Contacts of the helix formed by residues 196 - 210 (chain A) in PDB entry 2FE2
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 LYS 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A LEU* 4.0 24.5 - - - +
110A ASN 3.9 21.1 - - - +
111A LYS* 5.2 3.1 - - - +
112A LYS 5.9 0.2 - - - +
113A ALA* 4.2 7.0 - - + -
142A LYS* 2.8 11.5 + - - -
192A PRO 4.1 13.0 - - - +
193A LYS* 3.8 26.1 - - - +
194A ALA 2.7 11.0 + - - +
195A VAL* 1.4 77.9 - - - +
197A PRO* 1.3 73.9 - - + +
198A LYS* 3.6 23.1 - - + +
199A ALA 4.2 9.2 - - - +
200A ALA 3.0 13.2 + - - -
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Residues in contact with PRO 197 (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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110A ASN* 3.3 25.4 - - + +
111A LYS 3.9 20.2 - - - +
112A LYS 4.2 7.6 - - - +
113A ALA* 4.2 6.5 - - - +
114A ALA 5.5 0.2 - - - +
115A SER* 5.4 2.5 - - - +
142A LYS* 3.2 41.4 - - + +
145A ALA* 4.1 6.7 - - + -
146A GLY* 6.1 0.4 - - - -
195A VAL 3.6 7.0 - - - +
196A LYS* 1.3 88.6 - - + +
198A LYS* 1.3 51.7 + - - +
200A ALA* 3.3 2.1 + - - +
201A LYS* 2.7 36.8 + - - +
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Residues in contact with LYS 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 2.9 36.8 - - + -
110A ASN* 3.7 27.1 - - + +
146A GLY* 6.0 3.6 - - - -
150A ALA* 4.2 21.1 - - + +
151A VAL* 5.0 2.7 - - - -
153A LYS* 3.4 19.2 - - + +
154A THR* 3.0 33.7 + - + +
175A LYS* 5.9 0.4 - - - +
193A LYS* 4.8 4.2 + - - +
196A LYS* 3.6 27.2 - - + +
197A PRO* 1.3 75.0 - - - +
199A ALA* 1.3 69.5 + - - +
201A LYS* 4.7 1.6 - - - -
202A PRO* 2.8 31.2 - - - +
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Residues in contact with ALA 199 (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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119A LYS* 5.1 3.2 + - - +
154A THR* 4.5 1.1 - - - -
174A LYS* 6.2 1.1 - - - -
175A LYS* 2.8 44.6 - - + +
177A LYS* 6.3 0.4 - - - +
193A LYS 3.8 22.4 - - - +
194A ALA* 3.8 16.2 - - + -
196A LYS* 3.2 6.4 + - + +
198A LYS* 1.3 91.0 - - - +
200A ALA* 1.3 61.6 + - - +
203A LYS* 3.1 8.2 + - - +
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Residues in contact with ALA 200 (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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118A ALA* 5.2 6.3 - - + -
119A LYS* 5.1 9.2 - - + +
142A LYS* 2.9 52.7 - - + +
195A VAL 5.2 1.9 - - - +
196A LYS 3.0 5.2 + - - +
199A ALA* 1.3 74.9 - - - +
201A LYS* 1.4 60.9 + - - +
203A LYS* 3.1 14.5 + - - +
204A ALA* 2.8 26.2 + - - +
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Residues in contact with LYS 201 (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 LYS 6.1 0.2 - - - -
142A LYS* 4.7 2.9 - - - +
143A LYS* 3.0 79.9 + - + +
146A GLY* 4.0 10.8 + - - +
147A ALA 4.9 3.8 + - - -
148A LYS* 5.3 2.6 - - - +
151A VAL* 3.2 29.4 - - + +
197A PRO 2.7 21.4 + - - +
198A LYS* 4.7 0.2 - - - -
199A ALA 3.3 0.2 - - - -
200A ALA* 1.4 72.0 - - - +
202A PRO* 1.3 67.9 - - + +
204A ALA* 2.8 11.8 + - + +
205A ALA* 2.8 29.1 + - + +
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Residues in contact with PRO 202 (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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151A VAL* 3.0 35.2 - - + +
154A THR* 2.9 21.3 - - - +
155A PRO* 3.1 28.5 - - + -
175A LYS* 3.5 11.2 - - + -
198A LYS 2.8 16.5 - - - +
201A LYS* 1.3 92.5 - - + +
203A LYS* 1.3 55.4 + - - +
205A ALA* 4.1 7.0 - - + -
206A LYS* 2.9 35.7 + - - +
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Residues in contact with LYS 203 (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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118A ALA* 5.1 6.1 + - - +
119A LYS* 3.3 39.4 - - - +
121A LYS* 3.7 30.7 - - - +
122A ALA* 4.3 7.0 - - - -
139A LYS* 6.0 1.6 - - - +
175A LYS* 3.6 14.0 - - - +
178A ALA* 2.9 30.7 - - + +
179A ALA* 3.4 11.4 - - - +
181A LYS* 5.6 0.2 - - - -
199A ALA 3.1 13.1 + - - +
200A ALA* 3.1 13.1 + - - +
202A PRO* 1.3 72.5 - - - +
204A ALA* 1.3 67.3 + - - +
207A PRO* 2.7 40.7 - - + +
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Residues in contact with ALA 204 (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 LYS* 4.4 7.2 + - - +
139A LYS* 4.0 32.2 + - + +
143A LYS* 6.0 4.7 - - + -
200A ALA 2.8 10.5 + - - +
201A LYS* 2.8 15.9 + - + +
203A LYS* 1.3 86.7 - - - +
205A ALA* 1.3 56.9 + - - +
207A PRO* 3.7 1.9 - - - +
208A LYS* 2.8 32.8 + - + +
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Residues in contact with ALA 205 (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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66A LYS* 6.2 0.2 - - - +
143A LYS* 6.5 0.7 - - - -
151A VAL* 6.0 3.8 - - + -
201A LYS* 2.8 18.4 + - + +
202A PRO* 3.8 10.5 - - + +
204A ALA* 1.3 78.0 - - - +
206A LYS* 1.3 59.5 + - + +
208A LYS* 3.0 9.1 + - - +
209A ALA* 2.8 32.3 + - - +
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Residues in contact with LYS 206 (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 6.5 - - + +
87A LYS* 5.4 6.6 - - + +
88A SER* 2.8 29.8 + - - +
155A PRO* 4.3 19.4 - - + +
158A ALA* 3.6 15.8 - - - +
175A LYS* 3.4 21.9 - - + +
176A ALA* 2.9 38.7 - - - +
179A ALA* 3.9 0.9 - - + -
202A PRO 2.9 18.2 + - - +
205A ALA* 1.3 76.8 - - + +
207A PRO* 1.3 70.4 - - + +
209A ALA* 3.7 5.2 - - - +
210A ALA* 2.8 27.5 + - - +
213A LYS* 3.2 14.6 + - - +
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Residues in contact with PRO 207 (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 LYS* 4.5 12.8 - - - +
179A ALA* 3.0 35.9 - - + +
181A LYS* 5.0 3.4 - - + +
203A LYS* 2.7 32.5 - - + +
204A ALA 3.8 1.8 - - - +
205A ALA 3.3 0.2 - - - -
206A LYS* 1.3 82.2 - - + +
208A LYS* 1.3 67.6 + - - +
209A ALA 3.2 0.2 + - - -
210A ALA 3.3 4.9 + - - +
213A LYS* 2.7 58.4 - - + +
214A ALA 5.4 1.8 - - - +
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Residues in contact with LYS 208 (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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5A PRO* 4.7 8.6 - - - +
7A GLU* 2.5 35.0 - - - +
66A LYS* 3.0 73.3 - - + +
67A ALA* 4.0 20.6 - - - +
139A LYS* 6.1 4.5 - - - +
143A LYS* 4.2 18.9 - - - +
204A ALA* 2.8 21.1 + - + +
205A ALA* 3.0 10.5 + - - +
207A PRO* 1.3 75.8 - - - +
209A ALA* 1.3 51.0 + - - +
213A LYS 5.0 0.4 - - - -
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Residues in contact with ALA 209 (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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7A GLU* 2.5 22.6 - - - +
10A THR* 4.3 7.5 + - + -
60A SER* 4.1 13.0 + - - -
62A ALA* 3.7 4.9 + - - +
66A LYS* 5.2 3.1 - - - +
87A LYS* 2.9 46.9 + - + +
205A ALA 2.8 17.5 + - - +
206A LYS* 3.7 3.6 - - - +
208A LYS* 1.3 72.7 - - - +
210A ALA* 1.4 59.6 + - - +
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Residues in contact with ALA 210 (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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7A GLU* 3.0 19.8 - - - +
59A LEU 5.7 0.4 - - - -
60A SER* 6.0 1.1 - - - +
62A ALA* 3.3 1.8 - - - -
79A ASN* 3.2 8.5 - - - +
83A LYS* 3.5 20.4 - - + -
84A LEU* 3.7 11.7 - - - +
87A LYS* 5.5 3.6 - - + -
206A LYS 2.8 14.8 + - - +
207A PRO 3.3 3.3 + - - +
209A ALA* 1.4 75.4 - - + +
211A LYS* 1.4 67.4 + - - +
213A LYS* 2.9 29.5 + - + -
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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