Contacts of the strand formed by residues 178 - 184 (chain L) in PDB entry 3GHG
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 PHE 178 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205K VAL 6.1 1.3 - - - +
207K SER* 6.6 0.2 - - - -
168L PHE* 3.4 8.9 - - - -
169L ILE* 3.0 39.9 + - + +
171L PRO* 4.2 19.7 - - + -
176L GLN 4.6 5.8 - - - -
177L GLN* 1.3 79.3 - - - +
179L LEU* 1.3 63.9 + - - +
180L VAL* 3.2 30.2 + - + -
228L LEU* 3.6 13.5 - - + -
232L LYS* 3.7 49.1 - - + +
235L LEU* 4.7 9.2 - - + -
236L ILE* 4.0 22.0 - - + -
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Residues in contact with LEU 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203K ILE* 3.7 25.8 - - + -
205K VAL 5.2 4.7 + - - +
226K LEU* 4.6 4.7 - - + -
145L ILE* 3.3 26.7 - - + -
166L LEU* 3.6 15.9 - - + +
167L TYR 2.9 36.1 - - - +
168L PHE* 3.4 23.3 - - + -
178L PHE* 1.3 79.4 - - - +
180L VAL* 1.3 72.6 + - - +
218L LEU* 3.1 33.6 - - + +
228L LEU* 4.1 8.1 - - - +
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Residues in contact with VAL 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L CYS* 3.6 31.4 - - - -
166L LEU* 3.4 4.2 - - - +
167L TYR 2.9 32.6 + - - +
169L ILE* 3.1 36.3 - - + -
178L PHE* 3.2 25.1 - - + +
179L LEU* 1.3 79.1 - - - +
181L TYR* 1.3 65.4 + - - +
182L CYS* 3.8 6.1 - - - -
192L THR* 4.0 10.3 - - + -
193L VAL 5.5 1.3 - - - +
218L LEU* 4.4 9.0 - - - -
226L PHE* 6.1 0.2 - - - -
228L LEU* 4.5 9.0 - - + -
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Residues in contact with TYR 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L CYS* 3.9 0.2 - - - -
164L SER* 2.8 20.6 + - - -
165L GLY* 3.2 24.9 - - - -
166L LEU* 4.0 4.7 - - + -
180L VAL* 1.3 80.6 - - - +
182L CYS* 1.3 62.8 + - - +
183L GLU* 4.4 14.5 - - + +
193L VAL* 3.2 45.3 + - + +
196L LYS* 3.7 25.1 + - - -
218L LEU* 4.2 9.4 - - + +
219L SER 3.5 24.2 - - - -
220L PRO 3.6 15.3 + - - -
221L THR 4.1 2.8 + - - -
222L GLY* 3.3 19.0 + - - -
226L PHE* 4.4 22.9 - + + -
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Residues in contact with CYS 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L CYS* 2.0 49.6 - - - -
156L ILE* 4.1 6.3 - - - -
164L SER* 3.0 15.4 + - - -
165L GLY 2.8 22.4 + - - +
167L TYR* 4.0 26.2 - - + -
180L VAL* 3.8 8.9 - - - +
181L TYR* 1.3 80.1 - - - +
183L GLU* 1.3 60.2 + - - +
184L ILE* 3.6 20.4 - - + -
191L TRP 3.2 4.3 - - - +
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Residues in contact with GLU 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164L SER* 3.6 10.9 - - - +
181L TYR* 4.4 11.2 - - + +
182L CYS* 1.3 74.2 - - - +
184L ILE* 1.3 73.7 + - - +
185L ASP* 5.2 2.3 - - - +
191L TRP* 2.9 49.8 + - + +
193L VAL* 3.9 19.3 - - + -
196L LYS* 6.0 1.1 - - - +
249L GLU* 4.9 0.5 - - - +
385L LYS* 2.7 32.6 + - + -
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Residues in contact with ILE 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L CYS 5.1 0.7 - - - +
156L ILE* 5.0 2.2 - - + -
157L ALA* 4.2 7.9 - - + -
161L ALA* 3.7 25.8 - - + +
162L LYS* 3.9 28.0 - - + +
163L GLN 3.7 22.4 - - - +
164L SER* 3.9 12.2 + - - +
167L TYR* 5.0 0.7 - - + -
182L CYS* 3.6 30.5 - - + -
183L GLU* 1.3 85.3 + - - +
185L ASP* 1.3 75.2 + - - +
188L GLY* 5.4 2.0 - - - -
189L ASN 3.6 9.9 - - - +
190L GLY* 4.1 12.6 - - - -
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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