIS* 1.3 63.2 + - - +
192K TYR 2.8 0.3 + - - -
193K VAL* 3.0 8.5 + - - +
194K ASP* 2.8 23.9 + - - +
328K SER* 5.3 0.8 - - - -
332K LEU* 4.2 15.3 - - - -
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Residues in contact with HIS 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K LYS* 3.6 23.8 - - + -
129K VAL 4.4 2.2 - - - -
130K LYS* 4.3 11.7 + - - +
131K GLN* 3.4 35.1 + - - -
132K ASN* 3.8 35.5 + - + +
188K GLN 4.8 2.9 - - - +
189K ALA 3.2 0.8 - - - -
190K SER* 1.3 79.1 + - - +
192K TYR* 1.3 68.3 + - + +
194K ASP* 3.5 16.1 - - - +
195K LEU* 3.5 18.2 - - - +
500K NAI 3.2 21.9 + - - -
550K HP7 3.6 35.4 + - + -
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Residues in contact with TYR 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K ASN* 4.6 8.8 + - - -
158K VAL* 4.1 20.3 - - + +
160K VAL* 3.6 26.9 - - + -
162K TRP* 3.6 32.8 - + - -
188K GLN 4.5 0.7 - - - -
189K ALA* 2.8 17.3 + - - +
191K HIS* 1.3 88.2 - - + +
193K VAL* 1.3 66.2 + - - +
194K ASP 3.3 0.4 - - - -
195K LEU* 3.4 31.8 + - + +
196K LEU* 3.9 5.9 + - - +
237K ILE* 3.9 10.6 - - + +
250K GLY* 3.9 20.5 - - - -
251K SER 4.8 0.7 - - - -
267K ALA* 3.2 33.6 - - - +
268K VAL* 3.7 25.0 - - + +
550K HP7 5.1 0.2 - - - -
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Residues in contact with VAL 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185K PHE* 4.2 16.4 - - + +
189K ALA* 2.9 15.8 + - + +
190K SER* 3.5 10.3 - - - +
192K TYR* 1.3 75.3 - - - +
194K ASP* 1.3 63.7 + - - +
195K LEU 3.1 1.1 + - - -
196K LEU* 3.3 22.3 + - + +
197K ASP* 4.2 1.0 + - - +
237K ILE* 3.9 18.6 - - + -
328K SER* 4.4 9.1 - - - +
331K LEU* 4.0 31.2 - - + +
332K LEU* 4.1 29.6 - - + -
335K ILE* 4.6 8.5 - - + -
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Residues in contact with ASP 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K LYS* 3.1 38.3 - - + +
133K ARG* 2.7 51.8 + - - +
190K SER 2.8 14.0 + - - +
191K HIS 3.5 13.2 - - - +
193K VAL* 1.3 73.4 - - - +
195K LEU* 1.3 64.1 + - - +
196K LEU 3.5 0.2 + - - -
197K ASP* 3.7 4.3 + - - +
198K TRP* 3.2 19.1 + - - +
324K GLU 5.1 1.2 - - - +
327K GLN* 6.1 0.2 - - - +
328K SER* 4.0 16.1 + - - -
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Residues in contact with LEU 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K ASN* 5.8 3.4 - - + +
133K ARG* 5.6 2.2 - - + -
138K LEU* 3.9 38.4 - - + -
158K VAL* 5.5 1.8 - - + -
191K HIS 3.5 14.4 - - - +
192K TYR* 3.4 36.6 - - + +
193K VAL 3.1 1.0 - - - -
194K ASP* 1.3 79.9 - - - +
196K LEU* 1.3 66.3 + - - +
198K TRP* 4.0 21.1 - - + -
199K LEU* 2.9 49.3 + - + +
200K VAL* 4.9 0.3 - - - +
252K ILE* 4.6 17.7 - - + -
268K VAL* 4.8 4.7 - - + -
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Residues in contact with LEU 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156K VAL* 4.5 5.6 - - + -
158K VAL* 3.8 28.0 - - + -
192K TYR 4.1 4.9 - - - +
193K VAL* 3.3 18.8 + - + +
195K LEU* 1.3 78.5 - - - +
197K ASP* 1.3 58.0 + - - +
200K VAL* 3.2 27.3 - - - +
201K GLY 3.6 0.3 - - - +
203K VAL* 4.6 2.2 - - + -
227K LEU* 3.8 33.7 - - + -
229K TRP* 3.3 37.6 + - + -
236K SER 5.3 0.9 - - - +
237K ILE* 4.0 21.3 - - + -
252K ILE* 5.4 1.1 - - + -
331K LEU* 4.2 15.5 - - + -
335K ILE* 5.5 1.6 - - + -
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Residues in contact with ASP 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K ARG* 5.7 1.6 + - - +
193K VAL 4.2 1.2 + - - +
194K ASP* 3.7 6.3 + - - +
195K LEU 3.3 0.4 - - - -
196K LEU* 1.3 78.8 - - - +
198K TRP* 1.3 66.5 + - - +
201K GLY* 2.9 39.7 + - - +
202K PRO* 3.6 15.3 - - - +
203K VAL* 4.2 6.4 + - + +
324K GLU* 5.1 5.4 - - - +
327K GLN* 3.3 39.7 - - + +
328K SER* 5.7 2.0 - - - +
331K LEU* 5.0 11.7 - - + -
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Residues in contact with TRP 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133K ARG* 3.5 83.5 - - + +
138K LEU* 4.1 13.0 - - + -
139K GLN* 4.3 7.4 - - - -
142K LYS* 2.8 71.7 + - + +
194K ASP* 3.2 17.0 + - - +
195K LEU* 4.0 17.5 - - + -
197K ASP* 1.3 83.7 + - - +
199K LEU* 1.3 84.2 + - + +
201K GLY 4.7 0.3 + - - -
324K GLU* 4.3 6.7 - - - +
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Residues in contact with LEU 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138K LEU* 4.1 10.8 - - + +
141K VAL* 3.8 21.8 - - + -
142K LYS* 3.7 38.8 + - + +
145K ILE* 3.2 32.8 - - + +
195K LEU* 2.9 33.0 + - + +
198K TRP* 1.3 103.3 - - + +
200K VAL* 1.3 69.7 + - + +
201K GLY 3.7 0.2 - - - -
252K ILE* 4.1 23.3 - - + -
254K ILE* 4.7 1.6 - - + -
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Residues in contact with VAL 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145K ILE* 4.9 4.2 - - + +
153K ILE* 4.7 12.8 - - + +
156K VAL* 3.9 30.7 - - + -
195K LEU 4.9 0.7 - - - +
196K LEU* 3.2 18.0 + - - +
199K LEU* 1.3 87.6 - - + +
201K GLY* 1.3 57.1 + - - +
229K TRP* 3.1 33.9 - - + +
231K HIS* 2.8 28.6 + - + +
252K ILE* 5.3 1.8 - - + -
254K ILE* 4.3 15.3 - - + -
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Residues in contact with GLY 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197K ASP* 2.9 31.1 + - - -
198K TRP 4.7 0.2 + - - -
199K LEU 3.7 0.8 - - - -
200K VAL* 1.3 79.6 - - - +
202K PRO* 1.3 75.6 - - - +
203K VAL 3.6 0.3 + - - -
229K TRP* 3.2 14.7 + - - -
231K HIS* 4.6 2.9 - - - -
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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