Contacts of the strand formed by residues 179 - 188 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LYS* 6.0 4.0 - - - -
111A GLU* 3.3 35.0 + - - +
144A ASN 3.2 5.1 + - - -
145A PHE* 2.7 57.9 + - + +
146A TYR* 3.8 17.7 - + - -
148A LYS* 3.7 43.9 - - + +
169A TRP* 6.3 2.0 - - + -
170A THR* 4.0 19.1 - - - +
171A ASP* 4.5 0.7 - - - -
172A GLN* 3.4 46.3 + - + +
178A THR* 1.3 74.8 - - - +
180A SER* 1.3 63.4 + - - +
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Residues in contact with SER 180 (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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142A LEU 3.3 5.6 - - - -
143A ASN* 3.4 10.5 - - - -
144A ASN* 3.0 21.3 + - - -
145A PHE* 3.9 3.2 - - - -
169A TRP* 3.5 4.9 - - - +
170A THR* 3.0 38.2 + - - +
178A THR* 5.0 0.3 + - - -
179A TYR* 1.3 73.4 + - - +
181A MET* 1.3 62.4 + - - +
175B HIS* 3.2 26.8 - - - -
177B PHE* 3.6 17.0 - - - -
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Residues in contact with MET 181 (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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140A CYS 3.9 0.5 - - - +
141A PHE* 3.5 2.6 - - - -
142A LEU* 2.7 60.8 + - + +
145A PHE* 4.0 13.7 - - + -
150A ILE* 4.1 13.2 - - - -
152A VAL* 3.5 33.7 - - + -
167A ASN* 4.7 2.2 - - - +
168A SER 3.4 9.0 - - - +
169A TRP* 3.3 44.2 - - + +
180A SER* 1.3 76.6 - - - +
182A SER* 1.3 64.5 + - - +
183A SER* 3.7 22.7 - - - +
177B PHE* 3.5 7.4 - - - -
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Residues in contact with SER 182 (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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139A VAL* 4.3 1.6 - - - +
140A CYS 3.6 3.3 + - - -
141A PHE* 3.6 9.8 - - - -
166A LEU 3.9 0.9 - - - +
167A ASN* 3.3 6.1 - - - +
168A SER* 2.7 40.4 + - - +
181A MET* 1.3 74.9 - - - +
183A SER* 1.3 59.7 + - - +
184A THR* 4.1 9.6 + - - -
177B PHE* 3.5 33.2 - - - -
189B SER* 2.8 21.5 + - - -
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Residues in contact with SER 183 (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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139A VAL* 3.5 2.6 - - - +
140A CYS* 2.8 47.3 + - - -
152A VAL* 4.3 10.0 - - - +
154A TRP* 2.8 33.1 + - - -
165A VAL* 3.7 0.5 - - - +
167A ASN* 2.7 25.4 + - - +
181A MET* 3.7 15.0 - - - -
182A SER* 1.3 72.5 + - - +
184A THR* 1.3 62.0 + - - +
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Residues in contact with THR 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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137A SER* 3.8 17.3 - - - +
138A VAL 3.2 9.2 - - - +
139A VAL* 3.9 17.4 - - + +
154A TRP* 4.6 1.8 - - - -
164A GLY 3.3 5.0 - - - +
165A VAL* 3.3 2.0 - - - -
166A LEU* 2.9 43.6 + - - +
182A SER* 4.1 10.4 + - - -
183A SER* 1.3 75.4 + - - +
185A LEU* 1.3 60.3 + - - +
186A THR* 3.8 17.8 + - - +
152B LEU* 4.7 12.8 - - + +
182B GLN* 5.5 1.3 - - - +
187B THR* 5.5 6.8 - - + +
189B SER* 4.9 1.6 + - - -
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Residues in contact with LEU 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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136A ALA 3.6 3.3 - - - +
137A SER* 3.4 1.2 - - - -
138A VAL* 2.7 41.1 + - + +
154A TRP* 3.9 43.2 - - + +
156A ILE* 3.7 31.0 - - + -
161A ARG* 3.8 12.8 - - + +
163A ASN 3.5 25.6 - - - +
164A GLY* 3.7 4.3 - - - -
165A VAL* 3.8 14.4 - - + +
184A THR* 1.3 69.0 - - - +
186A THR* 1.3 62.3 + - - +
187A LEU* 3.9 17.6 + - + +
198A TYR* 4.8 4.5 - - + -
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Residues in contact with THR 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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130A GLN* 5.0 1.6 - - - +
135A GLY* 6.1 0.7 - - - -
136A ALA 3.7 4.9 - - - +
137A SER* 2.8 26.2 + - - +
161A ARG* 5.2 2.4 + - - -
163A ASN 4.8 0.3 - - - +
164A GLY* 3.0 31.4 + - - -
166A LEU* 5.1 0.8 - - - +
184A THR* 3.8 9.2 + - - +
185A LEU* 1.3 72.4 - - - +
187A LEU* 1.3 71.2 + - - +
154B LYS* 4.2 9.9 - - - +
182B GLN* 3.3 32.6 + - - +
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Residues in contact with LEU 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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135A GLY* 4.3 2.4 - - - -
136A ALA 3.0 31.2 + - - +
138A VAL* 4.3 11.7 - - + -
156A ILE* 4.0 11.4 - - + -
161A ARG* 3.9 27.8 - - - +
185A LEU* 3.9 29.6 - - + +
186A THR* 1.3 83.5 - - - +
188A THR* 1.3 72.8 - - - +
191A GLU* 3.8 35.2 - - + +
192A TYR* 4.3 8.3 - - + +
195A HIS* 5.1 2.5 - - + +
198A TYR* 4.4 10.1 - - + +
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Residues in contact with THR 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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134A GLY 3.7 10.8 - - - +
135A GLY* 4.6 0.2 - - - -
136A ALA* 3.6 4.4 - - - +
187A LEU* 1.3 78.6 - - - +
189A LYS* 1.4 63.2 + - - +
190A ASP* 3.9 6.6 + - - +
191A GLU* 3.2 37.2 + - - +
192A TYR* 3.1 23.6 + - - +
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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