Contacts of the helix formed by residues 193 - 208 (chain A) in PDB entry 4DTR
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 ASN 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A LEU* 3.4 10.1 - - - -
153A ASN 4.4 2.5 - - - -
191A PHE* 3.3 2.9 - - - +
192A ASP* 1.3 88.8 - - - +
194A GLU* 1.3 65.6 + - - +
195A LYS* 3.4 11.8 + - + +
196A GLU* 2.9 58.1 + - - +
197A LEU* 3.1 19.9 + - - +
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Residues in contact with GLU 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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132A PRO* 3.5 14.7 - - + +
133A ILE 2.9 29.4 + - - +
151A LEU* 3.4 21.9 - - + +
153A ASN 4.7 1.2 + - - +
193A ASN* 1.3 73.9 - - - +
195A LYS* 1.3 63.1 + - + +
197A LEU* 3.2 5.8 + - + +
198A LEU* 2.9 36.3 + - + +
229A ARG* 2.7 52.7 + - - +
233A ILE* 3.6 10.7 - - + +
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Residues in contact with LYS 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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193A ASN* 3.3 9.4 + - - +
194A GLU* 1.3 77.4 - - + +
196A GLU* 1.3 62.0 + - - +
198A LEU* 3.4 1.1 + - - -
199A MET* 3.0 37.8 + - + +
233A ILE* 3.8 37.3 - - + +
234A PHE* 3.7 20.1 - - + -
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Residues in contact with GLU 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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191A PHE* 3.8 14.8 - - + -
192A ASP* 4.7 10.4 + - - +
193A ASN* 2.9 39.4 + - - +
194A GLU 3.3 0.2 - - - -
195A LYS* 1.3 72.1 - - - +
197A LEU* 1.3 66.5 - - - +
199A MET* 3.9 17.2 - - + +
200A GLU* 3.0 27.4 + - - +
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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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133A ILE* 4.3 12.6 - - + +
134A ASP 4.7 2.2 - - - +
135A ALA 5.0 0.2 - - - +
136A ILE* 3.9 28.7 - - + -
149A PHE* 4.0 22.6 - - + +
150A ASP 3.9 6.7 - - - +
151A LEU* 3.6 39.9 - - + +
191A PHE* 3.6 24.8 - - + -
193A ASN 3.1 12.2 + - - +
194A GLU* 3.2 9.2 + - - +
196A GLU* 1.3 77.0 - - - +
198A LEU* 1.3 70.0 + - + +
200A GLU* 3.7 1.7 - - - +
201A TYR* 2.8 29.6 + - + +
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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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133A ILE* 4.2 21.5 - - + -
136A ILE* 4.6 9.2 - - + -
194A GLU* 2.9 45.0 + - + +
195A LYS 4.0 2.9 - - - +
197A LEU* 1.3 88.7 - - + +
199A MET* 1.3 58.5 + - - +
201A TYR* 3.3 5.5 + - + +
202A LEU* 3.0 35.4 + - - +
226A VAL* 5.1 2.2 - - + -
229A ARG* 4.3 8.3 - - + -
230A ILE* 4.1 28.0 - - + +
233A ILE* 3.9 17.7 - - + -
234A PHE* 4.0 15.7 - - + -
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Residues in contact with MET 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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195A LYS* 3.0 34.8 + - + +
196A GLU* 4.0 17.9 - - + +
198A LEU* 1.3 72.2 - - - +
200A GLU* 1.3 66.5 + - - +
202A LEU* 3.5 10.4 + - + +
203A ASN* 3.0 32.6 + - - +
234A PHE* 3.7 26.7 - - + -
238A THR* 6.2 1.8 - - + -
241A ARG* 4.9 4.3 + - - +
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Residues in contact with GLU 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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149A PHE* 4.4 7.4 - - + -
189A MET* 5.2 6.7 - - - +
191A PHE* 3.6 30.3 - - + -
196A GLU 3.0 19.1 + - - +
197A LEU 3.8 0.2 - - - +
199A MET* 1.3 78.4 - - - +
201A TYR* 1.3 56.2 + - - +
203A ASN* 3.2 13.7 + - - +
204A PHE* 2.8 38.7 + - - +
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Residues in contact with TYR 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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113A PHE* 3.5 18.2 - + - -
136A ILE* 3.8 38.8 - - + +
138A HIS* 2.8 31.9 + - + -
149A PHE* 3.6 38.3 - + + -
197A LEU 2.8 19.2 + - - +
198A LEU* 3.6 11.0 - - + +
199A MET 3.3 0.4 - - - -
200A GLU* 1.3 75.9 - - - +
202A LEU* 1.3 55.0 + - + +
204A PHE* 3.3 11.3 + + - +
205A TRP* 2.8 64.1 + + - +
226A VAL* 4.6 19.3 - - + -
230A ILE* 5.5 0.9 - - + -
242A LEU* 4.8 4.9 - - + -
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Residues in contact with LEU 202 (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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198A LEU 3.0 22.3 + - - +
199A MET* 3.7 7.0 - - - +
201A TYR* 1.3 73.0 - - + +
203A ASN* 1.3 62.0 + - - +
205A TRP* 3.2 6.3 + - + +
206A GLN* 2.9 28.4 + - - +
230A ILE* 3.9 21.3 - - + -
234A PHE* 5.6 1.6 - - + -
238A THR* 3.5 43.3 - - + +
241A ARG* 3.7 38.1 + - + +
242A LEU* 3.8 33.4 - - + +
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Residues in contact with ASN 203 (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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199A MET* 3.0 22.7 + - - +
200A GLU* 3.5 21.6 - - - +
202A LEU* 1.3 71.5 - - - +
204A PHE* 1.3 67.5 + - - +
206A GLN* 3.4 8.8 + - - +
207A GLN* 3.1 26.8 + - - +
241A ARG* 3.0 25.2 - - - +
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Residues in contact with PHE 204 (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 HIS* 3.4 50.3 - + + -
140A ASP* 5.3 0.4 - - + -
147A TYR* 3.4 43.3 - + + -
149A PHE* 3.8 22.2 - + + -
189A MET* 5.6 1.1 - - + -
200A GLU* 2.8 21.4 + - - +
201A TYR* 3.3 17.9 - + - +
203A ASN* 1.3 76.9 - - - +
205A TRP* 1.3 56.0 + - - +
207A GLN* 3.0 9.5 + - - +
208A LYS* 2.8 62.8 + - + +
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Residues in contact with TRP 205 (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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113A PHE* 5.2 7.2 - + - -
138A HIS* 4.0 18.4 - + - -
201A TYR* 2.8 61.3 + + + +
202A LEU* 3.2 11.4 + - + +
204A PHE* 1.3 79.0 - - - +
206A GLN* 1.3 59.2 + - - +
208A LYS 4.3 4.3 - - - -
209A THR* 2.9 45.7 + - + +
210A PRO* 3.6 24.0 - - + +
213A LEU* 3.7 30.5 - - + -
223A ILE* 6.0 0.2 - - + -
241A ARG 3.8 18.2 - - - -
242A LEU* 3.0 46.5 + - + -
265A LEU* 4.5 6.3 - - + -
268A ILE* 4.1 8.3 - - + +
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Residues in contact with GLN 206 (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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202A LEU 2.9 12.3 + - - +
203A ASN* 3.6 12.2 + - - +
204A PHE 3.3 0.2 - - - -
205A TRP* 1.3 79.9 - - - +
207A GLN* 1.3 66.3 + - + +
209A THR* 3.1 15.4 + - - +
241A ARG* 3.7 24.0 + - - +
246A ARG* 3.6 28.3 + - - +
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Residues in contact with GLN 207 (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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109A ARG* 4.6 6.6 + - - -
203A ASN 3.1 15.8 + - - +
204A PHE* 3.0 11.7 + - - +
206A GLN* 1.3 83.6 + - - +
208A LYS* 1.3 75.3 + - + +
209A THR 3.7 1.1 + - - -
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Residues in contact with LYS 208 (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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109A ARG* 3.5 29.7 - - - +
138A HIS* 4.6 6.1 + - - -
140A ASP* 3.7 8.5 - - - +
143A ASP* 2.7 34.9 + - - +
147A TYR* 3.6 14.8 + - + -
204A PHE* 2.8 43.4 + - + +
205A TRP* 3.1 7.8 - - - +
207A GLN* 1.3 90.8 - - + +
209A THR* 1.3 62.3 + - - +
210A PRO* 3.3 10.6 - - - +
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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