Contacts of the strand formed by residues 179 - 186 (chain G) in PDB entry 7GCH
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 ALA 179 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100F ASN* 3.7 14.5 + - - +
101F ASN* 2.8 32.9 + - - +
177G LYS 3.3 1.4 + - - -
178G ASP* 1.3 73.8 - - - +
180G MET* 1.3 57.8 + - - +
229G ALA* 3.5 5.2 - - - +
230G ARG* 2.6 30.2 + - - -
233G ALA* 3.8 24.9 - - + -
234G LEU* 4.2 7.8 - - + +
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Residues in contact with MET 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F THR 4.0 9.9 - - - +
99F ILE 3.8 18.2 - - - +
100F ASN* 3.1 22.9 - - - +
165G ASN* 3.3 12.1 - - - +
175G LYS 3.4 15.3 - - - +
176G ILE* 4.0 5.6 - - + -
177G LYS* 3.0 49.4 - - + +
178G ASP 3.2 1.8 - - - -
179G ALA* 1.3 80.0 - - - +
181G ILE* 1.3 62.2 + - - +
214G SER* 6.0 0.4 - - - +
215G TRP* 3.9 24.2 - - - +
227G VAL* 4.0 9.2 - - + -
228G TYR 3.1 13.0 - - - +
229G ALA* 5.4 0.7 - - - -
230G ARG* 3.0 24.4 + - - +
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Residues in contact with ILE 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F PHE* 4.9 8.5 - - + +
162G LEU* 4.3 24.2 - - + -
163G LEU 4.1 12.6 - - - +
165G ASN* 4.3 0.7 - - - +
180G MET* 1.3 76.2 - - - +
182G CYS* 1.3 74.7 + - - +
199G LEU* 4.6 5.8 - - + -
210G VAL* 4.0 18.4 - - + +
211G GLY* 4.3 2.2 - - - -
227G VAL* 4.6 0.2 - - - -
228G TYR* 2.7 48.4 + - + +
229G ALA 3.6 20.2 - - - +
230G ARG* 3.5 40.3 - - + +
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Residues in contact with CYS 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162G LEU* 3.4 4.0 - - - +
163G LEU* 3.0 29.3 + - + +
164G SER 4.8 2.7 - - - +
165G ASN* 4.4 5.3 - - - +
168G CYS* 2.1 52.7 - - + -
172G TRP* 5.1 0.2 - - - -
176G ILE* 4.2 8.1 - - - -
180G MET 5.6 0.2 - - - -
181G ILE* 1.3 84.5 - - - +
183G ALA* 1.3 62.2 + - - +
225G PRO* 4.6 6.7 - - + -
226G GLY 3.5 9.0 - - - +
227G VAL* 3.8 23.6 - - - -
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Residues in contact with ALA 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G LEU* 4.2 16.1 - - + +
161G PRO 3.1 23.3 - - - +
162G LEU* 3.9 12.6 - - + -
163G LEU* 4.5 3.1 - - - +
182G CYS* 1.3 76.0 - - - +
184G GLY* 1.3 60.3 + - - +
199G LEU* 4.3 14.1 - - + -
225G PRO* 4.3 2.7 - - - -
226G GLY* 2.9 33.1 + - - +
228G TYR* 3.7 11.2 + - + -
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Residues in contact with GLY 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G LEU* 4.1 12.8 - - - +
161G PRO* 3.2 18.5 + - - +
163G LEU* 3.7 14.7 - - - +
183G ALA* 1.3 78.2 - - - +
185G ALA* 1.3 75.3 - - - +
186G SER* 3.0 15.8 + - - -
188G VAL 4.7 3.8 - - - -
225G PRO* 4.3 0.9 - - - -
226G GLY 4.8 0.4 - - - -
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Residues in contact with ALA 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G LEU* 4.9 5.4 - - + -
171G TYR* 4.3 9.4 - - + +
184G GLY* 1.3 75.8 - - - +
186G SER* 1.3 59.5 + - - +
188G VAL 4.2 4.2 + - - -
222G THR 3.6 14.1 - - - -
223G SER* 3.4 27.9 - - - +
224G THR 4.1 3.4 + - - -
225G PRO* 3.6 30.1 - - + +
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Residues in contact with SER 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G SER 5.5 0.2 - - - -
160G LEU* 4.0 1.7 - - - +
161G PRO* 3.6 28.6 - - - +
184G GLY* 3.5 9.9 - - - -
185G ALA* 1.3 79.2 - - - +
187G GLY* 1.3 58.2 + - - +
188G VAL* 3.2 29.1 + - - +
222G THR 3.5 0.8 + - - -
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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