Contacts of the strand formed by residues 210 - 221 (chain F) in PDB entry 6CU0
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 GLN 210 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133F LEU 3.7 1.6 - - - +
134F VAL* 3.5 1.7 - - - -
135F VAL* 2.9 37.8 + - + +
167F LEU* 3.9 37.5 - - + +
168F GLN 3.4 12.9 - - - +
169F PRO* 3.2 31.5 - - - +
171F ARG* 5.4 6.9 - - - +
205F HIS 5.0 1.6 + - - -
206F LEU* 4.4 10.8 - - + +
207F SER* 3.2 49.7 + - - +
208F ALA 3.3 2.0 - - - -
209F GLY* 1.3 77.4 - - - +
211F ARG* 1.3 61.4 + - - +
212F LEU* 3.9 1.3 + - + +
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Residues in contact with ARG 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F GLU* 3.7 31.4 - - + +
133F LEU 3.2 7.9 - - - +
134F VAL* 4.5 10.3 - - + +
166F HIS 3.9 0.2 - - - +
168F GLN* 2.9 45.9 + - + +
209F GLY 3.7 3.9 + - - +
210F GLN* 1.3 72.5 - - - +
212F LEU* 1.3 61.7 + - - +
213F GLY 3.9 1.2 + - - -
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Residues in contact with LEU 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F GLU* 3.3 5.1 - - - -
133F LEU* 2.8 51.1 + - + +
135F VAL* 5.6 6.7 - - + -
165F LEU* 4.0 20.9 - - + -
166F HIS 3.7 4.9 - - - -
167F LEU* 4.5 13.9 - - + -
206F LEU* 6.1 3.1 - - + -
210F GLN* 3.9 3.9 + - + +
211F ARG* 1.3 71.2 - - - +
213F GLY* 1.3 58.1 + - - +
214F VAL* 5.7 0.4 - - - -
235F LEU* 5.3 4.5 - - + -
237F LEU* 5.8 7.2 - - + -
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Residues in contact with GLY 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F TRP* 5.9 0.4 - - - -
131F LYS 4.2 13.5 - - - -
132F GLU* 4.7 7.8 + - - +
164F ALA 3.7 0.5 - - - +
165F LEU* 3.5 2.9 - - - +
166F HIS* 2.8 39.6 + - - +
211F ARG 3.9 1.0 + - - -
212F LEU* 1.3 74.2 - - - +
214F VAL* 1.3 65.6 + - - -
215F HIS* 5.8 1.3 - - - -
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Residues in contact with VAL 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F PRO* 3.4 6.7 - - - +
107F LEU* 3.0 45.8 + - + +
109F TRP* 3.6 33.6 - - + +
131F LYS 4.9 1.8 + - - -
145F PHE* 4.1 11.9 - - + -
163F LEU* 4.1 24.0 - - + -
164F ALA 3.4 9.0 - - - +
165F LEU* 3.7 19.7 - - + -
213F GLY* 1.3 76.9 - - - -
215F HIS* 1.3 65.4 + - - +
235F LEU* 3.8 14.1 - - + -
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Residues in contact with HIS 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F GLY* 3.7 18.9 - - - -
106F PRO* 3.3 43.4 - - + +
162F SER 3.5 5.0 - - - +
163F LEU* 3.5 1.7 - - - -
164F ALA* 2.8 40.7 + - + +
166F HIS* 4.2 21.2 - + + +
213F GLY 5.8 0.8 - - - -
214F VAL* 1.3 75.8 + - - +
216F LEU* 1.3 62.7 + - - +
217F HIS* 4.0 1.1 + - - +
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Residues in contact with LEU 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F ASN* 5.9 0.2 - - + -
101F LEU 4.5 3.8 - - - +
102F LEU* 4.1 18.4 - - + -
103F ILE 3.8 29.8 - - - +
104F ASP* 3.4 4.1 - - - +
105F GLY 3.1 37.8 + - - +
107F LEU* 3.8 24.6 - - + +
161F VAL* 3.5 28.0 - - + -
162F SER 3.3 4.0 - - - +
163F LEU* 3.5 24.5 - - + -
214F VAL 4.3 0.6 + - - -
215F HIS* 1.3 76.3 - - - +
217F HIS* 1.3 64.4 + - - +
218F THR* 4.8 2.5 - - + -
228F LEU* 4.6 11.7 - - + -
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Residues in contact with HIS 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F ASP* 3.4 25.6 + - - +
161F VAL* 3.4 2.6 - - - +
162F SER* 2.7 54.5 + - - +
215F HIS 5.3 1.1 - - - +
216F LEU* 1.3 75.5 + - - +
218F THR* 1.3 83.7 + - - +
219F GLU* 4.4 4.9 + - + -
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Residues in contact with THR 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LEU* 4.1 33.1 - - + +
103F ILE 4.5 1.1 - - - +
104F ASP* 2.9 31.1 + - - +
160F SER 3.4 12.3 + - - -
161F VAL* 4.2 14.2 - - - +
162F SER* 5.4 0.2 - - - -
185F LEU* 5.8 1.0 - - - +
216F LEU* 4.8 5.8 - - + -
217F HIS* 1.3 86.6 + - - +
219F GLU* 1.3 58.3 + - - +
220F ALA* 3.2 22.5 + - + +
223F ARG* 4.5 8.1 - - + +
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Residues in contact with GLU 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F SER 4.0 1.0 - - - +
159F GLY* 3.7 7.8 - - - -
160F SER* 3.0 40.2 + - - +
185F LEU* 5.8 0.5 - - - +
217F HIS* 4.4 6.7 - - + +
218F THR* 1.3 69.4 + - - +
220F ALA* 1.3 62.4 + - - +
221F ARG* 3.5 2.9 + - - +
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Residues in contact with ALA 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F THR* 3.2 14.8 + - + +
219F GLU* 1.3 69.6 - - - +
221F ARG* 1.3 60.5 + - - +
222F ALA 3.8 0.9 - - - +
223F ARG* 3.6 31.6 - - + +
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Residues in contact with ARG 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F GLY* 3.5 0.7 - - - -
158F SER* 3.1 54.0 + - - +
159F GLY* 5.3 1.8 - - - -
219F GLU 3.5 0.8 + - - +
220F ALA* 1.3 72.8 - - - +
222F ALA* 1.3 66.4 + - - +
223F ARG 4.3 0.6 - - - +
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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