Contacts of the strand formed by residues 142 - 149 (chain C) in PDB entry 6NQN
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 SER 142 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C KZ4 2.8 39.2 + - - +
140C GLU 3.6 0.4 + - - -
141C PRO* 1.3 76.5 - - - +
143C THR* 1.3 62.5 + - - +
144C GLU 4.1 0.2 - - - -
157C VAL* 4.0 9.1 - - - +
158C ASN 5.7 0.2 - - - -
159C THR* 3.7 20.2 - - - -
192C ASP* 3.3 5.0 - - - +
193C HIS* 2.7 40.2 + - - +
145E LYS* 5.7 2.0 - - - -
190E PHE* 4.3 7.0 - - - -
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Residues in contact with THR 143 (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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142C SER* 1.3 74.0 + - - +
144C GLU* 1.3 55.6 + - - +
145C LYS* 2.5 30.6 + - - +
157C VAL* 3.2 11.3 - - - +
190C PHE* 3.9 26.9 - - + -
191C VAL 3.6 3.6 - - - +
192C ASP* 2.6 26.9 + - - +
216C HIS* 4.1 1.8 - - - +
143E THR* 3.6 43.1 + - - +
145E LYS* 3.8 4.1 + - - +
190E PHE* 4.7 7.6 - - - -
216E HIS* 4.8 4.5 - - - -
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Residues in contact with GLU 144 (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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63C KZ4 5.9 1.8 - - - -
66C ARG* 3.2 17.3 + - - -
142C SER 4.1 0.6 - - - -
143C THR* 1.3 73.5 - - - +
145C LYS* 1.3 65.4 + - - +
146C LEU* 3.7 20.0 - - + +
155C GLY* 3.5 16.3 - - - +
156C ASP 3.9 11.7 - - - +
157C VAL* 3.7 19.0 - - + +
175C THR* 4.7 2.6 + - - -
177C TYR* 2.6 25.6 + - - -
190C PHE* 3.1 10.7 - - - +
191C VAL* 2.9 34.9 + - - +
193C HIS* 2.8 27.6 + - + +
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Residues in contact with LYS 145 (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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143C THR* 2.5 33.2 + - + +
144C GLU* 1.3 72.9 - - - +
146C LEU* 1.3 61.5 + - - +
147C TYR* 4.1 6.6 - - + -
154C LYS 3.8 0.5 - - - +
155C GLY* 3.3 3.1 - - - -
156C ASP* 2.9 46.3 + - + +
157C VAL* 4.6 3.2 - - - +
188C TYR* 3.3 29.8 - - + +
189C HIS 3.7 2.9 - - - -
190C PHE* 3.4 33.2 - - + -
141E PRO 5.3 0.7 - - - +
142E SER* 5.6 1.3 - - - -
143E THR* 3.9 10.2 + - - +
145E LYS* 2.9 25.7 - - - +
157E VAL* 4.9 2.2 - - - +
158E ASN 3.3 25.1 - - - +
159E THR* 5.2 0.9 - - - -
170E ARG* 6.4 1.1 - - - -
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Residues in contact with LEU 146 (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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66C ARG* 5.0 1.1 - - + -
71C TYR* 4.4 1.3 - - - +
79C PHE* 4.2 10.8 - - + -
144C GLU* 3.7 29.6 - - + +
145C LYS* 1.3 78.6 - - - +
147C TYR* 1.3 62.0 + - - +
153C LEU* 3.9 21.3 - - + -
154C LYS 3.1 7.2 - - - +
177C TYR* 3.9 27.6 - - + -
187C ASP 4.2 0.4 - - - +
188C TYR* 3.4 7.3 - - - -
189C HIS* 2.9 55.2 + - + +
190C PHE 4.0 3.8 - - - -
191C VAL* 3.6 30.7 - - + +
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Residues in contact with TYR 147 (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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145C LYS* 4.1 9.2 - - + -
146C LEU* 1.3 78.3 - - - +
148C VAL* 1.3 68.7 + - - +
149C ARG* 4.0 30.9 + - - -
153C LEU* 3.6 8.3 - - - +
154C LYS* 2.7 63.9 + - + +
156C ASP* 2.8 39.2 + - + -
174C LYS* 5.7 0.2 - - - +
186C PRO 5.3 1.3 - - - -
188C TYR* 3.6 35.9 - + + +
168E HIS* 4.3 20.4 - - + +
170E ARG* 3.9 19.7 - - + +
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Residues in contact with VAL 148 (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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147C TYR* 1.3 83.4 - - - +
149C ARG* 1.3 68.8 + - - +
150C ASP 4.7 0.4 - - - +
151C GLY 4.2 8.5 - - - +
152C VAL 3.3 12.3 - - - +
153C LEU* 4.1 9.9 - - + -
185C LEU* 3.7 42.6 - - + -
186C PRO* 3.5 24.8 + - + +
188C TYR 5.8 0.2 - - - +
227D LEU* 4.3 9.5 - - + +
167E GLY* 5.6 1.2 - - - -
168E HIS* 4.9 9.6 + - - -
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Residues in contact with ARG 149 (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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147C TYR* 3.8 25.9 + - + -
148C VAL* 1.3 74.2 + - - +
150C ASP* 1.3 78.8 + - + +
151C GLY 3.2 1.6 - - - -
152C VAL* 2.9 26.9 + - - +
154C LYS* 3.8 34.1 - - + +
226D GLU 4.0 12.9 + - - +
227D LEU* 3.1 28.0 + - + +
228D TYR 5.4 1.0 - - - -
96E GLU* 2.8 41.6 + - - -
168E HIS* 3.0 21.2 + - - +
170E ARG* 4.3 3.8 - - - +
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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