Contacts of the helix formed by residues 183 - 188 (chain A) in PDB entry 2G8N
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 CYS 183 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 3.9 7.6 - - - +
79A GLY* 4.0 12.3 - - - +
159A VAL* 4.5 12.3 - - - -
180A SER* 3.7 19.2 + - - +
181A ALA 3.2 4.7 + - - +
182A PHE* 1.3 78.0 - - - +
184A LEU* 1.3 73.2 - - + +
185A GLU* 3.5 1.6 + - - -
186A ALA* 2.8 15.8 + - - +
187A VAL* 3.2 15.2 + - - +
3001A SAH 3.3 51.1 - - - +
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Residues in contact with LEU 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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78A ILE* 5.0 0.2 - - + -
159A VAL* 4.2 22.2 - - + -
180A SER* 4.7 4.5 + - - +
183A CYS* 1.3 81.3 - - + +
185A GLU* 1.3 66.8 + - - +
187A VAL* 3.0 14.9 + - - +
188A SER* 2.9 21.1 + - - -
194A PHE* 3.5 25.6 - - + +
197A ALA* 4.0 19.5 - - + -
198A LEU* 3.8 39.3 - - + +
201A ILE* 4.1 20.4 - - + -
213A LEU* 4.4 20.6 - - + +
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Residues in contact with GLU 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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182A PHE* 3.4 19.1 - - - +
183A CYS 4.4 0.3 + - - -
184A LEU* 1.3 79.8 + - - +
186A ALA* 1.3 64.3 + - + +
187A VAL 3.4 0.9 + - - -
188A SER 3.4 4.3 - - - +
194A PHE* 3.5 19.0 - - + -
213A LEU* 6.0 1.0 - - - +
214A ILE 4.8 1.2 - - - +
215A GLY* 3.1 13.4 - - - -
216A ALA* 2.7 44.6 + - + +
231A VAL* 3.2 26.5 - - + +
232A VAL* 3.2 40.9 + - + +
234A VAL* 4.6 6.5 - - + -
273A PHE* 4.4 6.8 - - - -
2001A F83 5.2 1.0 + - - +
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Residues in contact with ALA 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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23A VAL* 5.1 0.5 - - - +
27A TYR* 2.5 36.7 + - - +
182A PHE 3.2 24.2 - - - +
183A CYS 2.8 4.9 + - - +
185A GLU* 1.3 81.6 - - + +
187A VAL* 1.3 56.2 + - - +
188A SER 3.6 0.4 - - - -
222A TYR* 4.0 9.4 - - + +
229A LEU* 5.0 0.3 - - - +
230A THR 3.9 13.1 - - - +
231A VAL* 4.1 9.2 - - - -
2001A F83 4.0 17.3 - - - +
3001A SAH 4.3 3.1 - - + -
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Residues in contact with VAL 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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23A VAL* 3.8 21.8 - - + +
27A TYR* 4.0 4.7 - - + +
159A VAL* 3.6 30.3 - - + -
160A HIS* 2.8 36.5 + - + +
183A CYS* 3.4 12.3 - - - +
184A LEU* 3.0 15.6 + - - +
186A ALA* 1.3 83.1 - - - +
188A SER* 1.3 61.0 + - - +
189A PRO* 4.1 1.6 - - - +
197A ALA* 5.3 0.2 - - + -
3001A SAH 3.4 48.0 - - + +
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Residues in contact with SER 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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23A VAL* 5.2 2.5 - - - -
160A HIS* 4.8 0.9 - - - -
184A LEU 2.9 19.8 + - - -
185A GLU 3.4 5.9 + - - +
186A ALA 3.6 0.4 - - - -
187A VAL* 1.3 83.8 + - - +
189A PRO* 1.3 67.9 - - - +
190A ASP 3.9 4.7 - - - -
193A SER* 3.6 7.5 + - - -
194A PHE* 3.3 39.4 + - - -
197A ALA* 4.3 5.0 - - - +
230A THR 4.8 1.4 - - - +
231A VAL* 4.3 2.3 - - - -
232A VAL* 3.3 22.7 + - - +
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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