Contacts of the strand formed by residues 207 - 216 (chain B) in PDB entry 6I53
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 ARG 207 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU* 3.4 29.3 - - - +
153B GLU* 3.3 25.2 + - - +
154B ILE 3.3 13.7 - - - +
155B GLU* 2.5 36.7 + - + +
166B PHE* 4.8 0.4 - - - +
194B VAL 4.0 0.3 - - - +
195B SER* 3.9 0.9 - - - -
196B ARG* 2.8 61.2 + - + +
198B VAL* 3.4 35.2 - - + +
200B PHE* 3.4 24.2 - - - -
205B TYR 3.7 0.2 + - - -
206B PRO* 1.3 76.7 - - - +
208B LEU* 1.3 74.6 + - - +
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Residues in contact with LEU 208 (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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40B MET* 3.7 30.1 - - + -
152B LEU 4.5 0.2 - - - -
153B GLU* 3.6 0.5 - - - -
154B ILE* 2.8 38.6 + - + +
166B PHE* 3.7 33.3 - - + -
167B TYR* 4.3 11.2 - - - +
168B TRP* 3.4 44.9 - - + +
194B VAL 3.4 2.7 - - - -
195B SER* 3.6 29.6 - - - +
207B ARG* 1.3 80.8 - - - +
209B SER* 1.3 64.2 + - - +
210B LEU 4.4 0.2 - - - -
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Residues in contact with SER 209 (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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151B THR* 5.3 2.5 - - - -
152B LEU 3.3 6.3 - - - -
153B GLU* 3.3 30.3 - - - -
168B TRP* 4.0 4.0 - - - -
192B ARG 3.6 5.5 - - - +
193B LEU* 3.9 0.7 - - - -
194B VAL* 3.1 46.7 + - - +
196B ARG* 5.0 2.8 + - - -
207B ARG* 5.3 0.4 - - - -
208B LEU* 1.3 79.9 - - - +
210B LEU* 1.3 63.5 + - - +
211B SER* 3.8 3.1 + - - -
1J NAG 5.4 0.2 + - - -
2J NAG 4.2 8.8 + - - -
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Residues in contact with LEU 210 (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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42B ILE* 4.4 13.2 - - + -
44B ILE* 3.9 7.9 - - + -
59B LEU* 5.3 1.3 - - + -
150B CYS 4.4 0.2 - - - +
151B THR* 3.3 2.4 - - - -
152B LEU* 2.7 53.4 + - + +
154B ILE* 5.4 0.8 - - + +
168B TRP* 4.2 15.3 - - + -
175B VAL* 3.8 31.9 - - + -
191B HIS* 4.3 10.1 - - + -
192B ARG 3.7 5.4 - - - +
193B LEU* 3.7 22.2 - - + -
209B SER* 1.3 71.2 - - - +
211B SER* 1.3 69.1 + - - +
212B PHE* 3.7 31.6 - - + -
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Residues in contact with SER 211 (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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150B CYS 3.8 5.2 - - - -
151B THR* 3.8 18.2 - - - +
191B HIS* 3.3 25.3 - - - +
192B ARG* 3.3 29.3 + - - +
194B VAL* 5.7 1.5 - - - +
209B SER* 3.8 4.5 + - - -
210B LEU* 1.3 75.0 - - - +
212B PHE* 1.3 68.3 + - - +
1J NAG 3.4 32.9 + - - +
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Residues in contact with PHE 212 (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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44B ILE* 3.6 26.5 - - + -
47B ILE* 4.7 20.4 - - + -
57B TYR* 4.9 15.7 - + - -
59B LEU* 5.0 7.4 - - + -
148B GLN 4.1 0.4 - - - -
149B ASN* 3.1 28.8 - - - +
150B CYS* 3.1 22.5 + - + +
152B LEU* 5.8 0.4 - - + -
178B VAL* 4.0 25.1 - - + -
181B ILE* 5.1 0.4 - - + -
188B ILE* 4.3 19.3 - - + -
190B GLU 3.7 4.5 - - - -
191B HIS* 4.0 11.0 - - + -
210B LEU* 3.7 23.8 - - + -
211B SER* 1.3 80.2 - - - +
213B ARG* 1.3 61.4 + - - +
214B LEU* 3.9 18.2 - - + -
1J NAG 3.7 6.3 - - - +
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Residues in contact with ARG 213 (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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147B GLU* 3.4 39.2 + - + +
148B GLN 3.3 6.1 - - - +
149B ASN* 4.9 4.4 - - + +
188B ILE* 3.8 1.1 - - - +
189B VAL* 3.0 45.2 + - + +
190B GLU* 3.1 43.5 + - + +
192B ARG* 4.2 7.9 - - - +
212B PHE* 1.3 73.2 - - - +
214B LEU* 1.3 61.4 - - - +
215B LYS 3.5 1.2 + - - -
1J NAG 3.3 27.4 + - + +
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Residues in contact with LEU 214 (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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47B ILE* 5.3 5.6 - - + -
50B VAL* 4.3 30.1 - - + -
57B TYR* 5.9 2.5 - - + -
147B GLU* 3.3 2.2 - - - -
148B GLN* 2.6 50.6 + - + +
150B CYS* 4.4 25.4 - - + -
183B LEU* 3.8 17.7 - - + -
186B PHE* 3.9 18.2 - - + -
187B SER 4.0 1.6 - - - -
188B ILE* 3.7 30.3 - - + -
212B PHE* 4.6 13.0 - - + -
213B ARG* 1.3 71.0 - - - +
215B LYS* 1.3 61.7 + - - +
216B ARG 3.8 0.9 + - - -
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Residues in contact with LYS 215 (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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146B ASP 3.9 5.2 - - - +
147B GLU* 4.0 29.9 + - + +
186B PHE* 3.4 1.7 - - - -
187B SER* 2.8 49.6 + - - +
189B VAL* 3.7 19.7 - - + -
213B ARG 3.5 1.8 + - - -
214B LEU* 1.3 72.4 - - - +
216B ARG* 1.3 72.8 + - - +
217B ASN* 4.5 4.0 - - - +
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Residues in contact with ARG 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU* 2.6 43.2 + - - +
138B MET* 4.9 0.8 - - - -
140B LEU* 4.1 3.8 - - - +
143B TYR* 3.4 20.4 - - - -
144B PRO* 3.4 37.4 - - - +
145B LEU* 5.5 1.2 - - - -
146B ASP* 3.1 39.4 + - - +
148B GLN* 4.7 4.2 - - - +
185B GLN* 3.1 28.0 - - + +
186B PHE* 3.3 37.5 - - + -
214B LEU 3.8 1.2 + - - -
215B LYS* 1.3 83.4 - - - +
217B ASN* 1.3 71.9 + - - +
218B ILE* 4.1 3.6 + - - +
221B PHE* 3.9 6.3 - - - -
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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