Contacts of the strand formed by residues 152 - 163 (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 VAL 152 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TYR* 4.5 8.5 - - - +
148E VAL* 3.3 9.0 - - - +
149E ARG 2.9 38.2 + - - +
150E ASP* 3.3 6.7 - - + +
151E GLY* 1.3 82.7 - - - +
153E LEU* 1.3 61.8 + - - +
154E LYS* 4.7 7.2 - - - -
176E THR* 3.8 23.6 - - + -
177E TYR 3.6 9.6 - - - +
178E LYS* 4.1 22.4 - - + -
185E LEU* 5.3 1.1 - - - -
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Residues in contact with LEU 153 (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* 3.8 34.6 + - + -
79E PHE* 3.7 30.7 - - + -
146E LEU* 3.9 15.7 - - + -
147E TYR* 3.5 33.7 - - - +
148E VAL* 4.1 5.6 - - + +
152E VAL* 1.3 74.8 - - - +
154E LYS* 1.3 64.1 + - - +
176E THR* 3.5 3.1 - - - +
177E TYR* 2.7 49.6 + - + +
186E PRO* 3.9 22.9 - - + -
189E HIS* 5.0 0.9 - - + -
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Residues in contact with LYS 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASN* 4.6 15.6 + - - +
126B PRO* 5.9 6.8 - - - +
145E LYS 4.4 0.2 - - - -
146E LEU* 3.1 8.1 - - - +
147E TYR* 2.7 64.8 + - + +
149E ARG* 4.0 34.8 - - + +
152E VAL* 4.7 7.4 - - + +
153E LEU* 1.3 78.2 - - - +
155E GLY* 1.3 58.8 + - - +
156E ASP* 4.9 2.0 - - - +
175E THR 3.3 5.2 - - - +
176E THR* 2.8 38.6 + - + +
177E TYR* 4.2 3.8 - - - -
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Residues in contact with GLY 155 (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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144E GLU* 3.4 24.0 - - - -
145E LYS 3.2 8.1 - - - -
146E LEU* 4.4 0.7 - - - -
154E LYS* 1.3 74.8 - - - +
156E ASP* 1.3 64.2 + - - +
157E VAL* 5.7 0.4 - - - -
173E PHE* 3.9 1.7 - - - +
174E LYS* 3.7 1.4 - - - -
175E THR* 2.8 42.9 + - - -
177E TYR* 3.9 5.7 - - - -
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Residues in contact with ASP 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ASN* 4.8 3.1 - - + +
170C ARG* 2.5 46.3 + - - +
144E GLU* 4.3 0.4 - - - +
145E LYS* 2.8 46.6 + - + +
147E TYR* 2.6 27.0 + - + -
154E LYS* 4.9 1.6 - - - +
155E GLY* 1.3 84.4 + - - +
157E VAL* 1.3 62.8 + - - +
173E PHE 3.4 6.7 - - - +
174E LYS* 3.9 22.0 + - - +
175E THR 4.3 1.2 + - - +
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Residues in contact with VAL 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C LYS* 4.9 1.3 - - - +
158C ASN* 5.2 0.7 - - - -
63E KZ4 3.5 21.3 - - + -
142E SER* 4.1 17.3 - - - -
143E THR 3.3 24.9 - - - +
144E GLU* 3.8 17.9 - - + -
145E LYS* 4.5 5.8 - - - +
155E GLY 5.7 0.4 - - - +
156E ASP* 1.3 78.4 - - - +
158E ASN* 1.3 80.3 + - - +
159E THR* 3.9 2.6 + - + -
171E CYS 3.8 1.4 - - - +
172E ASP* 3.8 0.3 - - - -
173E PHE* 2.9 51.3 + - + +
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Residues in contact with ASN 158 (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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145C LYS* 3.3 31.6 - - - +
156C ASP* 4.8 5.8 - - + +
157C VAL 3.9 2.8 + - - -
158C ASN* 2.2 61.8 + - - +
173C PHE 5.5 0.3 - - - +
174C LYS* 4.9 2.5 + - - -
145E LYS* 4.8 3.6 - - - +
157E VAL* 1.3 77.8 + - - +
159E THR* 1.3 60.3 - - - +
170E ARG* 3.2 36.3 + - - +
171E CYS 3.7 1.1 - - - -
172E ASP* 2.7 28.8 + - - -
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Residues in contact with THR 159 (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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145C LYS* 5.2 1.3 - - - +
188C TYR* 4.1 8.8 + - - -
63E KZ4 4.1 14.8 + - + +
139E TRP* 3.7 24.7 - - + -
140E GLU 4.0 9.4 + - - -
141E PRO 4.2 3.6 + - - -
142E SER* 3.7 25.0 - - - -
157E VAL* 4.2 3.6 - - + +
158E ASN* 1.3 75.3 - - - +
160E ALA* 1.3 74.9 + - - +
170E ARG* 2.7 25.6 + - - -
171E CYS 3.0 18.8 + - - +
173E PHE* 3.9 15.0 - - + -
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Residues in contact with ALA 160 (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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147C TYR* 6.0 0.2 - - + -
188C TYR* 3.9 26.7 + - + +
139E TRP* 3.5 12.9 - - - -
140E GLU* 3.1 26.8 + - - +
159E THR* 1.3 86.2 + - - +
161E LEU* 1.3 60.0 + - - +
168E HIS* 4.2 15.0 - - + -
169E TYR 3.3 17.3 - - - +
170E ARG* 4.2 9.6 - - - -
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Residues in contact with LEU 161 (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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55E ASP* 3.5 30.3 - - + +
56E ILE* 4.9 5.2 - - + -
95E TYR* 4.0 18.8 - - + +
136E THR* 3.9 19.3 - - + -
138E LYS 3.4 17.9 - - - +
139E TRP* 3.5 35.4 - - + -
160E ALA* 1.3 72.1 - - - +
162E SER* 1.3 66.5 + - - +
163E LEU* 3.7 0.4 + - + -
168E HIS* 3.2 5.2 - - - -
169E TYR* 2.8 64.4 + - + +
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Residues in contact with SER 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E THR* 3.8 0.9 - - - -
137E VAL* 2.9 41.7 + - - +
138E LYS* 2.9 23.8 + - - +
140E GLU* 3.7 23.4 - - - +
160E ALA 4.1 0.8 + - - -
161E LEU* 1.3 73.8 - - - +
163E LEU* 1.3 64.5 + - - +
166E GLY* 5.5 1.6 - - - -
167E GLY 3.4 7.2 - - - -
168E HIS* 3.7 10.8 - - - -
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Residues in contact with LEU 163 (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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224D MET 6.0 0.7 - - - +
227D LEU* 4.4 4.7 - - - -
228D TYR* 3.8 29.2 - - - +
130E PRO* 3.8 26.0 - - + -
135E ARG* 3.5 21.8 - - + +
136E THR* 4.1 11.0 - - + -
137E VAL* 3.6 8.2 - - - +
161E LEU 4.0 2.5 - - - +
162E SER* 1.3 82.8 - - - +
164E GLU* 1.3 70.2 + - - +
165E GLY 3.0 4.2 + - - -
166E GLY* 3.0 12.7 + - - -
167E GLY* 2.8 24.7 + - - +
168E HIS 4.6 0.7 - - - -
169E TYR* 3.8 23.8 - - + -
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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