Contacts of the strand formed by residues 210 - 220 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C LEU 3.9 0.5 - - - +
134C VAL* 3.3 5.0 - - - +
135C VAL* 2.9 31.5 + - + -
167C LEU* 4.2 21.2 - - + +
169C PRO* 3.2 44.8 + - - +
205C HIS 4.2 3.6 - - - +
206C LEU* 3.5 23.6 - - + -
207C SER* 2.6 54.0 + - - +
208C ALA 3.3 0.4 - - - -
209C GLY* 1.3 78.5 - - - +
211C ARG* 1.3 68.0 + - - +
212C LEU* 3.9 8.4 - - + +
60F ARG* 4.5 6.2 + - - +
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Residues in contact with ARG 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C GLU* 3.2 33.9 + - + +
133C LEU 3.7 4.5 - - - +
134C VAL* 3.9 20.9 - - + -
166C HIS 3.6 0.5 - - - +
167C LEU* 3.5 5.7 - - - -
168C GLN* 3.1 52.8 + - + +
169C PRO* 3.9 14.3 - - - +
209C GLY 3.2 17.5 - - - -
210C GLN* 1.3 77.8 - - - +
212C LEU* 1.3 62.5 + - - +
213C GLY 4.1 0.4 - - - -
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Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TRP* 5.8 1.0 + - - -
131C LYS 4.4 0.3 - - - +
132C GLU* 3.2 20.4 - - - +
133C LEU* 3.1 39.0 + - + +
135C VAL* 3.7 26.9 - - + -
143C VAL* 4.8 6.1 - - + -
165C LEU* 4.1 26.9 - - + -
166C HIS 3.4 4.9 - - - +
167C LEU* 3.6 18.6 - - + -
204C LEU* 5.9 0.4 - - + -
206C LEU* 4.0 22.9 - - + -
210C GLN* 3.9 12.1 - - + +
211C ARG* 1.3 78.1 - - - +
213C GLY* 1.3 59.7 + - - +
214C VAL* 5.4 0.4 - - - +
235C LEU* 5.3 1.0 - - + +
237C LEU* 4.3 13.0 - - + -
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Residues in contact with GLY 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TRP* 6.0 0.2 - - - -
131C LYS 4.2 7.0 - - - -
132C GLU* 4.0 12.1 - - - +
164C ALA 4.3 0.2 - - - -
165C LEU* 3.2 8.1 - - - +
166C HIS* 3.0 34.4 + - - -
168C GLN* 4.7 9.6 - - - +
211C ARG 4.1 0.4 - - - -
212C LEU* 1.3 75.1 - - - +
214C VAL* 1.3 67.0 + - - +
215C HIS* 4.7 7.0 - - - -
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Residues in contact with VAL 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C PRO* 3.3 6.0 - - - +
107C LEU* 3.0 50.3 + - + -
109C TRP* 3.5 31.2 - - + +
131C LYS 4.8 3.4 + - - -
145C PHE* 3.8 31.4 - - + -
163C LEU* 4.2 9.6 - - + -
164C ALA 3.2 6.3 - - - +
165C LEU* 4.6 1.3 - - + -
212C LEU 5.4 0.2 - - - +
213C GLY* 1.3 79.7 - - - +
215C HIS* 1.3 65.8 + - - +
235C LEU* 3.8 21.1 - - + -
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Residues in contact with HIS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C GLY* 3.7 7.4 - - - -
106C PRO* 3.6 36.8 - - + +
162C SER 3.6 1.4 - - - +
163C LEU* 3.4 4.2 - - - -
164C ALA* 2.8 40.7 + - + +
166C HIS* 3.7 33.2 + + + -
168C GLN* 5.1 12.3 - - - -
213C GLY* 4.7 2.4 - - - -
214C VAL* 1.3 83.0 + - - +
216C LEU* 1.3 60.7 + - - +
217C HIS* 3.8 3.9 + - + +
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Residues in contact with LEU 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LEU 5.4 3.1 - - - +
102C LEU* 3.8 27.6 - - + +
103C ILE 4.3 5.8 - - - +
104C ASP* 3.2 13.2 - - - +
105C GLY 3.0 26.7 + - - +
107C LEU* 3.8 20.1 - - + +
161C VAL* 3.8 23.3 - - + -
162C SER 3.3 3.6 - - - -
163C LEU* 3.7 23.6 - - + -
214C VAL 4.2 0.4 + - - -
215C HIS* 1.3 69.9 - - - +
217C HIS* 1.3 60.8 + - - +
218C THR* 3.9 7.6 - - + -
228C LEU* 3.7 41.1 - - + -
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Residues in contact with HIS 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ASP* 3.3 17.9 + - + -
160C SER 4.6 0.2 - - - +
162C SER* 2.9 41.4 + - - +
215C HIS* 3.8 4.1 + - + +
216C LEU* 1.3 73.3 - - - +
218C THR* 1.3 61.0 + - - +
219C GLU* 3.8 34.3 + - + +
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Residues in contact with THR 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 3.2 40.5 - - + +
104C ASP* 2.9 17.8 + - - +
160C SER 3.4 6.2 + - - -
161C VAL* 3.3 35.4 - - - +
216C LEU* 3.9 2.5 - - + -
217C HIS* 1.3 75.8 - - - +
219C GLU* 1.3 65.2 + - - +
220C ALA* 4.0 9.2 - - - +
223C ARG* 2.9 36.2 + - - +
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Residues in contact with GLU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C GLY* 3.5 2.1 - - - -
160C SER* 3.0 37.6 + - - +
217C HIS* 3.8 27.1 + - + -
218C THR* 1.3 71.7 - - - +
220C ALA* 1.3 60.7 + - - +
223C ARG* 4.8 2.0 - - - +
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Residues in contact with ALA 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 5.0 0.7 - - + -
158C SER 3.2 17.9 - - - +
159C GLY* 3.9 5.4 - - - -
185C LEU* 4.3 11.4 - - + -
218C THR* 4.0 14.3 + - - +
219C GLU* 1.3 74.6 - - - +
221C ARG* 1.3 67.4 + - - +
223C ARG* 4.3 26.8 + - + +
226C TRP* 6.2 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