Contacts of the strand formed by residues 210 - 221 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D LEU 3.7 1.2 - - - +
134D VAL* 3.5 1.9 - - - -
135D VAL* 2.9 32.9 + - + +
167D LEU* 3.9 38.1 - - + +
168D GLN 3.3 19.2 - - - +
169D PRO* 3.4 25.4 + - - +
205D HIS 4.9 1.8 + - - -
206D LEU* 4.4 13.8 - - + +
207D SER* 3.2 48.8 + - - +
208D ALA 3.3 2.0 - - - -
209D GLY* 1.3 76.3 - - - +
211D ARG* 1.3 62.1 + - - +
212D LEU* 3.9 2.6 + - + +
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Residues in contact with ARG 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLU* 3.7 31.8 - - + +
133D LEU 3.2 7.6 - - - +
134D VAL* 4.5 10.1 - - + +
166D HIS 3.9 0.3 - - - +
168D GLN* 2.9 47.3 + - + +
209D GLY 3.6 3.7 + - - +
210D GLN* 1.3 72.3 - - - +
212D LEU* 1.3 62.4 + - - +
213D GLY 3.9 1.4 + - - -
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Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLU* 3.4 4.1 - - - -
133D LEU* 2.8 55.8 + - + +
165D LEU* 4.1 20.4 - - + -
166D HIS 3.7 5.4 - - - -
167D LEU* 4.3 14.8 - - + -
206D LEU* 6.1 3.6 - - + -
210D GLN* 3.9 3.5 + - + +
211D ARG* 1.3 71.9 - - - +
213D GLY* 1.3 57.9 + - - +
235D LEU* 5.2 4.9 - - + +
237D LEU* 5.8 4.7 - - + -
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Residues in contact with GLY 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D TRP* 5.9 0.4 - - - -
131D LYS 4.3 12.8 - - - -
132D GLU* 4.7 7.2 + - - -
164D ALA 3.7 0.2 - - - +
165D LEU* 3.5 2.5 - - - -
166D HIS* 2.8 39.5 + - - +
211D ARG 3.9 1.0 + - - -
212D LEU* 1.3 74.2 - - - +
214D VAL* 1.3 65.7 + - - -
215D HIS 4.3 0.2 + - - -
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Residues in contact with VAL 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PRO* 3.4 7.6 - - - +
107D LEU* 3.0 30.1 + - + +
109D TRP* 3.6 37.6 - - + +
131D LYS 4.9 1.8 + - - -
145D PHE* 4.1 21.3 - - + -
163D LEU* 4.1 26.9 - - + -
164D ALA 3.4 8.3 - - - +
165D LEU* 3.7 19.5 - - + -
213D GLY* 1.3 77.3 - - - -
215D HIS* 1.3 63.4 + - - +
235D LEU* 3.8 13.7 - - + -
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Residues in contact with HIS 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D GLY* 4.9 2.5 - - - -
106D PRO* 4.1 14.1 - - + -
162D SER 3.5 4.3 - - - +
163D LEU* 3.5 1.8 - - - -
164D ALA* 2.8 40.2 + - + +
166D HIS* 4.2 20.2 - - + +
214D VAL* 1.3 76.8 - - - +
216D LEU* 1.3 61.2 + - - +
217D HIS* 4.0 0.9 + - - +
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Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ASN* 5.9 2.9 - - + -
101D LEU 4.6 2.9 - - - +
102D LEU* 4.1 13.5 - - + -
103D ILE 3.8 29.8 - - - +
104D ASP* 3.4 3.7 - - - +
105D GLY* 3.1 37.8 + - - +
107D LEU* 5.0 7.7 - - + +
161D VAL* 3.5 28.7 - - + -
162D SER 3.3 3.4 - - - +
163D LEU* 3.5 27.1 - - + +
214D VAL 4.3 0.4 + - - -
215D HIS* 1.3 73.8 - - - +
217D HIS* 1.3 62.6 + - - +
218D THR* 4.7 1.6 - - + -
228D LEU* 4.6 22.2 - - + -
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Residues in contact with HIS 217 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104D ASP* 3.4 26.2 + - - +
161D VAL* 3.4 2.8 - - - +
162D SER* 2.7 53.5 + - - +
215D HIS 5.3 1.1 - - - +
216D LEU* 1.3 74.9 - - - +
218D THR* 1.3 83.9 + - - +
219D GLU* 4.5 3.6 + - + +
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Residues in contact with THR 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LEU* 4.1 34.9 - - + +
103D ILE 4.5 1.1 - - - +
104D ASP* 2.9 32.4 + - - +
160D SER 3.4 12.4 + - - -
161D VAL* 4.2 14.8 - - - +
162D SER* 5.4 0.2 - - - -
216D LEU* 4.7 5.6 - - + -
217D HIS* 1.3 87.4 + - - +
219D GLU* 1.3 59.8 + - - +
220D ALA* 3.2 22.5 + - + +
223D ARG* 4.6 4.8 - - + +
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Residues in contact with GLU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D SER 4.0 0.9 - - - +
159D GLY* 3.7 7.6 - - - -
160D SER* 3.0 41.1 + - - +
217D HIS* 4.5 6.7 - - + +
218D THR* 1.3 68.1 + - - +
220D ALA* 1.3 63.4 + - - +
221D ARG* 3.5 3.1 + - - +
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Residues in contact with ALA 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D SER 4.9 0.2 - - - -
218D THR* 3.2 15.7 + - + +
219D GLU* 1.3 69.9 - - - +
221D ARG* 1.3 62.8 + - - +
222D ALA 3.8 1.3 - - - +
223D ARG* 3.6 31.2 - - + +
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Residues in contact with ARG 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B SER* 5.5 11.9 + - - -
191B GLU* 6.1 1.4 - - - +
157D GLY* 3.5 0.7 - - - -
158D SER* 3.1 54.4 + - - +
159D GLY* 5.2 1.3 - - - -
219D GLU 3.5 1.1 + - - +
220D ALA* 1.3 74.0 - - - +
222D ALA* 1.3 67.6 + - + +
223D ARG 4.2 0.4 - - - +
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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