Contacts of the helix formed by residues 189 - 201 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H VAL* 3.8 27.1 - - + -
184H ALA 2.9 21.2 + - - +
185H PHE* 3.5 10.1 - - + +
188H GLN* 1.3 71.3 - - - +
190H SER* 1.3 56.5 + - - +
191H HIS 3.0 3.1 - - - -
192H TYR* 2.7 29.6 + - + -
193H VAL* 2.8 14.0 + - - +
237H ILE* 5.0 1.6 - - + -
239H VAL* 4.0 20.9 - - + -
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Residues in contact with SER 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H LYS* 3.2 20.1 - - - -
104H PRO* 4.9 3.6 - - - -
130H LYS* 3.3 21.7 + - - -
185H PHE 3.0 9.8 + - - -
186H MET 3.1 22.4 - - - -
187H ASN 3.2 11.8 + - - -
188H GLN 3.4 0.4 - - - -
189H ALA* 1.3 76.9 - - - +
191H HIS* 1.3 59.6 + - - +
193H VAL* 3.7 7.3 - - - +
194H ASP 2.9 24.4 + - - -
328H SER* 4.7 1.6 - - - -
332H LEU* 4.3 13.9 - - - -
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Residues in contact with HIS 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H LYS* 3.5 26.9 - - + +
129H VAL 4.9 0.7 - - - -
130H LYS* 4.3 9.6 - - - +
131H GLN* 3.6 13.8 + - - -
132H ASN* 3.5 34.7 + - + +
188H GLN 3.8 11.0 - - - -
189H ALA 3.0 0.2 - - - -
190H SER* 1.3 88.2 + - - +
192H TYR* 1.3 65.6 + - + +
194H ASP* 3.4 11.0 - - - +
195H LEU* 3.3 23.2 - - - +
500H NAI 3.5 13.6 + - - -
550H HP7 2.6 53.6 + - + -
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Residues in contact with TYR 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H ASN* 4.1 12.0 + - - -
158H VAL* 3.9 19.5 - - + +
160H VAL* 3.5 29.6 - - + -
162H TRP* 3.1 41.8 - + - -
188H GLN 4.3 1.8 - - - -
189H ALA* 2.7 18.8 + - - +
191H HIS* 1.3 85.0 - - + +
193H VAL* 1.3 67.7 + - - +
194H ASP 3.1 1.1 - - - -
195H LEU* 3.1 33.4 + - + +
196H LEU* 3.7 9.7 + - - +
237H ILE* 4.2 5.8 - - + +
250H GLY* 4.2 14.1 - - - -
267H ALA* 3.4 21.7 - - - +
268H VAL* 3.7 28.5 - - + -
550H HP7 4.8 0.8 + - - -
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Residues in contact with VAL 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185H PHE* 4.2 14.8 - - + -
189H ALA 2.8 14.2 + - - +
190H SER* 3.7 9.9 - - - +
192H TYR* 1.3 77.2 - - - +
194H ASP* 1.3 63.2 + - - +
196H LEU* 3.2 25.6 + - + +
197H ASP* 4.1 1.4 + - - +
237H ILE* 3.9 16.6 - - + -
328H SER* 4.2 14.0 - - - +
331H LEU* 3.4 36.9 - - + +
332H LEU* 4.0 24.9 - - + +
335H ILE* 4.5 8.1 - - + -
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Residues in contact with ASP 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H LYS* 4.0 25.7 - - + +
133H ARG* 3.1 49.7 + - - +
190H SER 2.9 17.9 + - - +
191H HIS* 3.4 11.1 - - - +
193H VAL* 1.3 73.2 - - - +
195H LEU* 1.3 67.9 + - - +
196H LEU 3.0 3.3 + - - -
197H ASP* 3.3 5.7 + - - +
198H TRP* 3.1 19.1 + - - +
324H GLU 4.8 3.3 - - - +
327H GLN* 5.8 0.7 - - - +
328H SER* 3.9 19.6 + - - -
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Residues in contact with LEU 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H ASN* 5.4 5.8 - - + +
133H ARG* 5.5 2.0 - - + -
138H LEU* 4.1 26.2 - - + -
158H VAL* 5.3 1.6 - - + -
191H HIS 3.3 16.8 - - - +
192H TYR* 3.1 31.6 + - + +
194H ASP* 1.3 80.2 - - - +
196H LEU* 1.3 65.4 + - + +
198H TRP* 3.8 17.3 - - + -
199H LEU* 2.8 46.2 + - + +
200H VAL* 3.7 1.0 + - - +
252H ILE* 4.2 35.7 - - + -
268H VAL* 4.6 3.4 - - + -
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Residues in contact with LEU 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H VAL* 4.5 5.6 - - + -
158H VAL* 3.9 28.0 - - + -
192H TYR 3.8 6.5 - - - +
193H VAL* 3.2 19.5 - - + +
194H ASP 3.0 1.0 + - - -
195H LEU* 1.3 81.1 - - - +
197H ASP* 1.3 61.4 + - - +
200H VAL* 3.4 13.3 + - - +
201H GLY 3.4 0.2 + - - -
203H VAL* 4.6 2.9 - - + -
227H LEU* 3.6 32.5 - - + -
229H TRP* 3.1 46.1 + - + -
236H SER 5.7 0.2 - - - +
237H ILE* 4.5 11.2 - - + -
252H ILE* 5.1 1.3 - - + -
331H LEU* 3.7 25.8 - - + -
335H ILE* 5.7 0.2 - - + -
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Residues in contact with ASP 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193H VAL 4.1 1.8 + - - +
194H ASP* 3.3 8.3 + - - +
196H LEU* 1.3 80.6 - - + +
198H TRP* 1.3 66.5 + - - +
201H GLY* 3.1 36.7 + - - +
202H PRO* 3.4 16.8 - - - +
203H VAL* 3.7 8.7 + - - +
327H GLN* 3.5 45.1 + - + +
328H SER* 5.4 1.1 - - - +
331H LEU* 5.2 8.7 - - + +
347H LEU* 6.2 0.2 - - - +
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Residues in contact with TRP 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H ARG* 2.8 94.6 - - + +
138H LEU* 4.3 13.9 - - + -
139H GLN* 4.1 9.0 - - - -
142H LYS* 3.2 69.7 + - + +
194H ASP* 3.1 14.8 + - - +
195H LEU* 4.4 12.8 - - + -
197H ASP* 1.3 82.4 - - - +
199H LEU* 1.3 87.4 + - + +
201H GLY* 5.6 0.2 - - - -
319H GLU* 4.6 6.5 + - - -
324H GLU* 4.5 2.7 - - - +
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Residues in contact with LEU 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H LEU* 3.9 25.6 - - + +
141H VAL* 4.2 10.1 - - + -
142H LYS* 3.7 44.2 + - + +
145H ILE* 3.2 33.4 - - + +
195H LEU* 2.8 25.4 + - + +
198H TRP* 1.3 101.2 - - + +
200H VAL* 1.3 63.1 + - + +
201H GLY 3.7 0.2 - - - -
252H ILE* 4.0 25.8 - - + -
254H ILE* 4.4 7.9 - - + -
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Residues in contact with VAL 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H ILE* 4.9 4.2 - - + +
153H ILE* 4.1 22.8 - - + +
156H VAL* 3.9 28.7 - - + -
195H LEU 4.8 1.3 - - - +
196H LEU* 3.4 14.5 + - - +
199H LEU* 1.3 83.2 - - + +
201H GLY* 1.3 59.9 + - - +
229H TRP* 3.7 17.9 - - + +
231H HIS* 2.8 46.4 + - + +
233H ALA* 4.8 0.2 - - + -
252H ILE* 5.0 1.8 - - + -
254H ILE* 4.2 22.7 - - + -
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Residues in contact with GLY 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196H LEU 3.4 0.4 + - - -
197H ASP* 3.1 31.6 + - - +
199H LEU 3.7 0.2 - - - -
200H VAL* 1.3 83.1 - - - +
202H PRO* 1.3 77.6 - - - +
203H VAL 3.5 0.2 + - - -
229H TRP* 3.1 13.3 + - - -
231H HIS* 4.6 1.3 - - - -
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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