Contacts of the helix formed by residues 197 - 213 (chain D) in PDB entry 3E2A
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 SER 197 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D TRP* 3.4 29.4 - - - -
195D ALA* 3.9 0.3 - - - +
196D THR* 1.3 80.2 - - - +
198D ARG* 1.3 63.8 + - - +
199D GLU* 3.0 18.8 + - - +
200D THR* 2.9 35.2 + - - +
201D LEU 3.0 8.0 + - - -
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Residues in contact with ARG 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D TYR* 3.8 5.9 + - - -
159D GLY 3.7 19.3 - - - -
160D ARG* 4.0 8.9 - - - +
165D LYS* 3.4 38.7 - - + +
168D TRP* 3.3 14.8 - - + +
197D SER* 1.3 75.1 - - - +
199D GLU* 1.3 71.5 + - - +
201D LEU* 3.4 17.1 - - - +
202D GLU* 3.1 50.9 + - + +
231D SO4 2.9 42.2 + - - -
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Residues in contact with GLU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D SER* 3.0 24.0 + - - +
198D ARG* 1.3 80.7 + - - +
200D THR* 1.3 65.2 + - + +
202D GLU* 3.2 8.4 + - - +
203D ILE* 3.1 27.7 + - + +
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Residues in contact with THR 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D MET* 4.4 4.0 - - - -
195D ALA* 4.4 3.6 - - - -
196D THR* 2.9 39.0 + - - +
197D SER* 2.9 21.6 + - - +
199D GLU* 1.3 74.7 - - + +
201D LEU* 1.3 57.2 + - - +
203D ILE* 4.2 6.0 - - - +
204D SER* 2.7 36.5 + - - -
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Residues in contact with LEU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D VAL* 3.8 22.9 - - + +
156D TYR* 3.8 29.2 - - + +
159D GLY* 3.4 38.4 - - - +
160D ARG* 3.9 1.3 - - + +
168D TRP* 4.4 1.1 - - + -
176D LEU* 4.5 0.2 - - + -
193D VAL* 4.3 10.9 - - + +
195D ALA* 3.6 26.2 - - + +
197D SER 3.0 10.6 + - - +
198D ARG* 3.4 27.4 - - - +
199D GLU 3.2 0.2 - - - -
200D THR* 1.3 74.9 + - - +
202D GLU* 1.3 65.8 + - - +
204D SER* 4.0 1.7 + - - -
205D TYR* 3.0 28.6 + - - +
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Residues in contact with GLU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D TYR* 2.4 41.4 + - - -
198D ARG* 3.1 29.4 + - + +
199D GLU* 3.2 10.5 + - - +
201D LEU* 1.3 79.3 - - - +
203D ILE* 1.3 63.3 + - + +
205D TYR* 3.9 2.0 - - - +
206D ARG* 2.9 80.0 + - - +
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Residues in contact with ILE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D GLU* 3.1 15.9 + - + +
200D THR* 4.2 5.4 - - - +
201D LEU 3.3 0.2 - - - -
202D GLU* 1.3 77.7 - - + +
204D SER* 1.3 58.8 + - - +
206D ARG* 3.3 24.6 + - + +
207D ASN* 2.8 58.1 + - - +
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Residues in contact with SER 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D GLY 3.6 19.9 - - - +
193D VAL* 3.9 4.5 - - - +
194D MET* 2.8 27.9 + - - -
200D THR 2.7 24.7 + - - -
201D LEU* 4.0 1.2 + - - -
203D ILE* 1.3 76.4 - - - +
205D TYR* 1.3 61.7 + - - +
207D ASN* 3.7 9.0 - - - +
208D ALA* 2.8 32.1 + - - +
211D ARG* 4.7 0.4 + - - -
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Residues in contact with TYR 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C PHE* 6.2 3.8 - + - -
129D LYS* 3.0 22.8 + - - -
130D HIS* 4.2 1.2 + - - -
152D ALA 3.9 13.0 - - - -
153D GLU* 2.5 39.1 + - - -
156D TYR* 3.6 52.5 - + + -
193D VAL* 3.9 16.0 - - + +
201D LEU 3.0 19.8 + - - +
202D GLU* 3.9 2.5 - - - +
204D SER* 1.3 74.6 + - - +
206D ARG* 1.3 77.5 + - + +
208D ALA* 3.1 1.6 + - - +
209D ILE* 3.0 50.2 + - + +
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Residues in contact with ARG 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D GLU* 2.9 51.7 + - - +
203D ILE* 3.8 23.5 - - - +
205D TYR* 1.3 89.1 - - + +
207D ASN* 1.3 64.7 + - - +
209D ILE* 4.2 3.9 - - - +
210D ALA* 3.2 24.3 + - - +
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Residues in contact with ASN 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D ILE* 2.8 49.0 + - - +
204D SER* 3.7 8.5 - - - +
206D ARG* 1.3 76.6 - - - +
208D ALA* 1.3 56.8 + - - +
210D ALA* 3.5 6.0 + - - +
211D ARG* 3.0 46.5 + - - +
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Residues in contact with ALA 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ALA* 5.0 3.8 - - + -
191D GLN 3.5 18.8 - - - +
193D VAL* 3.5 27.6 - - + +
204D SER 2.8 22.8 + - - +
205D TYR 3.1 0.9 + - - +
207D ASN* 1.3 70.6 - - - +
209D ILE* 1.3 62.1 + - - +
211D ARG* 3.3 16.0 + - - +
212D LEU* 2.8 36.3 + - + +
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Residues in contact with ILE 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D HIS* 3.7 34.8 - - + +
149D ILE* 4.7 13.0 - - + -
152D ALA* 4.1 20.0 - - + -
153D GLU* 4.3 1.3 - - - +
205D TYR* 3.0 47.9 + - + +
206D ARG* 4.2 4.7 - - - +
208D ALA* 1.3 73.3 - - - +
210D ALA* 1.3 61.4 + - - +
212D LEU* 3.2 6.7 + - + +
213D SER* 2.8 44.1 + - - +
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Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ARG 3.2 17.9 + - - +
207D ASN* 3.6 6.5 - - - +
209D ILE* 1.3 80.5 - - - +
211D ARG* 1.3 64.5 + - - +
213D SER* 3.2 13.6 + - - -
214D ILE* 3.6 14.5 + - - +
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Residues in contact with ARG 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D GLN 5.0 5.7 + - - -
192D GLY* 4.2 18.5 + - - -
204D SER* 5.9 0.2 - - - -
207D ASN* 3.0 26.3 + - - +
208D ALA* 3.4 31.8 - - - +
209D ILE 3.2 0.2 - - - -
210D ALA* 1.3 76.1 - - - +
212D LEU* 1.3 70.2 + - + +
213D SER 3.2 1.2 + - - -
214D ILE* 3.3 32.1 + - + +
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Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LEU* 3.9 7.5 - - + +
145D MET* 3.8 31.0 - - + +
148D LYS* 3.8 42.2 - - + +
149D ILE* 3.9 26.7 - - + +
152D ALA* 5.7 2.0 - - + -
191D GLN* 4.3 24.9 - - + +
208D ALA* 2.8 25.4 + - + +
209D ILE* 3.6 9.2 - - + +
211D ARG* 1.3 80.7 - - + +
213D SER* 1.3 58.6 + - - +
214D ILE 3.3 6.9 + - - +
215D LEU* 5.7 0.2 - - - +
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Residues in contact with SER 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D HIS* 5.2 0.9 + - - -
133D LEU* 3.7 35.9 - - - +
209D ILE* 2.8 35.6 + - - +
210D ALA* 3.8 9.4 - - - -
211D ARG 3.2 1.2 - - - -
212D LEU* 1.3 72.5 - - - +
214D ILE* 1.3 60.7 + - - +
215D LEU* 3.5 3.8 + - - +
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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