Contacts of the strand formed by residues 179 - 188 (chain F) in PDB entry 3Q3G
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 179 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109F LYS* 6.0 5.9 - - - -
111F GLU* 3.2 34.0 + - - +
144F ASN 3.2 4.5 + - - -
145F PHE* 2.8 60.2 + - + +
146F TYR* 3.8 17.5 - + - -
148F LYS* 3.7 43.4 - - + +
169F TRP* 6.4 1.1 - - + -
170F THR* 4.0 18.2 - - - +
171F ASP* 4.5 0.9 - - - -
172F GLN* 3.4 47.3 + - + +
177F SER 4.3 0.2 - - - -
178F THR* 1.3 73.7 - - - +
180F SER* 1.3 63.5 + - - +
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Residues in contact with SER 180 (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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142F LEU 3.3 6.1 - - - -
143F ASN* 3.7 14.4 - - - -
144F ASN* 3.0 22.3 + - - -
145F PHE* 3.9 2.2 - - - -
169F TRP* 3.5 4.5 - - - +
170F THR* 3.0 41.2 + - - +
178F THR* 5.3 0.3 + - - -
179F TYR* 1.3 72.5 + - - +
181F MET* 1.3 63.3 + - - +
175H HIS* 3.1 24.2 + - - -
177H PHE* 3.7 11.2 - - - -
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Residues in contact with MET 181 (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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140F CYS 3.9 0.5 - - - +
141F PHE* 3.5 3.1 - - - -
142F LEU* 2.7 60.6 + - + +
145F PHE* 4.1 10.5 - - + -
150F ILE* 4.1 12.3 - - - -
152F VAL* 3.5 34.3 - - + -
167F ASN* 4.7 2.5 - - - +
168F SER 3.4 9.2 - - - +
169F TRP* 3.3 44.0 - - + +
180F SER* 1.3 75.3 - - - +
182F SER* 1.3 63.1 + - - +
183F SER* 3.7 23.1 - - - +
177H PHE* 3.4 7.8 - - - -
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Residues in contact with SER 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F VAL* 4.3 1.4 - - - +
140F CYS 3.6 4.2 + - - -
141F PHE* 3.6 9.7 - - - -
166F LEU 3.9 0.5 - - - +
167F ASN* 3.3 5.9 - - - +
168F SER* 2.7 39.0 + - - -
181F MET* 1.3 74.5 - - - +
183F SER* 1.3 60.7 + - - +
184F THR* 4.1 9.2 + - - -
177H PHE* 3.4 34.5 - - - -
189H SER* 2.8 20.5 + - - -
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Residues in contact with SER 183 (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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139F VAL* 3.5 2.1 - - - +
140F CYS* 2.8 48.9 + - - -
152F VAL* 4.3 10.0 - - - +
154F TRP* 2.8 33.8 + - - -
165F VAL* 3.7 0.3 - - - +
166F LEU 3.6 0.2 - - - -
167F ASN* 2.7 25.4 + - - +
181F MET* 3.7 15.0 - - - +
182F SER* 1.3 72.5 + - - +
184F THR* 1.3 60.9 + - - +
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Residues in contact with THR 184 (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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137F SER* 3.8 21.1 - - - +
138F VAL 3.3 3.1 - - - +
139F VAL* 3.8 20.0 - - + +
154F TRP* 4.6 1.6 - - - -
164F GLY 3.3 5.4 - - - +
165F VAL* 3.3 1.9 - - - -
166F LEU* 2.9 43.8 + - + +
182F SER* 4.1 9.9 + - - -
183F SER* 1.3 74.8 + - - +
185F LEU* 1.3 60.4 + - - +
186F THR* 3.8 17.8 + - - +
152H LEU* 4.7 12.4 - - + +
154H LYS* 6.0 0.2 - - - -
187H THR* 5.5 6.4 - - + +
189H SER* 4.9 2.1 + - - -
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Residues in contact with LEU 185 (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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136F ALA 3.6 2.6 - - - +
137F SER* 3.4 1.2 - - - -
138F VAL* 2.8 43.3 + - + +
154F TRP* 3.8 39.7 - - + +
156F ILE* 3.9 21.3 - - + -
161F ARG* 3.8 28.9 - - + +
163F ASN 3.8 13.7 - - - +
164F GLY 3.8 2.7 - - - -
165F VAL* 3.9 10.3 - - + +
184F THR* 1.3 70.3 - - - +
186F THR* 1.3 61.9 + - - +
187F LEU* 3.8 26.1 + - + +
198F TYR* 4.2 9.0 - - + -
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Residues in contact with THR 186 (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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130F GLN* 4.9 1.8 - - - +
135F GLY* 6.0 1.1 - - - -
136F ALA 3.6 5.2 - - - +
137F SER* 3.2 22.8 + - - +
161F ARG* 5.2 2.1 + - - -
163F ASN 4.7 1.7 - - - +
164F GLY* 3.0 32.0 + - - -
166F LEU* 5.1 6.5 - - - +
184F THR* 3.8 12.0 + - - +
185F LEU* 1.3 73.4 - - - +
187F LEU* 1.4 70.3 + - - +
154H LYS* 4.1 21.6 - - - +
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Residues in contact with LEU 187 (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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135F GLY* 4.1 2.6 - - - -
136F ALA 2.9 26.7 + - - +
138F VAL* 4.4 6.5 - - + -
156F ILE* 4.0 11.0 - - + -
161F ARG* 3.9 30.7 - - - +
185F LEU* 3.8 35.0 - - + +
186F THR* 1.4 81.7 - - - +
188F THR* 1.3 73.8 + - - +
191F GLU* 4.0 35.0 - - + +
192F TYR* 4.3 9.2 - - + +
195F HIS* 5.1 0.9 - - - +
198F TYR* 4.3 13.2 - - + +
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Residues in contact with THR 188 (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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134F GLY 3.7 9.6 - - - +
135F GLY* 4.4 1.1 - - - -
136F ALA* 3.8 4.2 - - - +
187F LEU* 1.3 79.1 - - - +
189F LYS* 1.3 62.9 + - - +
190F ASP* 3.9 6.0 + - - +
191F GLU* 3.2 38.1 + - - +
192F TYR* 3.1 24.1 + - - +
194F ARG* 5.3 0.2 + - - -
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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