Contacts of the helix formed by residues 189 - 201 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A VAL* 4.0 16.2 - - + -
184A ALA 3.0 17.8 + - - +
185A PHE* 3.5 9.6 - - - +
187A ASN 3.4 0.2 - - - -
188A GLN* 1.3 73.6 - - - +
190A SER* 1.3 61.0 + - - +
191A HIS 3.1 2.7 - - - -
192A TYR* 2.7 26.0 + - + -
193A VAL* 2.8 17.4 + - + +
237A ILE* 5.1 0.4 - - + -
239A VAL* 3.8 30.7 - - + -
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Residues in contact with SER 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 3.4 16.8 - - - -
104A PRO* 4.7 4.0 - - - -
130A LYS* 3.8 14.2 + - - -
185A PHE 3.1 9.7 + - - -
186A MET 3.3 17.6 + - - -
187A ASN 2.7 17.9 + - - -
188A GLN 3.3 0.4 - - - -
189A ALA* 1.3 79.5 - - - +
191A HIS* 1.3 52.6 + - - +
192A TYR 2.9 0.2 - - - -
193A VAL* 3.8 7.0 - - - +
194A ASP* 2.8 33.8 + - - +
328A SER* 4.8 1.2 - - - -
332A LEU* 3.9 15.7 - - - -
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Residues in contact with HIS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 3.6 32.1 - - + +
130A LYS* 4.3 10.0 + - - +
131A GLN* 3.8 14.8 + - - -
132A ASN* 3.4 33.1 + - + +
188A GLN 3.5 16.6 - - - -
189A ALA 3.1 0.6 - - - -
190A SER* 1.3 77.2 + - - +
192A TYR* 1.3 66.3 + + + +
194A ASP* 3.5 13.2 - - - +
195A LEU* 3.5 20.6 - - - +
500A NAI 3.6 15.5 - - - -
550A HP7 2.5 50.0 + - + -
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Residues in contact with TYR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ASN* 4.0 13.5 + - - -
158A VAL* 3.8 18.1 - - + +
160A VAL* 3.6 29.6 - - + -
162A TRP* 3.5 30.0 - + - -
188A GLN 4.5 0.4 - - - -
189A ALA* 2.7 16.8 + - - +
191A HIS* 1.3 93.9 - + + +
193A VAL* 1.3 65.7 + - - +
194A ASP 3.2 0.7 - - - -
195A LEU* 2.9 33.7 + - + +
196A LEU* 3.9 7.8 + - - +
237A ILE* 4.1 5.0 - - + +
250A GLY* 3.9 16.2 - - - -
251A SER 4.6 0.4 - - - -
267A ALA* 3.2 34.0 - - - +
268A VAL* 3.9 26.5 - - + -
550A HP7 5.2 0.2 + - - -
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A PHE* 4.1 14.8 - - + -
189A ALA 2.8 20.0 + - - +
190A SER* 3.8 8.1 - - - +
192A TYR* 1.3 70.5 - - - +
194A ASP* 1.3 63.4 + - - +
195A LEU 2.9 1.6 + - - -
196A LEU* 3.0 29.4 + - + +
197A ASP 4.2 1.2 + - - -
237A ILE* 3.8 16.3 - - + +
328A SER* 4.0 14.1 - - - +
331A LEU* 3.6 35.3 - - + +
332A LEU* 4.0 25.1 - - + +
335A ILE* 4.5 7.2 - - + -
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Residues in contact with ASP 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LYS* 3.7 25.3 - - + +
133A ARG* 2.6 52.2 + - - +
190A SER 2.8 21.6 + - - +
191A HIS 3.5 10.6 - - - +
193A VAL* 1.3 73.5 - - - +
195A LEU* 1.3 64.5 + - - +
196A LEU 3.3 0.2 + - - -
197A ASP* 3.7 3.8 + - - +
198A TRP* 3.3 17.7 + - - +
324A GLU 4.6 2.4 - - - +
327A GLN* 5.6 1.2 - - - +
328A SER* 3.8 21.7 + - - -
331A LEU* 6.0 0.2 - - - -
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ASN* 5.5 3.4 - - + -
133A ARG* 5.9 1.6 - - + -
138A LEU* 3.7 31.6 - - + -
158A VAL* 5.4 2.0 - - + -
191A HIS 3.5 18.2 - - - +
192A TYR* 2.9 38.2 + - + +
194A ASP* 1.3 74.9 - - - +
196A LEU* 1.3 62.5 + - + +
197A ASP 3.3 0.2 - - - -
198A TRP* 4.1 17.3 - - + -
199A LEU* 2.7 47.4 + - + +
200A VAL* 3.7 0.9 + - - +
252A ILE* 4.3 33.8 - - + +
268A VAL* 4.4 4.7 - - + -
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A VAL* 4.7 5.2 - - + -
158A VAL* 3.8 29.8 - - + -
192A TYR 4.0 4.3 - - - +
193A VAL* 3.0 30.4 + - + +
195A LEU* 1.3 78.1 - - - +
197A ASP* 1.3 61.4 + - - +
200A VAL* 3.2 14.3 + - - +
201A GLY 3.2 2.9 - - - +
203A VAL* 4.2 8.1 - - + -
227A LEU* 4.0 31.6 - - + -
229A TRP* 3.1 48.0 + - + -
237A ILE* 4.5 12.3 - - + -
252A ILE* 5.3 0.9 - - + -
331A LEU* 4.5 9.4 - - + -
335A ILE* 5.6 1.6 - - + -
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Residues in contact with ASP 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A VAL 4.2 1.0 + - - -
194A ASP 3.7 4.7 + - - +
196A LEU* 1.3 80.4 - - - +
198A TRP* 1.3 67.2 + - - +
201A GLY* 3.2 34.1 + - - +
202A PRO* 3.4 17.0 - - - +
203A VAL* 4.2 2.6 + - + -
324A GLU* 5.4 2.9 - - - +
327A GLN* 2.7 44.1 + - + +
328A SER* 6.0 0.7 - - - -
331A LEU* 4.2 17.7 - - + +
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Residues in contact with TRP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ARG* 3.4 87.5 - - + +
138A LEU* 4.2 21.3 - - + -
139A GLN* 3.9 14.8 - - - -
142A LYS* 3.3 58.6 + - + +
194A ASP* 3.3 17.7 + - - +
195A LEU* 4.1 11.9 - - + -
197A ASP* 1.3 84.2 + - - +
199A LEU* 1.3 93.2 + - + +
319A GLU* 4.1 7.2 + - - +
324A GLU* 4.4 5.2 - - - -
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU* 4.4 19.7 - - + +
141A VAL* 4.2 17.5 - - + -
142A LYS* 3.7 38.5 + - + +
145A ILE* 3.4 31.8 - - + +
195A LEU* 2.7 29.9 + - + +
198A TRP* 1.3 103.4 - - + +
200A VAL* 1.3 69.2 + - + +
252A ILE* 4.0 24.7 - - + -
254A ILE* 4.5 1.6 - - + -
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 4.8 7.4 - - + +
153A ILE* 4.3 12.4 - - + +
156A VAL* 3.8 31.0 - - + -
195A LEU 4.7 2.0 - - - +
196A LEU* 3.2 13.5 + - - +
199A LEU* 1.3 91.6 - - + +
201A GLY* 1.3 58.2 + - - +
229A TRP* 3.3 34.5 - - + +
231A HIS* 3.0 36.4 + - + +
252A ILE* 5.2 1.6 - - + -
254A ILE* 4.2 17.0 - - + -
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Residues in contact with GLY 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU 3.2 6.6 - - - +
197A ASP* 3.2 25.9 + - - -
199A LEU 3.7 0.2 - - - -
200A VAL* 1.3 79.5 - - - +
202A PRO* 1.3 73.9 - - - +
203A VAL 3.4 0.9 + - - -
229A TRP* 3.0 20.4 + - - -
231A HIS* 4.6 0.9 - - - -
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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