Contacts of the helix formed by residues 180 - 196 (chain D) in PDB entry 5YL4
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 VAL 180 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ASN 3.8 21.3 - - - +
178D THR* 3.3 11.2 - - + -
179D VAL* 1.3 81.9 - - + +
181D GLU* 1.3 62.4 + - - +
182D PRO* 3.4 2.7 - - - -
183D TYR* 3.3 25.3 + - + +
184D ASN* 3.3 15.3 + - - +
388D MET* 4.4 5.4 - - + -
394D PHE* 3.8 42.4 - - + -
397D TRP* 3.9 20.0 - - + -
398D TYR* 3.8 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ASN* 5.9 0.3 + - - -
140D GLY* 3.1 27.5 - - - +
171D PRO* 3.4 24.8 - - + +
172D SER 4.4 2.4 + - - -
176D SER* 3.5 27.6 + - - +
178D THR* 3.4 25.4 - - + +
179D VAL 3.4 0.4 - - - -
180D VAL* 1.3 74.6 - - - +
182D PRO* 1.4 68.0 - - + +
184D ASN* 3.1 3.3 + - - +
185D ALA* 2.9 31.0 + - - +
501D GTP 2.7 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D PRO* 5.4 2.0 - - + -
173D PRO* 6.2 1.1 - - + -
178D THR 4.8 1.1 - - - +
179D VAL 3.6 14.8 - - - +
180D VAL* 3.6 0.9 - - - -
181D GLU* 1.4 94.3 - - + +
183D TYR* 1.3 58.4 + - - +
185D ALA* 4.7 0.9 - - + -
186D THR* 3.1 28.9 + - - -
381D ILE* 4.1 12.3 - - + +
384D GLN* 3.5 57.9 - - + +
385D PHE* 3.5 8.8 - - - +
388D MET* 5.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D VAL* 3.3 23.5 + - + +
181D GLU 3.2 0.6 - - - -
182D PRO* 1.3 78.4 - - - +
184D ASN* 1.3 63.1 + - - +
186D THR* 4.0 2.1 - - - -
187D LEU* 3.2 30.3 + - - +
385D PHE* 3.5 22.3 - + - -
388D MET* 3.3 40.6 - - + -
389D PHE* 3.3 21.8 + + + -
393D ALA 2.7 29.7 + - - -
394D PHE* 4.1 12.8 - - + -
395D LEU* 4.3 7.2 - - + +
398D TYR* 3.6 30.7 - + + +
408D PHE* 3.3 27.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ASN* 3.4 19.4 + - - +
101D TRP* 3.4 25.2 + - + +
139D LEU 3.2 14.8 - - - +
140D GLY 2.9 14.4 + - - +
141D GLY 2.7 26.6 + - - +
145D SER* 3.4 3.7 + - - +
180D VAL 3.5 12.0 + - - -
181D GLU* 3.1 6.5 + - - +
183D TYR* 1.3 74.7 - - - +
185D ALA* 1.3 60.8 + - - +
187D LEU* 3.5 2.9 + - - +
188D SER* 2.8 32.4 + - - -
398D TYR* 2.7 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LEU* 3.0 19.9 + - + +
170D MET* 4.7 4.9 - - + -
171D PRO* 3.8 28.0 - - + -
181D GLU 2.9 15.5 + - - +
184D ASN* 1.3 74.1 - - - +
186D THR* 1.3 56.0 + - - +
188D SER* 3.3 2.1 + - - -
189D VAL* 2.9 34.7 + - - +
381D ILE* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D PRO 3.1 18.7 + - - -
183D TYR 4.0 0.2 - - - -
184D ASN 3.3 0.4 - - - -
185D ALA* 1.3 75.7 - - - +
187D LEU* 1.3 64.9 + - - +
189D VAL* 3.5 7.8 + - - +
190D HIS* 3.2 21.0 + - - +
381D ILE* 3.4 6.8 - - - +
385D PHE* 3.4 32.3 - - + -
411D ALA* 3.7 29.9 - - + +
412D GLU* 4.0 3.6 - - - +
415D MET* 3.3 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D TRP* 3.6 53.5 - - + -
183D TYR 3.2 22.9 + - - +
184D ASN 3.9 2.0 - - - +
186D THR* 1.3 75.2 - - - +
188D SER* 1.3 62.9 + - - +
190D HIS* 3.4 15.6 - - + +
191D GLN* 3.5 13.2 + - - +
385D PHE* 5.8 0.7 - - + -
398D TYR* 4.4 5.2 - - + -
403D MET* 3.7 23.3 - - + -
407D GLU* 4.3 12.3 - - + +
408D PHE* 3.9 30.7 - - + -
411D ALA* 4.3 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D TRP* 3.1 12.7 + - - +
139D LEU* 3.7 26.0 - - - -
145D SER* 2.5 31.1 + - - -
149D THR* 4.0 12.7 - - - +
184D ASN 2.8 13.8 + - - -
185D ALA 3.6 4.0 - - - -
186D THR 3.3 0.2 - - - -
187D LEU* 1.3 74.3 - - - +
189D VAL* 1.3 59.9 + - - +
191D GLN* 2.9 21.4 + - - +
192D LEU* 2.9 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LEU* 4.4 15.9 - - + -
170D MET* 4.7 6.1 - - + -
185D ALA 2.9 22.7 + - - +
186D THR 3.8 4.3 - - - +
187D LEU 3.4 0.2 - - - -
188D SER* 1.3 74.4 - - - +
190D HIS* 1.3 57.6 + - - +
192D LEU* 3.8 9.6 - - + +
193D VAL* 2.9 45.6 + - + +
265D PHE* 5.2 2.7 - - + -
378D PHE* 3.9 26.9 - - + -
381D ILE* 6.0 0.7 - - + -
414D ASN* 5.9 0.2 - - - +
415D MET* 3.7 40.2 - - + +
418D LEU* 4.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D THR 3.2 11.0 + - - +
187D LEU* 3.4 11.2 - - + +
188D SER 3.2 0.8 - - - -
189D VAL* 1.3 79.3 - - - +
191D GLN* 1.3 77.4 + - - +
193D VAL 4.4 0.2 - - - -
194D GLU* 3.4 28.7 + - + +
407D GLU* 5.8 9.0 + - + +
410D GLU* 3.5 31.8 + - + +
411D ALA* 3.6 18.8 + - + +
414D ASN* 3.4 37.1 + - + +
126E LYS* 4.7 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D TRP* 4.0 15.8 - - + -
105D HIS* 3.7 19.2 + - - -
106D TYR* 5.4 2.2 + - - -
149D THR* 3.9 32.1 - - + +
152D ILE* 6.0 1.6 - - + -
153D SER* 4.6 1.9 + - - -
187D LEU 3.6 11.6 + - - +
188D SER 2.9 7.8 + - - +
190D HIS* 1.3 98.9 + - - +
192D LEU* 1.3 58.6 + - - +
193D VAL 3.4 0.2 - - - -
194D GLU* 3.4 2.2 + - - -
195D ASN* 2.9 46.5 + - + +
407D GLU* 5.4 2.0 + - - -
126E LYS* 3.5 38.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D HIS* 4.5 5.2 - - + -
139D LEU* 3.8 28.7 - - + -
149D THR* 4.6 5.2 - - + -
152D ILE* 3.9 18.8 - - + -
166D THR* 4.1 2.5 - - + +
168D SER* 3.7 24.9 - - - +
188D SER 2.9 19.5 + - - +
189D VAL* 3.2 7.6 + - + +
191D GLN* 1.3 75.0 - - - +
193D VAL* 1.3 62.4 + - - +
196D THR* 2.8 52.5 + - + +
199D THR* 4.0 12.8 - - + +
264D HIS* 2.8 8.7 + - - -
265D PHE* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D VAL* 2.9 26.0 + - + +
190D HIS 4.6 0.2 - - - +
192D LEU* 1.3 74.7 - - - +
194D GLU* 1.3 60.1 + - - +
261D PRO 4.7 0.7 - - - +
262D ARG* 3.2 60.1 - - + +
264D HIS* 3.3 21.7 - - - -
265D PHE* 3.5 22.9 - - + -
414D ASN* 3.9 15.5 - - - +
418D LEU* 3.7 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ARG* 4.9 5.7 + - - -
190D HIS* 3.4 23.9 - - + +
191D GLN* 3.4 6.0 + - - +
192D LEU 3.2 0.6 - - - -
193D VAL* 1.3 79.9 - - - +
195D ASN* 1.3 74.8 + - - +
196D THR 3.9 2.3 - - - +
262D ARG* 3.4 25.5 + - - +
414D ASN* 3.7 12.5 + - - +
122E ARG* 5.4 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D THR 5.3 0.2 - - - +
152D ILE* 3.6 27.4 - - + +
153D SER* 3.5 23.6 + - - -
156D ARG* 3.5 34.6 + - + +
164D MET* 4.0 2.6 - - - +
191D GLN* 2.9 30.7 + - - +
194D GLU* 1.3 93.0 + - - +
196D THR* 1.3 61.2 + - - +
123E LEU* 4.0 18.8 - - - +
126E LYS* 4.6 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D ILE* 4.0 7.0 - - + -
156D ARG* 4.3 2.8 + - - -
164D MET* 3.5 18.6 - - + -
166D THR* 3.7 17.9 - - + -
192D LEU* 2.8 36.9 + - + +
193D VAL 4.8 0.2 - - - +
194D GLU 5.0 1.2 - - - +
195D ASN* 1.3 82.5 + - - +
197D ASP* 1.3 65.1 + - - +
198D GLU 4.2 1.6 - - - -
199D THR* 3.2 11.9 + - - -
261D PRO 4.7 1.0 - - - +
264D HIS* 2.8 50.2 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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