Contacts of the helix formed by residues 179 - 190 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137H GLU* 2.9 13.7 - - - +
176H SER 4.1 4.3 - - - +
177H ALA 3.1 9.6 - - - +
178H PHE* 1.3 94.3 - - - +
180H PHE* 1.4 63.2 + - + +
182H GLN* 3.1 17.8 + - + +
183H GLU* 2.9 29.6 + - - +
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Residues in contact with PHE 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H GLU* 2.8 38.1 + - + +
140H LEU* 4.2 23.2 - - + +
141H ARG* 3.3 59.0 - - + -
144H GLY* 5.8 4.0 - - - -
179H PRO* 1.4 75.2 - - + +
181H LEU* 1.3 67.3 + - - +
183H GLU* 3.0 12.7 + - + +
184H TYR* 2.9 24.4 + - - +
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Residues in contact with LEU 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H PHE* 3.2 58.6 - - + +
136H PHE* 4.0 15.7 - - + -
137H GLU* 2.7 20.5 + - - +
140H LEU* 4.0 17.0 - - + -
160H LEU* 4.3 9.4 - - + -
164H ILE* 4.3 6.5 - - + -
175H LEU* 3.7 14.8 - - + -
178H PHE* 2.7 22.2 + - + +
180H PHE* 1.3 70.0 - - - +
182H GLN* 1.3 60.7 + - - -
184H TYR* 3.5 14.5 - - + +
185H THR* 2.9 29.9 + - - -
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Residues in contact with GLN 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175H LEU* 2.7 48.0 + - + +
176H SER* 2.9 24.4 + - - +
178H PHE 2.6 23.0 + - - +
179H PRO* 3.5 13.7 - - + +
180H PHE 3.0 0.4 - - - -
181H LEU* 1.3 75.2 - - - +
183H GLU* 1.3 64.1 + - - +
185H THR* 3.5 2.1 - - - -
186H VAL* 3.0 29.5 + - + +
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Residues in contact with GLU 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H PRO 2.9 16.4 + - - +
180H PHE* 3.0 10.2 + - + +
182H GLN* 1.3 77.5 - - - +
184H TYR* 1.3 55.5 + - - +
186H VAL* 2.8 30.0 + - + +
187H LYS* 3.0 38.2 + - + +
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Residues in contact with TYR 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140H LEU* 3.6 35.9 - - + -
146H SER 3.5 25.6 - - - -
148H LEU* 3.4 14.6 - - + +
157H ASP* 2.5 46.7 + - - -
160H LEU* 3.9 23.5 - - + +
161H LEU* 5.2 1.6 - - - -
164H ILE* 5.0 1.8 - - + -
180H PHE 2.9 15.7 + - - +
181H LEU* 3.5 11.7 - - + +
183H GLU* 1.3 73.0 - - - +
185H THR* 1.3 71.9 + - - +
186H VAL 3.2 0.5 + - - -
187H LYS* 3.2 16.5 + - - +
188H LEU* 2.9 48.0 + - + +
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Residues in contact with THR 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H LEU* 3.9 23.4 - - + +
164H ILE* 3.8 27.2 - - + +
165H LEU* 4.1 17.0 - - + -
168H GLU* 5.5 2.7 - - - +
175H LEU* 3.8 9.6 - - + +
181H LEU 2.9 18.8 + - - -
182H GLN* 3.5 4.7 - - - -
184H TYR* 1.3 81.4 - - - +
186H VAL* 1.3 60.7 + - + +
188H LEU* 3.5 1.9 + - - +
189H SER* 2.4 37.9 + - - +
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Residues in contact with VAL 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182H GLN* 3.0 17.4 + - + +
183H GLU* 2.8 13.6 + - + +
185H THR* 1.3 80.6 - - + +
187H LYS* 1.3 69.7 + - + +
189H SER* 2.9 11.7 + - - -
190H ASN* 2.9 34.1 + - - +
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Residues in contact with LYS 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H GLN 4.6 2.0 + - - -
146H SER* 3.2 43.2 + - - +
183H GLU* 3.0 36.3 + - + +
184H TYR* 3.7 22.5 - - - +
186H VAL* 1.3 85.2 - - + +
188H LEU* 1.3 60.6 + - + +
190H ASN* 2.8 25.2 + - - +
191H ILE* 3.3 8.2 + - - +
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Residues in contact with LEU 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H SER* 4.0 18.6 - - - +
147H PHE* 4.0 13.0 - - + -
153H LEU* 4.2 7.9 - - + -
157H ASP* 4.1 16.8 - - + +
161H LEU* 4.0 23.6 - - + -
184H TYR* 2.9 61.6 + - + +
185H THR 3.8 4.0 - - - +
187H LYS* 1.3 74.8 - - + +
189H SER* 1.3 61.1 + - - +
190H ASN 2.8 6.1 + - - -
191H ILE* 2.8 40.9 + - + +
194H ILE* 3.4 11.1 - - + +
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Residues in contact with SER 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H LEU* 4.0 12.2 - - - +
165H LEU* 5.2 3.0 - - - +
185H THR* 2.4 30.8 + - - +
186H VAL* 2.9 7.8 + - - -
188H LEU* 1.3 78.6 - - - +
190H ASN* 1.3 66.3 + - - +
191H ILE 3.4 0.2 - - - -
194H ILE* 3.7 10.0 - - - +
195H LYS* 3.4 24.4 + - - +
198H LEU* 3.5 21.2 - - - +
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Residues in contact with ASN 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186H VAL* 2.9 37.4 + - - +
187H LYS* 2.8 13.3 + - - +
189H SER* 1.3 83.7 - - - +
191H ILE* 1.3 64.8 + - - +
192H PRO* 3.0 7.3 - - - +
195H LYS* 3.7 30.3 - - + +
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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