Contacts of the helix formed by residues 177 - 198 (chain D) in PDB entry 4RDU
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 177 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LYS* 4.3 4.8 + - - +
171D ALA* 3.9 1.8 - - - -
176D LEU* 1.3 76.5 - - - +
178D GLN* 1.3 64.2 + - - +
179D THR* 3.5 8.6 + - - -
180D GLN* 2.8 44.1 + - - +
181D VAL* 3.1 22.2 + - - +
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Residues in contact with GLN 178 (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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164D LEU* 4.4 4.7 - - - +
167D ARG* 3.1 40.4 + - - +
168D ALA* 3.3 42.2 + - - +
171D ALA* 3.9 11.8 - - + +
177D THR* 1.3 70.8 - - - +
179D THR* 1.3 60.6 + - - +
181D VAL* 3.3 3.8 + - - +
182D LYS* 2.8 31.4 + - - +
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Residues in contact with THR 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LYS* 5.3 7.6 - - - +
167D ARG* 5.6 0.4 - - - +
177D THR* 3.2 8.8 + - - -
178D GLN* 1.3 78.8 - - - +
180D GLN* 1.3 62.5 + - - +
182D LYS* 3.6 21.8 + - - +
183D ILE* 3.0 37.6 + - + +
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Residues in contact with GLN 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LYS* 3.3 26.9 - - - +
142D THR* 2.9 40.3 + - - +
144D TYR* 3.4 22.8 + - - +
175D GLY 4.8 0.3 - - - +
176D LEU* 3.3 21.9 - - + +
177D THR* 2.8 50.5 + - - +
179D THR* 1.3 72.6 - - - +
181D VAL* 1.3 63.4 + - - +
183D ILE* 3.5 1.6 + - - +
184D TRP* 3.0 19.2 + - - +
7F A 4.4 8.4 + - - +
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Residues in contact with VAL 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D LEU* 4.2 11.7 - - + -
162D LEU* 3.7 29.4 - - + -
167D ARG* 4.3 9.6 - - + +
170D LEU* 4.6 5.4 - - + -
171D ALA* 3.7 26.7 - - + +
174D LEU* 5.4 0.2 - - + -
176D LEU* 4.0 20.4 - - + -
177D THR 3.1 13.2 + - - +
178D GLN* 3.8 6.7 - - - +
180D GLN* 1.3 77.1 - - - +
182D LYS* 1.3 62.9 + - - +
184D TRP* 3.3 6.4 + - - +
185D PHE* 3.1 32.6 + - + -
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Residues in contact with LYS 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D LEU* 6.2 0.4 - - - -
167D ARG* 3.8 34.0 - - - +
178D GLN 2.8 20.4 + - - +
179D THR* 3.6 19.4 + - - +
181D VAL* 1.3 73.6 - - - +
183D ILE* 1.3 74.3 + - - +
185D PHE* 3.4 6.3 + - - +
186D GLN* 2.9 54.5 + - + +
189D ARG* 5.0 0.7 + - - -
3E A 5.4 10.2 + - + +
4E C 6.2 0.4 - - - +
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Residues in contact with ILE 183 (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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179D THR* 3.0 32.8 + - + +
180D GLN 3.9 2.9 - - - +
182D LYS* 1.3 85.6 - - - +
184D TRP* 1.3 56.0 + - - +
186D GLN* 3.1 32.6 + - - +
187D ASN* 2.8 52.1 + - - +
6F A 4.5 1.3 - - + -
7F A 3.7 38.1 - - + +
8F T 3.7 17.9 - - + +
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Residues in contact with TRP 184 (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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144D TYR* 3.8 23.8 + + - +
149D LEU* 4.0 14.1 - - - +
152D LEU* 3.6 54.8 - - + +
153D GLN* 3.7 28.7 - - + -
156D PHE* 4.1 7.6 - + + -
180D GLN 3.0 14.4 + - - +
181D VAL* 3.5 11.7 - - - +
183D ILE* 1.3 75.1 - - - +
185D PHE* 1.3 82.1 + + + +
187D ASN* 3.3 3.4 + - - +
188D LYS* 2.8 66.6 + - + +
6F A 3.1 32.3 + - - -
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Residues in contact with PHE 185 (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 LEU* 4.0 27.6 - - + -
155D ARG* 4.1 15.0 - - + -
156D PHE* 3.7 16.2 - + - -
159D THR 3.5 22.7 - - - -
160D GLN 3.4 19.5 - - - -
161D TYR* 4.9 0.2 - - - -
162D LEU* 3.7 39.0 - - + +
170D LEU* 4.3 1.3 - - + -
181D VAL* 3.1 23.0 + - + +
182D LYS* 3.8 8.1 - - - +
184D TRP* 1.3 92.0 - + - +
186D GLN* 1.3 65.7 + - - +
188D LYS* 3.9 1.7 - - - +
189D ARG* 3.0 42.8 + - - +
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Residues in contact with GLN 186 (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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182D LYS* 2.9 44.6 + - + +
183D ILE* 3.1 29.9 + - - +
185D PHE* 1.3 77.8 - - - +
187D ASN* 1.3 67.4 + - - +
189D ARG* 3.8 20.6 - - - +
190D SER* 3.1 21.8 + - - -
4E C 4.6 9.7 - - - -
5E T 3.4 40.1 + - + +
6E A 4.8 3.0 + - - +
8F T 4.5 10.9 - - - +
9F T 5.0 1.6 - - - +
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Residues in contact with ASN 187 (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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183D ILE* 2.8 31.5 + - - +
184D TRP 3.8 3.1 - - - +
186D GLN* 1.3 74.1 - - - +
188D LYS* 1.3 61.2 + - - +
190D SER* 3.2 9.2 + - - -
191D LYS* 2.9 27.9 + - - +
7E A 4.6 2.6 + - - -
5F T 5.1 5.2 - - + -
6F A 3.4 32.7 + - + +
7F A 3.0 48.3 + - - +
8F T 4.6 2.6 - - - +
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Residues in contact with LYS 188 (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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159A THR* 4.8 9.5 + - - +
161A TYR 5.4 0.9 + - - -
163A ALA* 5.0 1.1 - - - +
166A GLU* 2.7 38.6 + - - -
153D GLN* 4.8 11.1 - - - +
156D PHE* 3.5 47.8 - - + -
184D TRP* 2.8 47.3 + - + +
185D PHE 3.9 1.1 - - - +
187D ASN* 1.3 76.8 - - - +
189D ARG* 1.3 64.3 + - - +
191D LYS* 3.2 18.5 + - + +
192D ILE* 3.0 30.8 + - + +
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Residues in contact with ARG 189 (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 PHE* 3.8 16.6 - - + -
160D GLN* 2.9 39.8 + - + +
161D TYR* 3.3 47.2 - - - +
162D LEU 5.0 1.0 - - - +
182D LYS* 5.0 1.2 + - - +
185D PHE* 3.0 39.0 + - - +
186D GLN* 3.8 22.9 - - - +
188D LYS* 1.3 77.1 - - - +
190D SER* 1.3 61.2 + - - +
192D ILE* 3.4 3.9 + - - +
193D LYS* 3.0 24.8 + - - +
4E C 3.9 18.8 + - - -
5E T 3.0 31.4 + - - +
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Residues in contact with SER 190 (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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186D GLN 3.1 15.1 + - - -
187D ASN* 3.2 12.1 + - - -
189D ARG* 1.3 75.7 - - - +
191D LYS* 1.3 62.6 + - - +
193D LYS* 3.4 7.1 + - - +
194D LYS* 3.0 43.6 + - - +
6E A 4.9 24.3 + - - +
7E A 5.4 3.9 + - - -
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Residues in contact with LYS 191 (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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155A ARG* 3.6 18.5 - - - +
159A THR* 4.8 2.4 + - - -
166A GLU* 2.9 27.8 + - - +
169A GLU* 6.0 0.4 - - - -
187D ASN 2.9 13.9 + - - +
188D LYS* 3.5 22.1 - - + +
190D SER* 1.3 73.1 + - - +
192D ILE* 1.3 67.0 + - + +
194D LYS* 3.1 12.6 + - + +
195D ILE* 3.0 36.9 + - + +
4F C 5.3 2.4 - - - -
5F T 2.9 31.9 + - - +
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Residues in contact with ILE 192 (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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163A ALA* 3.8 26.2 - - + -
165A PRO* 3.8 14.6 - - + -
166A GLU* 4.0 24.0 - - + +
156D PHE* 3.7 24.0 - - + -
188D LYS* 3.0 24.8 + - + +
189D ARG* 3.8 4.9 - - - +
191D LYS* 1.3 75.4 - - + +
193D LYS* 1.3 63.3 + - - +
195D ILE* 3.0 13.0 + - + +
196D MET* 2.9 45.7 + - + +
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Residues in contact with LYS 193 (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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189D ARG 3.0 17.2 + - - +
190D SER* 3.7 6.7 - - - +
191D LYS 3.3 0.2 - - - -
192D ILE* 1.3 78.8 - - - +
194D LYS* 1.3 60.5 + - + +
196D MET* 3.3 11.0 + - + +
197D LYS* 3.1 22.5 + - - +
6E A 4.2 22.4 - - - +
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Residues in contact with LYS 194 (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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190D SER* 3.0 33.8 + - - +
191D LYS* 3.1 12.7 + - + +
193D LYS* 1.3 73.6 - - + +
195D ILE* 1.3 67.3 + - + +
197D LYS* 3.3 9.2 + - - +
198D ASN 3.3 19.8 + - - +
6E A 5.6 2.4 - - - +
7E A 4.8 16.2 + - - -
8E T 5.0 15.3 - - - +
5F T 6.1 6.3 - - + -
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Residues in contact with ILE 195 (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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155A ARG* 5.6 0.2 - - - +
165A PRO* 3.8 28.3 - - + +
166A GLU* 3.8 30.7 - - + +
169A GLU* 3.9 35.7 - - + +
191D LYS* 3.0 35.3 + - + +
192D ILE* 3.0 16.8 + - + +
194D LYS* 1.3 76.3 - - + +
196D MET* 1.3 57.5 + - + +
198D ASN* 3.0 22.8 + - - +
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Residues in contact with MET 196 (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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165A PRO* 3.8 27.6 - - + -
192D ILE* 2.9 36.9 + - + +
193D LYS* 3.7 10.3 - - + +
194D LYS 3.2 0.4 - - - -
195D ILE* 1.3 73.6 - - - +
197D LYS* 1.3 60.8 + - - +
198D ASN* 3.3 3.3 - - - +
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Residues in contact with LYS 197 (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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193D LYS 3.1 12.4 + - - +
194D LYS* 3.7 11.7 - - - +
195D ILE 3.2 0.4 - - - -
196D MET* 1.3 74.5 - - - +
198D ASN* 1.3 71.6 + - - +
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Residues in contact with ASN 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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194D LYS 3.3 9.0 + - - +
195D ILE 3.0 18.8 + - - +
196D MET 4.7 2.9 - - - +
197D LYS* 1.3 84.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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