Contacts of the strand formed by residues 140 - 150 (chain A) in PDB entry 3N2Q
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 SER 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A PHE* 3.0 13.7 - - - -
132A GLY 2.8 35.6 + - - +
133A LYS* 5.8 0.2 - - - -
138A GLU* 3.2 8.0 + - - -
139A LEU* 1.3 74.3 - - - +
141A LEU* 1.3 67.1 + - - +
181A ASN* 4.0 8.1 + - - -
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Residues in contact with LEU 141 (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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104A TYR* 3.5 28.0 - - + +
129A ASP* 4.1 13.7 - - + -
130A TYR 3.3 27.1 - - - +
131A PHE* 3.5 19.2 - - + -
140A SER* 1.3 80.2 + - - +
142A SER* 1.3 58.1 + - - +
143A GLY 3.6 15.5 - - - +
144A VAL* 4.0 4.7 - - + -
180A TYR* 3.9 17.3 - - + -
181A ASN* 2.9 44.9 + - - +
183A SER* 3.0 15.3 + - - +
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Residues in contact with SER 142 (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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92A PHE* 4.4 14.3 - - - -
97A HIS* 3.6 23.7 - - - -
130A TYR 2.8 15.6 + - - -
132A GLY* 3.4 23.0 + - - -
133A LYS 5.2 2.6 + - - -
140A SER 3.7 0.5 + - - -
141A LEU* 1.3 71.4 + - - +
143A GLY* 1.3 55.5 + - - +
183A SER* 3.4 7.6 + - - -
184A PRO* 3.4 23.7 - - - +
211A LYS* 4.9 3.4 + - - +
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Residues in contact with GLY 143 (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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91A GLN* 5.7 0.2 - - - -
92A PHE* 4.4 12.1 - - - -
130A TYR* 3.0 30.7 + - - +
141A LEU* 3.6 3.0 - - - +
142A SER* 1.3 82.3 - - - +
144A VAL* 1.3 65.5 + - - -
145A MSE 4.8 6.3 - - - -
183A SER* 3.8 4.7 + - - -
184A PRO* 3.2 15.3 - - - -
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Residues in contact with VAL 144 (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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104A TYR* 4.3 8.1 - - + -
127A GLU* 4.0 10.3 - - + +
128A GLN 3.5 3.1 - - - -
129A ASP* 3.6 24.0 - - - +
141A LEU* 4.0 22.4 - - + -
143A GLY* 1.3 76.4 - - - +
145A MSE 1.3 68.2 + - - +
146A ILE* 3.9 28.5 - - + -
174A ILE* 4.6 6.3 - - + -
180A TYR* 4.4 13.7 - - + -
184A PRO 3.0 9.3 + - - +
185A ILE* 3.4 9.7 - - + -
186A THR* 2.9 25.3 + - - -
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Residues in contact with MSE 145 (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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84A LEU* 3.9 24.2 - - + +
87A ILE* 4.8 4.7 - - - -
88A ALA* 3.9 28.5 - - + -
91A GLN* 3.6 22.2 - - - +
92A PHE* 3.6 38.8 - - + -
126A ILE 3.8 0.3 - - - +
127A GLU* 3.5 2.4 - - - -
128A GLN* 2.7 45.2 + - + +
130A TYR* 3.5 22.0 - - + -
143A GLY* 4.8 3.8 - - - -
144A VAL* 1.3 83.0 - - - +
146A ILE* 1.3 62.5 - - - +
186A THR* 3.5 27.4 - - - -
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Residues in contact with ILE 146 (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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84A LEU* 4.0 3.8 - - - +
105A ILE* 4.2 12.8 - - + -
125A ILE* 3.9 11.9 - - + -
126A ILE 3.2 11.4 - - - +
127A GLU* 4.5 1.8 - - - -
144A VAL* 3.9 8.5 - - + -
145A MSE 1.3 79.8 - - - +
147A GLY* 1.3 61.1 + - - +
148A LEU* 3.7 27.0 + - + +
170A LEU* 3.9 2.9 - - + -
174A ILE* 3.8 20.9 - - + -
185A ILE* 3.6 21.5 - - + -
186A THR 2.9 9.0 + - - +
187A PHE* 3.4 33.9 - - + +
188A ALA* 2.9 29.5 + - - +
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Residues in contact with GLY 147 (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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80A TYR* 2.7 26.6 + - - -
84A LEU* 3.5 9.1 - - - +
125A ILE* 3.4 3.1 - - - -
126A ILE* 2.9 27.0 + - - +
146A ILE* 1.3 70.5 - - - +
148A LEU* 1.3 60.8 + - - +
188A ALA 3.7 4.5 - - - -
203A TYR* 3.7 22.4 - - - -
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Residues in contact with LEU 148 (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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80A TYR* 4.3 1.5 - - - -
122A LEU* 4.0 7.9 - - + -
124A ASN 3.7 1.3 - - - -
125A ILE* 3.9 18.4 - - + -
146A ILE* 3.8 25.8 - - + +
147A GLY* 1.3 70.6 - - - -
149A ALA* 1.3 61.6 + - - +
150A MSE 3.6 11.2 + - + +
163A GLY* 4.0 32.1 - - - +
166A VAL* 3.6 29.2 - - + -
167A ALA 4.8 0.2 - - - +
170A LEU* 4.0 3.8 - - + -
187A PHE* 4.5 19.7 - - + -
188A ALA 2.9 15.9 + - - +
189A ILE* 3.6 8.3 - - + -
190A PHE 2.8 27.3 + - - +
219A TRP* 4.9 1.1 - - + -
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Residues in contact with ALA 149 (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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80A TYR* 3.6 20.5 + - + +
122A LEU* 3.3 8.5 - - - +
123A THR* 2.8 44.5 + - - +
124A ASN* 3.0 26.5 + - + +
148A LEU* 1.3 70.3 - - - +
150A MSE 1.3 60.0 + - - +
190A PHE* 3.6 10.1 - - + +
192A GLN* 3.9 11.2 - - + +
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Residues in contact with MSE 150 (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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121A VAL* 3.5 6.3 - - - +
122A LEU* 3.9 20.4 - - + -
148A LEU* 4.1 22.4 - - + +
149A ALA* 1.3 79.2 - - - +
151A SER* 1.3 63.9 + - - +
154A VAL* 4.7 2.0 - - + -
159A ALA* 3.6 25.8 - - + +
162A LYS* 3.7 22.0 - - + +
163A GLY* 3.3 39.5 - - - +
166A VAL* 4.8 0.9 - - + -
189A ILE* 3.7 22.4 - - + -
190A PHE 2.8 12.9 + - - +
191A LYS* 3.8 4.4 - - + +
192A GLN* 2.9 35.1 + - - +
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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