Contacts of the helix formed by residues 188 - 199 (chain A) in PDB entry 2Q4E
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 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A PHE* 3.5 34.8 - - + +
161A SER* 5.4 0.2 - - - -
162A PHE* 5.7 2.2 - - + -
184A ALA* 2.6 21.4 + - + +
187A ASP* 1.3 79.3 - - - +
189A GLY* 1.3 66.8 + - - +
190A TRP 3.0 3.5 + - - -
191A TYR* 3.0 15.8 + - - +
192A ALA* 3.6 7.1 + - - +
241A CYS* 3.5 15.7 - - + -
242A SER 4.7 5.4 - - - +
243A PHE* 5.0 4.5 - - + -
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Residues in contact with GLY 189 (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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184A ALA 2.9 14.1 + - - -
185A LEU* 2.9 14.1 + - - -
188A ALA* 1.3 71.7 - - - +
190A TRP* 1.3 52.1 + - - +
192A ALA* 3.0 9.8 + - - +
193A ILE* 2.7 42.3 + - - +
239A ILE* 4.6 5.6 - - - -
241A CYS* 3.3 21.1 - - - +
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Residues in contact with TRP 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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102A LYS* 3.0 32.9 - - + +
103A PRO* 4.0 14.4 - - + -
104A VAL* 3.9 19.7 - - + -
127A ASP* 4.1 8.5 - - - -
129A THR* 2.6 25.3 + - + -
185A LEU 2.9 6.4 + - - +
186A GLY 3.1 20.9 - - - +
187A ASP 4.6 3.1 - - - +
188A ALA 4.5 1.6 - - - +
189A GLY* 1.3 75.1 - - - +
191A TYR* 1.3 64.1 + + - +
193A ILE* 3.3 10.8 + - - +
194A ARG* 2.8 44.4 + - + +
336A SER* 3.6 18.8 - - - -
339A THR* 3.5 26.2 + - + +
340A GLN* 3.4 35.9 - - - -
343A VAL* 3.5 12.8 - - + -
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Residues in contact with TYR 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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102A LYS* 2.6 39.3 + - - -
129A THR* 4.1 15.9 - - + -
130A MSE 5.0 7.7 + - + +
131A TRP* 3.7 21.8 - + - +
160A PHE* 3.5 26.0 - + - -
187A ASP* 3.3 29.9 + - - -
188A ALA 3.0 4.3 + - - +
190A TRP* 1.3 78.1 - + - +
192A ALA* 1.3 68.6 + - - +
194A ARG* 3.0 8.8 + - - +
195A ALA* 2.9 19.1 + - - +
265A PHE* 3.8 12.9 - - + -
266A ILE* 3.4 36.5 - - + +
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Residues in contact with ALA 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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158A SER* 2.8 35.3 + - - +
159A CYS* 4.7 3.6 - - - +
160A PHE* 5.5 1.7 - - + +
188A ALA 3.6 4.3 + - - +
189A GLY* 3.0 12.2 + - - +
191A TYR* 1.3 76.3 - - - +
193A ILE* 1.3 66.4 + - - +
195A ALA 3.0 2.8 + - - -
196A THR* 2.9 23.0 + - - -
239A ILE* 3.4 25.4 - - + -
240A TYR 4.3 7.0 - - - +
265A PHE* 4.3 2.4 - - - -
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Residues in contact with ILE 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 LEU* 4.5 4.7 - - + -
189A GLY 2.7 26.2 + - - +
190A TRP 3.4 6.5 - - - +
192A ALA* 1.3 71.1 - - - +
194A ARG* 1.3 63.4 + - - +
196A THR* 3.2 13.1 + - + -
197A LEU* 3.2 17.0 + - + +
239A ILE* 3.6 29.4 - - + +
339A THR* 3.7 19.1 - - - +
342A VAL* 3.4 39.9 - - + +
343A VAL* 3.4 40.6 - - + +
346A VAL* 4.4 2.9 - - + -
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Residues in contact with ARG 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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127A ASP* 2.8 26.1 + - - -
129A THR* 3.5 30.7 + - + +
131A TRP* 3.6 22.7 - - + +
132A VAL* 3.7 23.0 - - + +
190A TRP* 2.8 20.6 + - + +
191A TYR* 3.2 13.0 - - - +
193A ILE* 1.3 74.8 - - - +
195A ALA* 1.3 58.2 + - - +
197A LEU* 2.9 22.9 + - - +
198A LEU* 3.0 10.6 + - - +
202A PHE* 4.3 8.5 - - - -
332A TRP* 6.0 1.6 - - - -
335A ILE* 3.5 37.4 + - - +
336A SER* 3.9 1.8 - - - +
339A THR* 3.1 31.0 - - - +
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Residues in contact with ALA 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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131A TRP* 3.9 17.9 - - + -
156A VAL* 5.1 2.5 - - + -
158A SER* 4.3 6.3 - - - +
191A TYR 2.9 11.9 + - - +
192A ALA 3.6 6.1 - - - +
194A ARG* 1.3 70.7 - - - +
196A THR* 1.3 59.0 + - - +
197A LEU 2.8 11.6 + - - -
198A LEU* 2.9 3.1 + - - +
199A ALA* 2.9 26.6 + - - +
251A ILE* 3.7 39.2 - - + +
265A PHE* 4.2 2.9 - - + -
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Residues in contact with THR 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* 4.0 18.8 + - - +
158A SER* 4.5 2.6 - - - -
192A ALA 2.9 12.7 + - - -
193A ILE* 3.3 16.2 - - + +
195A ALA* 1.3 74.8 - - - +
197A LEU* 1.3 63.2 + - + +
199A ALA 4.3 0.4 - - - -
200A ASN* 3.0 25.3 + - - -
205A PRO* 5.7 0.2 - - + -
229A LEU* 3.3 29.4 - - + -
231A TRP* 3.8 17.5 - - + -
237A ALA* 3.9 14.5 - - + +
238A THR 4.2 1.9 + - - -
239A ILE* 3.8 12.0 - - - +
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Residues in contact with LEU 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 ILE* 3.2 17.7 - - + +
194A ARG* 2.9 9.6 + - - +
195A ALA 2.8 0.8 - - - -
196A THR* 1.3 85.3 - - + +
198A LEU* 1.3 59.8 + - - +
199A ALA 3.2 1.6 - - - -
200A ASN* 3.1 9.2 + - - +
202A PHE* 2.5 45.4 + - + +
203A GLU 4.1 24.5 - - - +
204A LEU* 4.6 4.5 - - + -
205A PRO* 4.4 15.7 - - + -
231A TRP* 5.4 0.2 - - + -
335A ILE* 3.7 19.5 - - + -
338A LYS* 4.1 4.7 - - + +
339A THR* 3.9 34.1 - - + +
342A VAL* 4.6 7.6 - - + -
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Residues in contact with LEU 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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131A TRP* 3.6 24.7 - - + -
132A VAL* 4.8 4.0 - - + -
137A THR* 3.3 31.0 - - + -
140A LEU* 4.2 15.7 - - + -
141A LYS* 3.9 35.3 - - + +
144A LEU* 4.9 4.7 - - + +
194A ARG 3.0 9.0 + - - +
195A ALA* 2.9 7.0 + - - +
197A LEU* 1.3 76.9 - - - +
199A ALA* 1.3 63.5 + - - +
201A ASN* 3.4 10.9 + - - -
202A PHE* 3.3 36.1 - - + -
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Residues in contact with ALA 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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144A LEU* 4.2 32.4 - - + +
150A PHE* 5.8 0.5 - - - -
153A LEU* 3.8 19.3 - - + +
156A VAL* 4.0 28.3 - - + -
195A ALA 2.9 15.3 + - - +
198A LEU* 1.3 79.4 - - + +
200A ASN* 1.3 62.3 - - - +
201A ASN 3.3 2.6 + - - -
251A ILE* 5.9 2.7 - - + -
253A ALA* 4.9 3.1 - - + -
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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