Contacts of the helix formed by residues 180 - 193 (chain A) in PDB entry 1UMD
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 GLU 180 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.7 29.4 - - + +
147A ALA* 3.8 12.3 - - + -
177A ALA 3.1 9.8 + - - +
179A SER* 1.3 80.1 - - - +
181A GLY* 1.3 69.4 + - - +
182A ASP* 4.3 5.3 + - + +
183A TRP* 3.1 17.5 + - - +
184A TYR 3.5 3.1 + - - -
1402A TPP 3.1 18.1 - - - +
184C TYR* 4.0 5.9 - - - -
58D LEU* 3.1 25.1 - - - +
59D SER* 3.5 9.8 + - - -
60D GLU* 2.7 29.5 + - - +
61D ALA* 5.2 0.3 + - - +
89D PRO* 4.0 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A SER 3.8 2.4 + - - -
180A GLU* 1.3 77.9 + - - +
182A ASP* 1.3 59.0 + - - +
184A TYR* 3.2 3.1 + - - +
185A ALA* 2.8 25.3 + - - +
181C GLY* 3.3 42.3 - - - -
182C ASP* 5.5 0.9 - - - -
184C TYR* 4.5 3.8 - - - -
185C ALA* 4.2 8.9 - - - +
59D SER* 4.7 0.4 + - - -
61D ALA* 6.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE 5.7 0.7 - - - +
147A ALA* 4.3 15.0 - - + +
148A SER* 5.0 1.2 - - - -
151A PRO* 3.4 21.4 - - + +
180A GLU* 3.2 2.8 - - + +
181A GLY* 1.3 75.1 - - - +
183A TRP* 1.3 65.2 + - - +
185A ALA* 3.8 6.1 - - - -
186A GLY* 3.0 18.0 + - - -
61B ALA* 3.2 23.2 - - - +
89B PRO 4.3 6.1 - - - +
90B GLY* 5.8 0.3 - - - -
92B ASP* 4.5 15.2 - - - +
93B GLN* 3.1 29.4 + - - +
181C GLY* 5.5 0.9 - - - -
89D PRO* 5.7 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA* 4.0 8.1 - - + +
150A VAL* 3.6 28.1 - - + +
173A PHE* 3.2 33.0 - + - -
177A ALA 3.3 22.2 - - - +
178A THR* 3.5 30.5 - - + +
180A GLU 3.1 13.2 + - - +
182A ASP* 1.3 81.8 - - - +
184A TYR* 1.3 79.5 + - + +
187A ILE* 3.3 45.2 + - + +
221A ILE* 4.8 0.7 - - + -
224A LYS* 3.6 31.0 - - + -
228A PHE* 3.9 24.5 - + - -
262A LEU* 4.1 18.2 - - + -
184C TYR* 3.8 19.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLU 3.5 0.8 + - - -
181A GLY 3.2 6.4 + - - +
183A TRP* 1.3 88.9 - - + +
185A ALA* 1.3 68.4 + - - +
187A ILE 3.5 0.3 + - - -
188A ASN* 3.0 29.7 + - + +
227A ALA* 4.1 16.8 - - + -
228A PHE* 3.3 36.5 - + - -
178C THR 2.5 29.3 + - - -
179C SER* 3.9 15.0 - - - -
180C GLU 4.0 10.5 - - - -
183C TRP* 3.7 8.2 - + - -
184C TYR* 3.5 54.7 - + + -
224C LYS* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLY 2.8 18.8 + - - +
182A ASP* 4.0 8.1 - - - +
184A TYR* 1.3 79.2 - - - +
186A GLY* 1.3 62.0 - - - +
188A ASN* 3.5 4.0 + - - +
189A PHE* 3.3 16.3 + - - +
59B SER* 3.2 25.5 - - - +
61B ALA* 4.3 9.6 - - + -
62B ALA* 3.7 13.8 - - - +
179C SER 4.1 11.1 - - - +
181C GLY* 4.2 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 4.4 3.1 - - - -
151A PRO* 4.0 26.9 - - - +
154A ALA* 3.5 15.2 - - - +
182A ASP 3.0 17.2 + - - -
183A TRP 4.1 0.4 - - - -
185A ALA* 1.3 74.5 - - - +
187A ILE* 1.3 64.5 + - - +
189A PHE* 3.3 4.2 + - - +
190A ALA 3.1 17.2 + - - -
199A PHE* 5.0 0.2 - - - -
62B ALA* 4.8 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 3.8 4.0 - - + +
183A TRP* 3.3 59.1 + - + +
186A GLY* 1.3 75.0 - - - +
188A ASN* 1.3 57.8 + - - +
190A ALA* 3.2 1.4 + - - +
191A ALA* 2.9 28.1 + - + +
199A PHE* 3.7 54.3 - - + -
228A PHE* 3.6 31.6 - - + -
230A ILE* 4.1 11.7 - - + -
260A PRO* 5.6 0.2 - - + -
262A LEU* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TYR* 3.0 30.2 + - + +
185A ALA* 3.6 7.3 + - - +
186A GLY 3.2 0.2 - - - -
187A ILE* 1.3 77.8 - - - +
189A PHE* 1.3 61.3 + - - +
191A ALA* 3.3 2.8 + - - +
192A VAL* 3.0 28.6 + - - +
228A PHE* 3.7 19.5 - - + -
57B PRO* 3.8 8.5 - - - +
59B SER* 6.2 0.2 - - - -
179C SER* 3.2 33.9 + - - +
215C GLN 3.2 11.3 + - - -
216C THR* 2.8 26.8 + - - -
217C HIS 4.4 1.2 + - - -
224C LYS* 3.9 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA* 5.2 2.7 - - + -
158A ILE* 3.5 20.2 - - + -
185A ALA 3.3 8.7 + - - +
186A GLY* 3.3 8.6 + - - +
187A ILE 3.3 0.4 - - - -
188A ASN* 1.3 76.7 - - - +
190A ALA* 1.3 67.4 + - - +
192A VAL* 3.2 1.7 + - + +
193A GLN* 3.1 45.1 + - + +
27B LEU* 4.3 10.1 - - + -
54B MET* 4.1 13.2 - - - -
56B THR* 3.8 22.2 - - + -
57B PRO* 3.3 36.6 - - + -
62B ALA* 4.0 20.0 - - + -
66B ALA* 3.5 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ALA* 3.7 27.5 - - + +
158A ILE* 5.2 1.6 - - - -
186A GLY 3.1 7.7 + - - +
187A ILE 3.2 8.0 + - - +
189A PHE* 1.3 76.0 - - - +
191A ALA* 1.3 58.1 + - - +
193A GLN* 3.4 1.8 + - - -
194A GLY 3.0 7.1 + - - -
195A ALA* 3.0 41.4 + - + -
197A ALA* 4.7 2.0 - - + -
199A PHE* 3.8 22.9 - - + -
260A PRO* 3.8 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ILE 2.9 17.0 + - - +
188A ASN* 3.7 4.5 - - - +
190A ALA* 1.3 76.4 - - - +
192A VAL* 1.3 66.4 + - - +
194A GLY* 3.0 13.2 + - - -
228A PHE* 3.7 21.1 - - + +
230A ILE* 3.6 28.0 - - + -
260A PRO* 3.6 13.0 - - + +
217C HIS* 3.8 19.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASN 3.0 19.0 + - - +
189A PHE 3.2 4.9 + - - +
191A ALA* 1.3 76.1 - - - +
193A GLN* 1.3 72.7 + - + +
194A GLY 3.5 0.3 + - - -
57B PRO* 4.2 8.3 - - + -
213C ARG* 3.7 19.3 - - - +
214C HIS* 3.7 24.9 - - + +
215C GLN 3.7 6.1 - - - +
216C THR* 3.3 38.4 - - - +
217C HIS* 3.5 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ILE* 4.0 25.8 - - + +
161A LYS* 2.7 38.4 + - + +
162A LEU* 5.9 2.3 - - - +
189A PHE* 3.1 45.1 + - + +
190A ALA 4.0 3.1 - - - +
192A VAL* 1.3 88.8 + - - +
194A GLY* 1.3 59.1 + - - +
195A ALA* 3.2 1.9 + - + +
50B PRO 5.7 0.3 - - - +
54B MET* 3.9 23.3 - - - +
55B ASP 4.3 12.7 + - - -
57B PRO* 5.8 0.2 - - - +
214C HIS* 5.3 8.5 + - - +
----------------------------------------------------------
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