Contacts of the helix formed by residues 194 - 208 (chain D) in PDB entry 5U03
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 THR 194 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C UTP 2.7 15.7 + - - +
183D VAL* 5.2 3.8 - - + -
192D GLN 4.5 4.9 - - - +
193D LYS* 1.3 74.8 - - - +
195D LYS* 1.3 60.3 + - - +
196D PRO* 3.3 3.1 - - - -
197D THR* 2.8 27.7 + - - +
198D GLN* 2.9 32.9 + - - +
226D VAL* 3.6 33.2 - - + +
229D LYS* 5.3 6.6 - - + +
230D ILE* 3.7 24.2 - - + +
233D PHE* 4.4 7.3 - - - -
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Residues in contact with LYS 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL 4.6 3.1 - - - +
11C ILE* 3.8 19.3 - - + -
12C SER 4.8 1.6 - - - +
150C THR* 2.9 37.0 - - + -
153C ASP* 2.7 30.9 + - - -
602C UTP 3.2 37.8 + - - +
194D THR* 1.3 77.9 + - - +
196D PRO* 1.3 69.3 - - + +
198D GLN* 2.9 21.6 + - - +
199D ASN* 2.8 47.5 + - - +
202D ARG* 5.7 0.6 - - - +
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Residues in contact with PRO 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 4.1 13.5 - - + +
11C ILE* 3.6 18.4 - - + -
10D VAL* 3.9 24.8 - - + +
182D LEU 4.4 6.7 - - - +
184D PRO* 3.8 22.9 - - + -
193D LYS 4.0 4.3 - - - +
194D THR 3.3 8.7 - - - +
195D LYS* 1.3 96.1 - - + +
197D THR* 1.3 56.5 + - - +
199D ASN* 3.2 13.5 + - + +
200D SER* 3.0 26.0 + - - -
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Residues in contact with THR 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D SER* 2.7 36.7 + - - +
182D LEU 2.9 17.3 + - - -
183D VAL* 4.6 7.2 - - - +
194D THR* 2.8 13.9 + - - -
196D PRO* 1.3 74.7 - - - +
198D GLN* 1.3 62.2 + - - +
200D SER* 3.0 1.4 + - - +
201D VAL* 2.8 44.6 + - + +
214D VAL* 4.5 9.6 - - + -
216D CYS* 5.3 5.0 - - - -
230D ILE* 5.3 9.9 - - + -
234D CYS* 4.8 8.5 - - - -
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Residues in contact with GLN 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602C UTP 2.8 30.0 + - - -
194D THR* 2.9 34.5 + - - +
195D LYS* 2.9 18.0 + - + +
197D THR* 1.3 75.5 - - + +
199D ASN* 1.3 58.6 + - - +
201D VAL* 4.2 3.5 - - - +
202D ARG* 2.9 42.5 + - - +
205D ARG* 5.6 0.9 + - - -
230D ILE* 6.2 0.4 - - + -
233D PHE* 3.4 45.8 - - + -
234D CYS* 5.3 5.4 - - - -
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Residues in contact with ASN 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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10C VAL* 4.5 8.7 + - - +
150C THR* 5.2 1.8 + - - -
151C VAL 5.8 1.6 + - - -
153C ASP* 4.9 0.5 - - - +
195D LYS* 2.8 48.4 + - - +
196D PRO* 3.4 11.2 - - + +
197D THR 3.0 0.2 - - - -
198D GLN* 1.3 75.1 - - - +
200D SER* 1.3 65.4 + - - +
202D ARG* 2.9 36.7 + - - +
203D GLU* 2.9 25.2 + - - +
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Residues in contact with SER 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLY* 3.7 12.2 - - - -
10D VAL* 4.3 16.6 - - - -
151D VAL* 4.2 8.9 - - - +
179D HIS* 2.9 28.7 + - - -
181D SER* 4.5 1.6 - - - -
196D PRO 3.0 13.4 + - - -
197D THR* 3.0 7.6 + - - -
199D ASN* 1.3 76.3 - - - +
201D VAL* 1.3 56.6 + - - +
203D GLU* 3.2 7.3 + - - +
204D LEU* 2.8 27.7 + - - +
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Residues in contact with VAL 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D HIS* 3.8 22.4 - - + -
197D THR* 2.8 39.3 + - + +
198D GLN* 4.2 1.8 - - - +
200D SER* 1.3 67.5 - - - +
202D ARG* 1.3 56.4 + - - +
204D LEU* 3.0 7.6 + - - +
205D ARG* 2.7 60.3 + - + +
211D PRO* 4.6 12.8 - - + -
214D VAL* 4.7 9.4 - - + -
234D CYS* 4.1 26.9 - - + +
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Residues in contact with ARG 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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152C GLY* 4.4 19.3 + - - -
153C ASP* 5.3 3.7 + - - -
195D LYS* 5.7 0.8 - - - +
198D GLN* 2.9 42.3 + - - +
199D ASN* 2.9 40.1 + - - +
201D VAL* 1.3 77.3 - - - +
203D GLU* 1.3 56.7 + - - +
205D ARG* 3.2 18.2 + - - +
206D GLY* 2.8 26.2 + - - -
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Residues in contact with GLU 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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151D VAL* 3.7 20.0 - - + -
152D GLY* 5.2 8.8 - - - -
199D ASN 2.9 17.4 + - - +
200D SER* 3.5 6.1 - - - +
202D ARG* 1.3 76.9 - - - +
204D LEU* 1.3 57.5 + - - +
206D GLY* 3.0 4.4 + - - +
207D LEU* 2.8 45.3 + - + +
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Residues in contact with LEU 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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7D THR* 4.1 9.0 - - - +
151D VAL* 4.0 21.1 - - + +
160D ILE* 4.7 3.8 - - + -
177D ASN* 4.3 7.0 - - - +
179D HIS* 3.6 27.4 - - + +
200D SER 2.8 14.5 + - - +
201D VAL* 3.4 8.5 - - - +
203D GLU* 1.3 77.2 - - - +
205D ARG* 1.3 57.9 + - - +
207D LEU* 3.0 19.0 + - + +
208D GLY 2.9 22.0 + - - -
209D LEU* 3.0 41.1 + - + +
211D PRO* 3.7 28.5 - - + -
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Residues in contact with ARG 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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161A GLU* 5.8 0.2 + - - -
164A ARG* 4.1 30.4 - - - +
206A GLY 3.8 1.7 - - - +
207A LEU 4.5 1.2 - - - +
208A GLY* 4.4 9.9 - - - -
198D GLN 5.6 0.6 + - - -
201D VAL* 2.7 39.6 + - + +
202D ARG* 3.8 17.1 - - - +
204D LEU* 1.3 68.4 - - - +
206D GLY* 1.3 65.7 + - - +
208D GLY* 3.2 11.3 + - - -
209D LEU 3.1 17.5 - - - +
210D SER* 4.3 20.6 - - - -
211D PRO* 4.5 1.6 - - + -
233D PHE 3.1 22.8 + - - -
234D CYS* 2.9 31.5 + - - +
235D HIS* 3.0 20.6 + - - +
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Residues in contact with GLY 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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205A ARG 3.8 0.3 - - - +
206A GLY* 1.5 42.4 - - - +
207A LEU* 4.6 6.5 - - - -
202D ARG 2.8 14.5 + - - -
203D GLU* 3.0 7.4 + - - -
205D ARG* 1.3 77.6 - - - +
207D LEU* 1.3 58.3 + - - +
208D GLY 3.1 1.2 + - - -
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Residues in contact with LEU 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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205A ARG 4.5 3.5 - - - +
206A GLY* 4.6 5.1 - - - -
151D VAL* 3.7 29.6 - - + -
152D GLY* 5.1 4.7 - - - +
157D MET* 5.7 13.7 - - + -
160D ILE* 3.8 41.7 - - + +
164D ARG* 4.1 13.7 - - - +
203D GLU* 2.8 29.3 + - + +
204D LEU* 3.0 17.9 + - + +
206D GLY* 1.3 73.6 - - - +
208D GLY* 1.3 57.6 + - - +
209D LEU 4.7 0.7 - - - +
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Residues in contact with GLY 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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205A ARG 4.4 9.4 - - - -
208A GLY* 5.6 1.6 - - - -
164D ARG* 4.0 11.5 - - - +
167D GLN* 4.0 8.3 + - - -
168D PHE* 5.5 2.6 - - - -
204D LEU 2.9 1.6 + - - -
205D ARG 3.2 9.4 + - - -
206D GLY 3.0 5.1 - - - -
207D LEU* 1.3 81.4 - - - +
209D LEU* 1.3 72.2 + - - +
210D SER 4.3 0.3 + - - -
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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