Contacts of the strand formed by residues 201 - 210 (chain F) in PDB entry 4GG6
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 TYR 201 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162F GLY 2.9 23.4 + - - -
163F PHE* 2.7 53.9 + - + +
164F TYR* 3.8 17.2 - + - -
165F PRO* 4.0 2.5 - - + -
166F ASP* 3.6 42.9 + - + -
189F PRO* 4.1 14.6 - - + -
190F LEU 3.1 20.0 - - - +
191F LYS* 3.4 36.9 - - + -
192F GLU* 3.9 3.1 - - - -
197F ASN 5.2 1.0 + - - -
199F SER 3.7 15.4 + - - -
200F ARG* 1.3 73.8 - - - +
202F ALA* 1.3 59.9 + - - +
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Residues in contact with ALA 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E TYR* 6.1 0.2 - - + -
193E TRP* 3.6 33.9 - - + -
160F ALA 3.3 9.0 - - - +
161F THR* 4.3 2.0 - - + +
163F PHE* 4.1 2.0 - - - -
189F PRO* 3.1 6.2 - - - +
190F LEU* 2.6 47.4 + - + +
192F GLU* 4.0 16.8 - - + +
201F TYR* 1.3 73.9 - - - +
203F LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E TRP* 5.5 1.1 - - - -
158F CYS 4.7 0.2 - - - -
159F LEU* 3.5 4.5 - - - +
160F ALA* 2.8 42.0 + - + +
163F PHE* 4.2 11.9 - - + -
168F VAL* 4.0 27.4 - - + +
170F LEU* 4.0 34.1 - - + +
185F THR* 4.2 8.1 - - + -
186F ASP* 3.9 34.5 - - + +
188F GLN 4.3 0.4 - - - -
189F PRO* 4.1 22.0 - - + -
202F ALA* 1.3 76.1 - - - +
204F SER* 1.3 66.1 + - - +
225F VAL* 5.9 0.2 - - + -
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Residues in contact with SER 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E THR* 3.3 16.3 - - - +
191E VAL* 4.1 10.8 - - - +
193E TRP* 4.6 0.2 - - - -
157F VAL* 4.8 2.0 - - - -
158F CYS 3.2 12.8 - - - -
159F LEU* 3.8 13.7 - - - -
170F LEU* 4.7 0.9 - - - -
185F THR* 3.4 5.3 - - - +
186F ASP* 2.6 53.7 + - - +
203F LEU* 1.3 77.6 - - - +
205F SER* 1.3 61.6 + - - +
206F ARG* 3.1 15.5 + - - -
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Residues in contact with SER 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F VAL* 3.3 9.0 - - - +
158F CYS* 2.8 30.2 + - - +
170F LEU* 3.7 20.3 - - - +
172F TRP* 2.8 32.9 + - - -
184F CYS 3.5 3.7 + - - -
185F THR* 2.6 28.1 + - - +
204F SER* 1.3 74.8 - - - +
206F ARG* 1.3 71.7 + - - +
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Residues in contact with ARG 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E LEU* 4.3 13.0 - - + -
173E THR* 3.1 20.2 + - - -
174E ASP 4.7 0.2 + - - -
176E CYS* 3.9 4.9 - - - +
189E SER* 3.1 42.0 + - - +
191E VAL* 3.3 24.8 - - + +
155F THR* 3.8 15.9 - - + -
156F LEU 3.3 4.3 - - - -
157F VAL* 4.3 7.0 - - + -
172F TRP* 3.8 8.3 + - - -
182F GLY 3.4 2.8 - - - +
183F VAL* 3.5 3.6 - - - -
184F CYS* 2.7 55.5 + - + +
186F ASP* 3.0 17.4 + - - +
204F SER* 3.1 42.4 + - - -
205F SER* 1.3 82.0 + - - +
207F LEU* 1.3 60.8 + - - +
208F ARG* 5.2 0.7 - - + +
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Residues in contact with LEU 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F THR* 3.3 2.0 - - - -
156F LEU* 2.8 47.2 + - + +
172F TRP* 3.5 41.0 - - + -
174F VAL* 4.0 14.1 - - + -
179F VAL* 4.2 10.1 - - + -
181F SER 3.7 23.8 - - - +
182F GLY 3.4 0.7 - - - +
183F VAL* 3.7 16.4 - - + -
206F ARG* 1.3 73.4 - - - +
208F ARG* 1.3 61.0 + - - +
209F VAL* 4.0 16.8 - - + -
221F PHE* 3.9 26.9 - - + -
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Residues in contact with ARG 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E TYR* 5.3 0.2 - - - -
152E LEU* 6.0 0.2 - - - +
154E THR* 4.1 14.5 + - - +
155E ASP* 2.9 38.0 + - - -
185E PHE* 3.5 49.7 - - + +
187E SER* 3.2 22.0 + - - +
147F GLU* 5.1 6.7 - - - +
151F THR* 3.8 17.0 + - - +
153F LYS* 3.4 32.7 + - + +
154F ALA 3.5 6.3 - - - +
155F THR* 3.0 30.8 + - + +
181F SER 4.5 0.7 - - - +
182F GLY* 2.9 22.0 + - - +
206F ARG* 4.1 0.4 - - + -
207F LEU* 1.3 72.3 - - - +
209F VAL* 1.3 64.9 + - - +
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Residues in contact with VAL 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E PHE* 4.0 11.4 - - + -
153F LYS* 3.9 1.4 - - - -
154F ALA* 2.9 39.6 + - - +
156F LEU* 4.4 6.5 - - + -
174F VAL* 5.5 2.0 - - + -
181F SER 5.6 0.7 - - - +
207F LEU* 4.0 24.5 - - + -
208F ARG* 1.3 79.2 - - - +
210F SER* 1.3 69.2 + - - +
213F PHE* 4.1 24.5 - - + -
214F TRP* 4.3 9.2 - - + -
221F PHE* 4.2 24.5 - - + -
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Residues in contact with SER 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E PHE* 3.5 24.6 - - - -
152F GLN 4.4 7.0 - - - -
153F LYS* 4.7 0.2 - - - +
209F VAL* 1.3 81.1 - - - +
211F ALA* 1.3 64.3 + - - +
212F THR* 4.1 5.8 + - - -
213F PHE* 3.1 24.5 + - - +
214F TRP* 3.1 18.5 + - - +
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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