Contacts of the helix formed by residues 179 - 189 (chain C) in PDB entry 1GSD
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C GLU* 3.4 8.5 - - - +
176C SER 4.5 3.1 - - - +
177C SER 3.3 9.9 - - - +
178C PHE* 1.3 88.4 - - - +
180C LEU* 1.3 64.7 + - + +
182C LYS* 3.1 22.1 + - - +
183C ALA* 2.8 29.9 + - - +
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C GLU* 2.9 25.5 + - + +
140C LEU* 3.5 27.7 - - + +
141C LYS* 3.5 46.2 - - + +
179C PRO* 1.3 82.2 - - + +
181C LEU* 1.3 55.9 + - - +
183C ALA* 3.4 9.0 + - + +
184C LEU* 3.0 22.0 + - - +
187C ARG* 4.9 3.1 + - - +
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Residues in contact with LEU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PHE* 3.7 52.7 - - + +
136C PHE* 3.9 22.7 - - + -
137C GLU* 3.0 17.2 + - - +
140C LEU* 3.6 21.5 - - + -
160C LEU* 3.9 18.6 - - + -
164C LEU* 3.5 14.9 - - + +
175C ILE* 3.9 10.1 - - + -
178C PHE* 3.2 15.7 + - + +
180C LEU* 1.3 73.6 - - - +
182C LYS* 1.3 61.0 + - - +
184C LEU* 3.4 3.3 + - + +
185C LYS* 2.9 29.1 + - - +
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Residues in contact with LYS 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C ILE* 3.5 39.5 - - + +
176C SER* 3.2 30.4 + - - +
178C PHE 3.1 6.5 + - - +
179C PRO* 3.1 28.8 + - - +
181C LEU* 1.3 73.8 - - - +
183C ALA* 1.3 65.6 + - - +
185C LYS* 3.1 7.1 + - - +
186C THR* 3.0 25.9 + - - -
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C PRO 2.8 15.8 + - - +
180C LEU* 3.6 12.8 - - + +
182C LYS* 1.3 76.3 - - - +
184C LEU* 1.3 56.7 + - - +
186C THR* 3.2 8.2 + - - -
187C ARG* 2.9 50.9 + - - +
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C LEU* 4.2 15.3 - - + -
146C ASP 3.4 24.9 - - - +
147C TYR* 4.9 0.4 - - - -
148C LEU* 4.4 9.6 - - + -
157C ASP* 3.9 15.0 - - - +
160C LEU* 3.6 35.4 - - + -
161C VAL* 4.1 7.0 - - + -
164C LEU* 5.2 0.7 - - + -
180C LEU 3.0 17.2 + - - +
181C LEU* 3.7 5.6 - - + +
182C LYS 3.3 0.2 - - - -
183C ALA* 1.3 75.3 - - - +
185C LYS* 1.3 59.1 + - - +
187C ARG* 3.4 12.3 - - - +
188C ILE* 2.8 62.0 + - + +
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Residues in contact with LYS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C VAL* 3.9 12.2 - - + +
164C LEU* 3.8 26.0 + - + +
165C TYR* 3.6 41.2 - - + +
168C GLU* 2.7 47.5 + - - +
175C ILE* 4.6 12.1 - - + +
181C LEU 2.9 15.2 + - - +
182C LYS* 3.1 10.5 + - - +
184C LEU* 1.3 78.6 - - - +
186C THR* 1.3 54.1 + - - +
188C ILE* 4.2 0.9 - - - +
189C SER* 2.5 38.1 + - - +
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Residues in contact with THR 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C LYS 3.0 13.8 + - - -
183C ALA* 3.5 9.5 - - - -
185C LYS* 1.3 74.4 - - - +
187C ARG* 1.3 67.4 + - - +
189C SER* 3.1 6.3 + - - -
190C ASN* 3.0 42.7 + - - +
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Residues in contact with ARG 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C LEU* 5.1 2.8 - - - +
145C GLN 4.6 2.8 + - - -
146C ASP* 2.8 71.9 + - - +
147C TYR* 5.0 10.3 - - + +
180C LEU* 4.9 3.0 + - - +
183C ALA* 2.9 34.6 + - - +
184C LEU* 3.4 31.0 - - - +
186C THR* 1.3 79.8 - - - +
188C ILE* 1.3 64.6 + - + +
190C ASN* 3.3 14.2 + - - +
191C LEU* 3.5 15.5 + - + +
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Residues in contact with ILE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C TRP* 5.7 0.7 - - + -
147C TYR* 4.0 13.9 - - + -
153C LEU* 3.6 28.3 - - + -
157C ASP* 3.9 10.5 - - + +
158C ILE* 4.3 11.7 - - + -
161C VAL* 3.6 33.0 - - + -
184C LEU* 2.8 41.3 + - + +
187C ARG* 1.3 73.0 - - + +
189C SER* 1.3 63.3 + - - +
191C LEU* 3.1 22.5 + - + +
194C VAL* 3.2 28.3 - - + +
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Residues in contact with SER 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C VAL* 4.3 1.9 - - - +
165C TYR* 2.7 36.0 + - - -
185C LYS* 2.5 24.3 + - - +
186C THR* 3.1 6.3 + - - -
188C ILE* 1.3 76.4 - - - +
190C ASN* 1.3 62.4 + - - +
194C VAL* 3.9 9.2 - - - -
195C LYS* 3.3 33.1 + - - +
198C LEU* 3.6 8.2 - - - +
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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