Contacts of the helix formed by residues 179 - 190 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A GLU* 2.9 13.9 - - - +
176A SER 4.1 4.0 - - - +
177A ALA 3.1 10.8 - - - +
178A PHE* 1.3 94.1 - - - +
180A PHE* 1.4 61.6 + - + +
182A GLN* 3.1 17.7 + - + +
183A GLU* 2.9 29.8 + - - +
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLU* 2.8 39.1 + - + -
140A LEU* 4.2 23.9 - - + +
141A ARG* 3.3 57.0 - - + -
144A GLY* 5.8 4.0 - - - -
179A PRO* 1.4 75.2 - - + +
181A LEU* 1.3 67.6 + - - +
183A GLU* 3.0 11.6 + - + +
184A TYR* 2.9 24.6 + - - +
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.2 58.1 - - + +
136A PHE* 4.0 15.9 - - + -
137A GLU* 2.7 19.2 + - - +
140A LEU* 4.0 17.3 - - + -
160A LEU* 4.3 10.1 - - + -
164A ILE* 4.3 6.3 - - + -
175A LEU* 3.7 14.6 - - + -
178A PHE* 2.7 21.8 + - + +
180A PHE* 1.3 72.0 - - - +
182A GLN* 1.3 60.8 + - - -
184A TYR* 3.5 13.8 - - + +
185A THR* 2.9 29.9 + - - -
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Residues in contact with GLN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LEU* 2.7 47.6 + - + +
176A SER* 2.9 24.2 + - - +
178A PHE 2.6 24.0 + - - +
179A PRO* 3.5 13.5 - - + +
180A PHE 3.0 0.4 - - - -
181A LEU* 1.3 74.6 - - - +
183A GLU* 1.3 64.8 + - - +
185A THR* 3.3 2.8 + - - -
186A VAL* 3.0 28.7 + - + +
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A PRO 2.9 16.6 + - - +
180A PHE* 3.7 9.8 - - + +
182A GLN* 1.3 77.1 - - - +
184A TYR* 1.3 53.9 + - - +
186A VAL* 2.8 30.4 + - + +
187A LYS* 3.0 38.3 + - + +
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Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.6 38.1 - - + -
146A SER 3.5 24.7 - - - -
148A LEU* 3.4 14.4 - - + +
157A ASP* 2.5 47.0 + - - -
160A LEU* 3.9 23.2 - - + +
161A LEU* 5.2 1.3 - - - -
164A ILE* 5.0 2.7 - - + -
180A PHE 2.9 16.1 + - - +
181A LEU* 3.5 11.9 - - + +
183A GLU* 1.3 73.3 - - - +
185A THR* 1.3 71.7 + - - +
186A VAL 3.2 0.5 + - - -
187A LYS* 3.2 16.7 + - - +
188A LEU* 2.9 47.1 + - + +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 3.9 23.0 - - + +
164A ILE* 3.8 26.5 - - + +
165A LEU* 4.1 17.3 - - + -
168A GLU* 5.5 2.5 - - - +
175A LEU* 3.8 9.7 - - + +
181A LEU 2.9 19.5 + - - -
182A GLN* 3.5 4.9 - - - +
184A TYR* 1.3 80.9 - - - +
186A VAL* 1.3 60.5 + - + +
188A LEU* 3.5 1.7 + - - +
189A SER* 2.4 38.0 + - - +
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLN* 3.0 17.6 + - + +
183A GLU* 2.8 13.2 + - + +
185A THR* 1.3 81.7 - - + +
187A LYS* 1.3 69.2 + - + +
189A SER* 2.9 11.8 + - - -
190A ASN* 2.9 34.3 + - - +
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Residues in contact with LYS 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLN 4.6 2.0 + - - -
146A SER* 3.2 44.8 + - - +
183A GLU* 3.0 36.9 + - + +
184A TYR* 3.7 22.5 - - - +
186A VAL* 1.3 85.5 - - + +
188A LEU* 1.3 61.3 + - + +
190A ASN* 2.8 25.5 + - - +
191A ILE* 3.3 8.3 + - - +
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A SER 4.0 19.3 - - - +
147A PHE* 4.0 13.0 - - + -
153A LEU* 4.2 8.5 - - + -
157A ASP* 4.1 16.8 - - + +
161A LEU* 4.0 22.2 - - + -
184A TYR* 2.9 61.9 + - + +
185A THR 3.8 3.8 - - - +
187A LYS* 1.3 73.9 - - + +
189A SER* 1.3 61.8 + - - +
190A ASN 2.8 5.7 + - - -
191A ILE* 2.8 40.6 + - + +
194A ILE* 3.4 10.9 - - + +
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Residues in contact with SER 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 4.0 12.1 - - - +
165A LEU* 5.2 3.2 - - - +
185A THR* 2.4 30.5 + - - +
186A VAL* 2.9 7.8 + - - -
188A LEU* 1.3 78.4 - - - +
190A ASN* 1.3 67.2 + - - +
194A ILE* 3.7 10.8 - - - +
195A LYS* 3.4 24.4 + - - +
198A LEU* 3.5 21.9 - - - +
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Residues in contact with ASN 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 2.9 38.2 + - - +
187A LYS* 2.8 12.0 + - - +
189A SER* 1.3 85.5 - - - +
191A ILE* 1.3 63.6 + - - +
192A PRO* 3.0 7.3 - - - +
195A 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