Contacts of the strand formed by residues 146 - 156 (chain B) 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 MET 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B GLN* 4.3 4.7 - - - +
144B ASN* 3.3 34.0 + - - +
145B SER* 1.4 88.7 + - - +
147B VAL* 1.3 60.6 - - - +
193B THR* 3.7 36.6 - - + +
194B VAL* 3.5 3.1 - - - -
195B PRO* 4.0 25.8 - - + -
196B SER* 3.5 7.1 + - - -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PRO* 4.3 12.6 - - + -
142B GLN* 3.9 28.5 - - + +
146B MET* 1.3 74.3 - - - +
148B THR* 1.3 69.0 + - - +
149B LEU* 4.0 7.2 + - + +
192B VAL 3.7 1.2 - - - +
193B THR* 3.4 2.5 - - - -
194B VAL* 2.7 56.2 + - + +
195B PRO 3.7 12.3 - - - +
196B SER* 4.1 12.3 - - - +
199B ARG* 4.1 23.1 - - + +
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A THR* 5.0 9.5 - - - +
122A SER* 3.4 25.4 + - - +
124A PHE* 3.1 20.8 - - + -
141A PHE* 4.0 9.6 - - + -
143A ASN* 4.5 6.5 + - - +
137B PRO* 4.2 0.2 - - - +
142B GLN* 3.1 25.6 + - - -
147B VAL* 1.3 72.7 - - - +
149B LEU* 1.3 70.7 + - - +
191B SER* 3.8 22.0 - - - +
192B VAL 3.3 4.7 - - - +
193B THR* 2.8 21.5 + - - +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 3.9 5.6 - - - -
141A PHE* 4.2 0.2 - - - -
135B LEU 3.5 5.4 - - - +
137B PRO* 3.6 29.4 - - + -
147B VAL* 4.5 6.7 - - + +
148B THR* 1.3 79.2 - - - +
150B GLY* 1.3 59.8 + - - +
191B SER* 3.5 3.3 - - - -
192B VAL* 2.8 42.7 + - + +
194B VAL* 4.4 8.5 - - + -
199B ARG* 3.6 48.2 - - + +
204B VAL* 3.8 26.9 - - + -
221B ILE* 3.8 18.2 - - + -
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Residues in contact with GLY 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 4.2 0.8 - - - -
141A PHE* 4.0 4.9 - - - -
135B LEU* 2.8 49.2 + - - +
149B LEU* 1.3 75.1 - - - +
151B CYS* 1.3 58.8 + - - -
165B TRP* 3.5 5.2 - - - -
190B SER 3.1 12.1 - - - -
221B ILE* 3.4 14.4 - - - +
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Residues in contact with CYS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B VAL* 3.6 21.1 - - - -
133B TYR 3.6 6.1 - - - -
135B LEU* 3.5 2.8 - - - +
150B GLY* 1.3 74.2 - - - -
152B LEU* 1.3 60.4 + - - +
153B VAL* 4.0 5.4 + - + +
163B VAL* 4.7 1.3 - - - -
165B TRP* 3.4 14.6 - - + -
189B SER* 3.2 6.8 - - - -
190B SER* 3.0 35.1 + - - +
206B CYS* 2.0 47.3 - - + -
208B VAL* 3.8 11.4 - - - -
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Residues in contact with LEU 152 (chain B).
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* 4.2 2.9 - - - +
137A SER* 3.8 31.0 - - - +
139A VAL* 4.4 16.6 - - + -
184A THR* 4.7 8.1 - - + +
131B SER 3.2 5.5 - - - +
132B VAL* 3.5 0.9 - - - -
133B TYR* 2.8 66.2 + - + +
135B LEU* 4.0 16.7 - - + +
151B CYS* 1.3 70.4 - - - +
153B VAL* 1.3 59.2 + - - +
154B LYS* 3.7 9.6 + - + -
187B THR* 3.8 20.2 - - + -
188B LEU 3.5 16.4 - - - +
189B SER* 4.3 10.5 - - - -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PRO* 3.5 25.6 - - + -
131B SER 3.6 4.0 - - - +
132B VAL* 4.7 2.0 - - + -
151B CYS* 4.5 9.0 - - - +
152B LEU* 1.3 70.8 - - - +
154B LYS* 1.3 57.4 + - - +
156B TYR* 3.8 16.9 - - + -
161B VAL* 4.1 9.2 - - + -
163B VAL* 4.1 4.0 - - + -
187B THR* 3.3 3.8 - - - -
188B LEU* 2.8 60.3 + - + +
208B VAL* 3.6 42.2 - - + -
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Residues in contact with LYS 154 (chain B).
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* 3.7 22.0 - - - +
137A SER* 3.6 21.1 - - - +
186A THR* 4.2 6.2 - - - +
130B PRO* 3.5 1.7 - - - +
131B SER* 2.8 44.8 + - - +
133B TYR* 4.1 18.2 - - + -
152B LEU* 4.5 8.3 - - + -
153B VAL* 1.3 72.5 - - - +
155B GLY* 1.3 69.2 + - - +
156B TYR 3.5 2.2 - - - -
182B GLN* 3.1 33.5 + - - +
186B TYR 3.8 0.2 - - - -
187B THR* 3.4 20.8 + - + +
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Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B THR* 3.2 23.6 - - - +
129B PRO 3.4 5.6 - - - +
131B SER* 5.6 0.8 + - - -
154B LYS* 1.3 82.3 - - - +
156B TYR* 1.3 58.5 + - - -
185B LEU* 3.8 24.6 - - - +
186B TYR 2.9 13.8 + - - -
187B THR* 3.7 2.1 + - - -
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B THR 3.4 12.1 - - - +
129B PRO 4.2 0.2 - - - -
130B PRO* 3.7 22.4 - - + -
153B VAL* 3.8 34.5 - - + -
155B GLY* 1.3 77.8 - - - +
157B PHE* 1.4 62.4 + - - +
158B PRO 3.4 25.6 - - - -
159B GLU* 2.7 30.5 + - - -
161B VAL* 3.8 18.0 - - + +
179B ALA* 3.2 14.6 - - - +
185B LEU* 3.6 2.4 - - - -
186B TYR* 2.8 70.4 + + + -
187B THR 4.1 1.3 - - - -
188B LEU* 3.6 15.0 - - + +
210B HIS* 3.9 9.6 - + - +
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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