Contacts of the strand formed by residues 210 - 220 (chain G) in PDB entry 6A3V
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134G VAL* 3.6 0.7 - - - -
135G VAL* 3.1 27.7 + - + +
167G LEU* 3.7 25.4 - - + +
169G PRO* 3.3 46.7 + - - +
205G HIS 4.9 1.0 - - - +
206G LEU* 4.1 15.1 - - + -
207G SER* 3.5 39.7 + - - +
208G ALA 3.2 2.8 - - - -
209G GLY* 1.3 74.8 - - - +
211G ARG* 1.3 62.2 + - - +
212G LEU* 3.5 23.1 - - + +
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Residues in contact with ARG 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G LYS* 6.0 3.5 - - + +
130G THR* 5.2 7.0 + - - +
132G GLU* 3.2 39.9 + - + +
133G LEU 3.5 3.1 - - - -
134G VAL* 3.7 25.6 - - + -
166G HIS 3.7 0.3 - - - +
167G LEU* 3.5 8.3 - - - +
168G GLN* 3.3 32.8 + - + +
169G PRO* 3.3 36.6 - - + +
209G GLY 3.2 23.8 + - - -
210G GLN* 1.3 73.4 - - - +
212G LEU* 1.3 62.2 + - - +
213G GLY 4.0 0.6 + - - -
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Residues in contact with LEU 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G TRP* 5.8 1.6 + - - -
131G LYS 4.6 0.2 - - - +
132G GLU* 3.5 5.1 - - - -
133G LEU* 3.1 48.0 + - + +
135G VAL* 4.2 7.9 - - + -
143G VAL* 4.4 9.9 - - + -
165G LEU* 4.1 28.5 - - + -
166G HIS 3.6 3.6 - - - -
167G LEU* 3.7 13.0 - - + -
204G LEU* 5.3 0.2 - - + -
206G LEU* 4.1 22.0 - - + -
210G GLN* 3.5 31.9 - - + +
211G ARG* 1.3 73.4 - - - +
213G GLY* 1.3 60.9 + - - +
214G VAL* 5.1 0.6 - - - +
235G LEU* 5.0 2.9 - - + +
237G LEU* 4.2 22.2 - - + -
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Residues in contact with GLY 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G PRO* 6.2 1.1 - - - -
131G LYS 4.5 5.2 - - - -
132G GLU* 4.0 9.9 - - - +
165G LEU* 3.2 7.4 - - - +
166G HIS 2.9 35.2 + - - -
168G GLN* 4.0 17.6 - - - +
211G ARG 4.0 1.4 - - - -
212G LEU* 1.3 74.7 - - - +
214G VAL* 1.3 64.3 + - - +
215G HIS* 4.2 4.9 - - - -
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Residues in contact with VAL 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G PRO* 3.3 5.0 - - - +
107G LEU* 3.0 41.3 + - + +
109G TRP* 3.5 40.2 - - + +
131G LYS 4.9 3.8 + - - -
145G PHE* 3.8 29.4 - - + -
163G LEU* 4.4 9.0 - - + -
164G ALA 3.1 8.3 - - - +
165G LEU* 4.3 3.6 - - + -
212G LEU 5.1 0.4 - - - +
213G GLY* 1.3 78.1 - - - +
215G HIS* 1.3 62.8 + - - +
235G LEU* 3.6 22.4 - - + -
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Residues in contact with HIS 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105G GLY* 4.0 8.1 - - - +
106G PRO* 4.0 31.7 - - + +
163G LEU* 3.3 5.0 - - - +
164G ALA* 2.7 42.1 + - + +
166G HIS* 3.1 42.2 + + + -
168G GLN* 3.8 24.9 - - - -
213G GLY* 4.4 0.4 - - - -
214G VAL* 1.3 84.7 + - - +
216G LEU* 1.3 61.6 + - - +
217G HIS* 4.2 0.6 + - + +
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Residues in contact with LEU 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101G LEU 5.1 1.1 - - - +
102G LEU* 4.7 3.8 - - - -
103G ILE 3.6 29.6 - - - +
104G ASP* 3.1 24.1 - - - +
105G GLY 3.2 17.5 + - - +
107G LEU* 3.9 30.0 - - + +
147G LEU* 4.9 0.2 - - + -
161G VAL* 4.3 18.4 - - + -
162G SER 3.4 10.1 - - - +
163G LEU* 3.9 17.0 - - + -
214G VAL 4.1 1.0 + - - -
215G HIS* 1.3 74.9 - - - +
217G HIS* 1.3 72.4 + - - +
218G THR* 4.3 6.5 - - + -
228G LEU* 4.1 25.6 - - + -
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Residues in contact with HIS 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G ASP* 2.5 26.4 + - + +
160G SER 4.2 0.3 - - - +
161G VAL* 3.7 0.3 - - - +
162G SER* 2.6 57.3 + - - +
215G HIS* 4.2 1.3 + - + +
216G LEU* 1.3 75.2 - - - +
218G THR* 1.3 66.9 + - - +
219G GLU* 4.0 24.7 + - + +
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Residues in contact with THR 218 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G LEU* 4.1 20.1 - - + +
104G ASP* 3.4 20.4 + - - +
160G SER 3.6 8.5 + - - -
161G VAL* 4.0 14.9 - - - +
216G LEU* 4.3 16.4 - - + -
217G HIS* 1.3 81.3 + - - +
219G GLU* 1.3 68.2 + - - +
220G ALA* 3.9 17.2 - - - +
223G ARG* 3.5 34.7 + - + +
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Residues in contact with GLU 219 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G GLY* 3.2 2.4 - - - -
160G SER* 2.7 47.2 + - - +
217G HIS* 4.0 23.1 + - + +
218G THR* 1.3 75.0 - - - +
220G ALA* 1.3 57.9 + - - +
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Residues in contact with ALA 220 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G LEU* 5.5 1.1 - - + -
158G SER 3.3 16.4 - - - +
159G GLY* 3.9 3.8 - - - -
185G LEU* 4.6 11.4 - - + -
218G THR* 3.9 12.8 + - - +
219G GLU* 1.3 76.0 - - - +
221G ARG* 1.3 67.9 + - - +
223G ARG* 3.6 36.0 + - - +
226G TRP* 6.0 0.9 - - + -
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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