Contacts of the helix formed by residues 179 - 190 (chain D) in PDB entry 1GUM
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 PRO 179 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D GLU* 2.9 13.9 - - - +
176D SER 4.1 3.8 - - - +
177D ALA 3.1 11.0 - - - +
178D PHE* 1.3 93.3 - - - +
180D PHE* 1.4 63.8 + - + +
182D GLN* 3.1 17.3 + - + +
183D GLU* 2.9 29.3 + - - +
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Residues in contact with PHE 180 (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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137D GLU* 2.8 39.0 + - + -
140D LEU* 4.2 23.4 - - + +
141D ARG* 3.3 59.2 - - + -
144D GLY* 5.8 3.6 - - - -
179D PRO* 1.4 75.7 - - + +
181D LEU* 1.3 66.6 + - - +
183D GLU* 3.0 12.2 + - + +
184D TYR* 2.9 24.6 + - - +
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Residues in contact with LEU 181 (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 PHE* 3.2 58.1 - - + +
136D PHE* 4.0 15.0 - - + -
137D GLU* 2.7 19.7 + - - +
140D LEU* 4.0 17.5 - - + -
160D LEU* 4.3 9.6 - - + -
164D ILE* 4.3 6.7 - - + -
175D LEU* 3.7 14.1 - - + -
178D PHE* 2.7 22.2 + - + +
180D PHE* 1.3 72.1 - - - +
182D GLN* 1.3 60.3 + - - -
184D TYR* 3.5 14.2 - - + +
185D THR* 2.9 30.1 + - - -
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Residues in contact with GLN 182 (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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175D LEU* 2.7 45.0 + - + +
176D SER* 2.9 24.9 + - - +
178D PHE 2.6 24.9 + - - +
179D PRO* 3.5 13.9 - - + +
180D PHE 3.0 0.4 - - - -
181D LEU* 1.3 74.1 - - - +
183D GLU* 1.3 65.6 + - - +
185D THR* 3.3 2.7 + - - -
186D VAL* 3.0 29.3 + - + +
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Residues in contact with GLU 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 PRO 2.9 17.3 + - - +
180D PHE* 3.0 10.0 + - + +
182D GLN* 1.3 75.9 - - - +
184D TYR* 1.3 55.2 + - - +
186D VAL* 2.8 30.1 + - + +
187D LYS* 3.0 39.2 + - + +
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Residues in contact with TYR 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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140D LEU* 3.6 37.9 - - + -
146D SER 3.5 25.6 - - - -
148D LEU* 3.4 14.4 - - + +
157D ASP* 2.5 46.3 + - - -
160D LEU* 3.9 23.9 - - + +
161D LEU* 5.2 1.8 - - - -
164D ILE* 5.0 1.8 - - + -
180D PHE 2.9 16.3 + - - +
181D LEU* 3.5 11.7 - - + +
183D GLU* 1.3 72.4 - - - +
185D THR* 1.3 71.2 + - - +
186D VAL 3.2 0.3 + - - -
187D LYS* 3.2 18.0 + - - +
188D LEU* 2.9 47.6 + - + +
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Residues in contact with THR 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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161D LEU* 3.9 22.6 - - + +
164D ILE* 3.8 26.8 - - + +
165D LEU* 4.1 17.0 - - + -
168D GLU* 5.5 2.2 - - - +
175D LEU* 3.8 10.4 - - + +
181D LEU 2.9 19.4 + - - -
182D GLN 3.5 4.5 - - - -
184D TYR* 1.3 80.6 - - - +
186D VAL* 1.3 60.2 + - + +
188D LEU* 3.8 1.8 - - - +
189D SER* 2.4 37.6 + - - +
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Residues in contact with VAL 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 GLN* 3.0 18.5 + - + +
183D GLU* 2.8 13.6 + - + +
185D THR* 1.3 79.9 - - + +
187D LYS* 1.3 70.3 + - + +
189D SER* 2.9 12.3 + - - -
190D ASN* 2.9 32.6 + - - +
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Residues in contact with LYS 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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145D GLN 4.6 2.6 + - - -
146D SER* 3.2 43.0 + - - +
183D GLU* 3.0 36.5 + - + +
184D TYR* 3.7 22.7 - - - +
186D VAL* 1.3 84.7 - - + +
188D LEU* 1.3 60.4 + - + +
190D ASN* 2.8 25.5 + - - +
191D ILE* 3.3 8.5 + - - +
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Residues in contact with LEU 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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146D SER* 4.0 19.3 - - - +
147D PHE* 4.0 12.3 - - + -
153D LEU* 4.2 8.5 - - + -
157D ASP* 4.1 16.4 - - + +
161D LEU* 4.0 22.9 - - + -
184D TYR* 2.9 62.5 + - + +
185D THR 3.8 3.6 - - - +
187D LYS* 1.3 74.1 - - + +
189D SER* 1.3 62.4 + - - +
190D ASN 2.8 5.9 + - - -
191D ILE* 2.8 40.4 + - + +
194D ILE* 3.4 10.6 - - + +
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Residues in contact with SER 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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161D LEU* 4.0 12.4 - - - +
165D LEU* 5.2 3.1 - - - +
185D THR* 2.4 30.9 + - - +
186D VAL* 2.9 7.9 + - - -
188D LEU* 1.3 78.6 - - - +
190D ASN* 1.3 66.9 + - - +
194D ILE* 3.7 9.6 - - - +
195D LYS* 3.4 24.4 + - - +
198D LEU* 3.5 21.5 - - - +
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Residues in contact with ASN 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 VAL* 2.9 38.4 + - - +
187D LYS* 2.8 13.1 + - - +
189D SER* 1.3 84.7 - - - +
191D ILE* 1.3 64.7 + - - +
192D PRO* 3.0 7.6 - - - +
195D LYS* 3.7 30.1 - - + +
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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