Contacts of the strand formed by residues 210 - 220 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60H ARG* 3.5 25.0 + - - +
134I VAL* 3.4 0.7 - - - -
135I VAL* 2.8 31.7 + - + -
167I LEU* 3.6 28.8 - - + +
169I PRO* 3.3 39.8 - - - +
205I HIS 5.0 0.4 + - - -
206I LEU* 4.0 24.5 - - + +
207I SER* 3.3 38.2 + - - +
208I ALA 3.2 3.0 - - - -
209I GLY* 1.3 75.8 - - - +
211I ARG* 1.3 61.4 + - - +
212I LEU* 3.6 8.9 - - + +
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Residues in contact with ARG 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127I LYS* 5.2 12.5 - - + +
130I THR* 5.1 5.7 + - - +
132I GLU* 3.2 40.4 + - + +
133I LEU 3.4 4.3 - - - -
134I VAL* 3.6 27.1 - - + +
167I LEU* 3.6 5.4 - - - +
168I GLN* 3.0 39.8 + - + +
169I PRO* 3.3 28.0 - - + +
209I GLY 3.3 22.0 + - - -
210I GLN* 1.3 71.3 - - - +
212I LEU* 1.3 61.3 + - - +
213I GLY 3.9 0.7 - - - -
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Residues in contact with LEU 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I TRP* 5.8 1.6 + - - -
131I LYS 4.7 0.3 - - - +
132I GLU* 3.5 14.3 - - - +
133I LEU* 2.9 39.2 + - + +
135I VAL* 3.8 16.8 - - + -
143I VAL* 4.5 10.1 - - + -
165I LEU* 4.0 28.5 - - + -
166I HIS 4.0 4.0 - - - -
167I LEU* 3.7 21.1 - - + -
204I LEU* 5.7 0.2 - - + -
206I LEU* 4.0 18.6 - - + -
210I GLN* 3.6 18.4 - - + +
211I ARG* 1.3 73.0 - - - +
213I GLY* 1.3 60.9 + - - +
214I VAL* 5.2 0.8 - - - +
235I LEU* 5.1 3.4 - - + +
237I LEU* 4.2 22.2 - - + -
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Residues in contact with GLY 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I LYS 4.7 3.1 - - - -
132I GLU* 4.2 6.7 - - - -
165I LEU* 3.3 8.3 - - - +
166I HIS 3.1 34.6 + - - +
168I GLN* 3.8 24.9 - - - +
212I LEU* 1.3 75.4 - - - +
214I VAL* 1.3 64.5 + - - +
215I HIS* 4.4 4.7 - - - -
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Residues in contact with VAL 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I PRO* 3.3 8.6 - - - +
107I LEU* 3.3 36.8 + - + +
109I TRP* 3.7 30.5 - - + +
131I LYS 5.1 3.6 + - - -
145I PHE* 3.8 25.1 - - + -
163I LEU* 3.8 26.9 - - + -
164I ALA 3.3 9.4 - - - +
165I LEU* 4.2 3.1 - - + -
212I LEU 5.2 0.9 - - - +
213I GLY* 1.3 79.3 - - - +
215I HIS* 1.3 64.7 + - - +
235I LEU* 4.1 16.2 - - + -
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Residues in contact with HIS 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I GLY* 4.1 6.3 - - - +
106I PRO* 3.5 36.3 - - + +
162I SER 3.9 1.0 - - - +
163I LEU* 4.0 0.3 - - - -
164I ALA* 3.0 33.2 + - + +
166I HIS* 3.3 35.4 + + + -
168I GLN* 4.2 26.8 + - - -
213I GLY* 5.1 0.2 - - - -
214I VAL* 1.3 83.8 + - - +
216I LEU* 1.3 62.2 + - - +
217I HIS* 4.0 1.9 + - + +
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Residues in contact with LEU 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101I LEU 5.9 0.2 - - - +
102I LEU* 4.2 24.7 - - + +
103I ILE 4.9 4.0 - - - +
104I ASP* 3.6 9.3 - - - +
105I GLY* 3.3 30.4 + - - +
107I LEU* 3.8 23.7 - - + +
147I LEU* 4.7 1.1 - - + -
161I VAL* 3.8 22.9 - - + -
162I SER 3.4 10.1 - - - +
163I LEU* 4.2 15.7 - - + -
214I VAL 4.4 0.2 + - - -
215I HIS* 1.3 73.4 - - - +
217I HIS* 1.3 69.2 + - - +
218I THR* 4.2 4.7 - - - +
228I LEU* 3.7 38.6 - - + -
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Residues in contact with HIS 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ASP* 3.4 14.1 + - - +
160I SER 5.0 0.2 - - - -
162I SER* 2.8 49.5 + - - +
215I HIS* 4.0 2.2 + - + +
216I LEU* 1.3 74.7 - - - +
218I THR* 1.3 78.0 + - - +
219I GLU* 4.3 5.7 + - + +
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Residues in contact with THR 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I LEU* 3.7 19.6 - - + +
104I ASP* 3.2 23.9 + - - +
160I SER 3.1 15.0 + - - -
161I VAL* 3.5 14.7 - - - +
216I LEU* 4.2 11.9 - - - +
217I HIS* 1.3 90.3 + - - +
219I GLU* 1.3 64.1 + - - +
220I ALA* 4.1 5.7 - - - +
223I ARG* 3.7 31.9 + - + +
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Residues in contact with GLU 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G ALA 5.6 3.6 + - - +
159I GLY* 3.3 2.3 - - - -
160I SER* 2.7 49.6 + - - +
217I HIS* 4.3 6.2 + - + +
218I THR* 1.3 73.7 - - - +
220I ALA* 1.3 59.2 + - - +
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Residues in contact with ALA 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I LEU* 5.4 1.3 - - + -
158I SER 3.2 17.3 - - - +
159I GLY* 4.0 4.7 - - - -
160I SER 4.9 0.2 - - - +
185I LEU* 5.1 7.6 - - + -
218I THR* 4.1 13.9 - - + +
219I GLU* 1.3 78.4 - - - +
221I ARG* 1.3 66.5 + - - +
222I ALA 4.5 0.4 - - - +
223I ARG* 4.1 25.6 + - + +
226I TRP* 6.5 0.2 - - + -
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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