Contacts of the strand formed by residues 168 - 179 (chain E) 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 HIS 168 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C TYR* 4.3 25.3 - - + +
148C VAL 4.9 8.7 + - - +
149C ARG* 3.0 12.4 + - - +
188C TYR* 3.2 40.7 - + + -
227D LEU* 2.8 28.5 - - - +
140E GLU* 2.7 36.5 + - + -
160E ALA* 4.2 8.7 - - + -
161E LEU 3.2 6.7 - - - -
162E SER* 3.7 15.6 - - - -
163E LEU* 4.3 3.3 - - - +
166E GLY 3.9 13.7 + - - -
167E GLY* 1.3 76.2 + - - -
169E TYR* 1.3 58.3 + - - +
170E ARG* 5.4 0.4 - - + -
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Residues in contact with TYR 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D TYR* 4.0 12.8 - - - +
95E TYR* 3.2 37.0 - + + +
96E GLU* 3.5 12.3 - - + -
97E ASP* 2.6 44.4 + - + -
125E PHE* 3.6 12.6 - - - -
130E PRO* 3.8 23.3 - - + -
131E VAL* 3.5 21.4 - - + +
136E THR* 5.0 0.9 - - + -
160E ALA* 3.3 1.7 - - - -
161E LEU* 2.8 51.8 + - + +
163E LEU* 3.8 22.2 - - + -
168E HIS* 1.3 73.1 - - - +
170E ARG* 1.3 64.9 + - - +
171E CYS* 4.9 1.2 - - - +
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Residues in contact with ARG 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C LYS* 6.4 1.3 - - - -
147C TYR* 3.9 27.4 - - + +
149C ARG* 4.3 4.5 - - - +
156C ASP* 2.3 33.9 + - - +
174C LYS* 3.8 23.4 - - - +
188C TYR* 5.7 1.3 - - - -
95E TYR* 3.4 6.1 - - - +
96E GLU* 2.7 56.3 + - + +
158E ASN* 3.2 24.7 - - - +
159E THR 2.7 43.3 + - - +
160E ALA* 4.2 9.4 - - + -
168E HIS 5.4 0.4 - - - -
169E TYR* 1.3 76.0 - - - +
171E CYS* 1.3 77.4 + - - +
172E ASP* 5.3 3.6 - - - +
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Residues in contact with CYS 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E MET* 3.8 2.9 - - - -
94E ASN 3.5 17.9 - - - -
95E TYR* 3.5 43.5 - - + -
139E TRP* 3.9 15.7 - - + -
157E VAL 3.8 1.2 - - - +
158E ASN* 3.7 0.5 - - - -
159E THR* 3.0 33.7 + - - +
169E TYR 3.9 0.6 + - - +
170E ARG* 1.3 81.3 + - - +
172E ASP* 1.3 62.3 + - - +
173E PHE* 3.4 25.0 + - + -
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Residues in contact with ASP 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ASN* 3.6 7.2 - - - +
170C ARG* 5.2 0.2 + - - -
172C ASP* 4.0 11.1 - - - +
174C LYS* 5.9 1.0 + - - -
92E SER 3.5 5.0 - - - +
93E MET* 3.5 0.2 - - - -
94E ASN* 2.8 48.0 + - + +
157E VAL 3.8 2.2 - - - -
158E ASN* 2.7 26.9 + - + +
170E ARG* 5.3 3.8 - - - +
171E CYS* 1.3 73.3 - - - +
173E PHE* 1.3 74.2 + - - +
174E LYS* 4.4 20.6 + - - +
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Residues in contact with PHE 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E THR* 3.3 33.0 - - + -
63E KZ4 3.7 26.7 - + + -
91E ARG* 4.0 21.3 - - - -
92E SER 3.5 3.8 - - - +
93E MET* 3.8 14.8 - - + -
139E TRP* 3.7 26.9 - + - -
155E GLY 4.4 1.1 - - - +
156E ASP* 3.4 6.6 - - - +
157E VAL* 2.9 41.3 + - + -
159E THR* 3.9 11.7 - - + -
171E CYS* 3.4 29.6 - - - -
172E ASP* 1.3 85.3 + - - +
174E LYS* 1.3 62.4 + - - +
175E THR* 4.2 4.3 - - - +
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Residues in contact with LYS 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLY* 5.2 16.2 - - - +
100B ILE* 6.1 3.1 - - + -
124B ASN* 3.1 19.4 + - - +
170C ARG* 4.3 19.6 - - - +
172C ASP* 5.1 3.6 + - - -
91E ARG* 3.1 1.3 - - - -
92E SER* 2.9 46.8 + - - +
155E GLY 3.7 3.1 - - - -
156E ASP* 3.9 13.3 + - - +
172E ASP* 4.4 19.0 + - - +
173E PHE* 1.3 78.3 - - - +
175E THR* 1.3 61.0 + - - +
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Residues in contact with THR 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E TRP* 4.2 6.5 - - + -
90E GLU 3.2 11.0 - - - +
91E ARG* 2.9 35.6 + - + +
144E GLU* 4.6 1.6 + - - -
154E LYS* 3.3 7.5 - - - +
155E GLY 2.8 39.0 + - - +
156E ASP* 4.3 0.5 + - - +
173E PHE* 4.9 4.3 - - - +
174E LYS* 1.3 73.4 + - - +
176E THR* 1.3 68.1 + - - +
177E TYR* 3.4 43.6 + - + +
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Residues in contact with THR 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ASN* 2.8 22.8 + - - +
89E TRP* 3.1 5.9 - - - +
90E GLU* 2.8 40.6 + - - +
152E VAL* 3.8 27.6 - - + -
153E LEU 3.5 3.6 - - - +
154E LYS* 2.8 30.5 + - + +
175E THR* 1.3 72.1 - - - +
177E TYR* 1.3 62.7 + - - +
178E LYS* 3.9 25.7 + - + +
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Residues in contact with TYR 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E ARG* 2.9 34.1 + - + -
78E TYR* 3.5 9.3 + - + -
79E PHE* 3.4 35.7 - + + -
87E TYR* 4.1 6.7 - + + -
88E SER 3.7 3.8 - - - +
89E TRP* 3.8 22.7 - + + -
91E ARG* 5.0 0.4 - - - -
144E GLU* 2.5 31.3 + - - -
146E LEU* 4.0 11.7 - - + -
152E VAL* 3.6 6.4 - - - +
153E LEU* 2.7 55.5 + - + +
154E LYS 4.3 0.7 - - - -
155E GLY 3.9 10.8 - - - -
175E THR* 3.4 26.0 + - + +
176E THR* 1.3 73.2 - - - +
178E LYS* 1.3 60.4 + - - +
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Residues in contact with LYS 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ASN* 3.9 18.4 + - - +
125B PHE 4.9 3.2 + - - -
127B ALA* 6.1 1.8 - - - +
78E TYR* 3.7 2.2 - - - -
87E TYR* 3.3 4.5 - - - -
88E SER* 2.8 49.3 + - - +
89E TRP* 6.4 0.2 - - - -
90E GLU* 2.8 31.0 + - - +
152E VAL* 4.1 18.6 - - + -
176E THR* 3.9 23.8 - - + +
177E TYR* 1.3 78.6 - - - +
179E ALA* 1.3 67.2 + - - +
180E LYS* 3.6 1.6 + - - +
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Residues in contact with ALA 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TYR* 2.9 26.3 + - + +
82E SER* 3.3 24.2 - - - +
86E GLY 4.0 0.2 - - - -
87E TYR* 3.7 9.9 - - - -
178E LYS* 1.3 77.5 - - - +
180E LYS* 1.3 63.6 + - - +
181E LYS 3.2 20.9 + - - +
183E VAL* 4.1 8.7 - - + -
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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