Contacts of the strand formed by residues 152 - 163 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D TYR* 4.1 10.8 - - - +
148D VAL* 3.3 8.6 - - - +
149D ARG 3.0 35.1 + - - +
150D ASP* 4.0 8.7 - - + +
151D GLY* 1.3 82.8 - - - +
153D LEU* 1.3 61.0 + - - +
154D LYS* 4.4 8.1 - - - +
176D THR* 3.9 23.3 - - + -
177D TYR 3.5 10.5 - - - +
178D LYS* 4.2 21.3 - - + -
185D LEU* 4.8 3.1 - - - -
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Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D TYR* 3.6 50.5 + - + -
79D PHE* 3.8 21.5 - - + -
146D LEU* 4.0 13.5 - - + -
147D TYR* 3.4 33.0 - - - +
148D VAL* 4.1 2.7 - - + +
152D VAL* 1.3 75.1 - - - +
154D LYS* 1.3 64.6 + - - +
176D THR* 3.7 2.9 - - - +
177D TYR* 2.7 41.4 + - + +
186D PRO* 3.8 26.9 - - + -
189D HIS* 4.7 2.5 - - + -
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Residues in contact with LYS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D LYS 3.8 0.2 - - - +
146D LEU* 3.1 9.0 - - - +
147D TYR* 2.8 70.9 + - + +
149D ARG* 3.8 40.3 + - + +
150D ASP* 5.9 0.8 - - - +
152D VAL* 4.4 3.8 - - + +
153D LEU* 1.3 76.4 - - - +
155D GLY* 1.3 58.2 + - - +
156D ASP* 4.8 1.6 - - - +
175D THR 3.3 6.7 - - - +
176D THR* 3.2 39.0 + - + +
177D TYR* 4.3 4.5 - - - -
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Residues in contact with GLY 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D GLU* 3.5 22.2 - - - -
145D LYS 3.2 6.7 - - - -
146D LEU* 4.3 1.3 - - - -
154D LYS* 1.3 76.3 - - - +
156D ASP* 1.3 63.9 + - - +
157D VAL* 5.8 0.4 - - - -
173D PHE* 3.9 1.6 - - - +
174D LYS* 3.6 1.4 - - - -
175D THR* 2.8 44.4 + - - -
177D TYR* 4.0 6.1 - - - -
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Residues in contact with ASP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D GLU* 4.3 0.6 - - - +
145D LYS* 2.8 41.5 + - + +
147D TYR* 3.0 36.0 + - + -
154D LYS* 4.8 1.4 - - - +
155D GLY* 1.3 81.2 + - - +
157D VAL* 1.3 63.7 + - - +
173D PHE 3.4 6.7 - - - +
174D LYS* 3.4 31.5 - - + +
175D THR 4.5 1.0 + - - +
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Residues in contact with VAL 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D KZ4 3.5 23.3 - - + -
142D SER* 4.0 19.3 - - - -
143D THR 3.3 27.1 - - - +
144D GLU* 3.7 18.6 - - + -
145D LYS* 5.6 1.3 - - - -
155D GLY 5.7 0.2 - - - +
156D ASP* 1.3 76.9 - - - +
158D ASN* 1.3 75.4 + - - +
159D THR* 3.8 3.7 + - + -
171D CYS 3.8 0.3 - - - +
172D ASP* 3.7 1.0 - - - -
173D PHE* 2.9 50.0 + - + -
145F LYS* 4.8 2.2 - - - +
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Residues in contact with ASN 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D SER* 5.7 0.2 - - - -
157D VAL* 1.3 73.5 - - - +
159D THR* 1.3 60.6 + - - +
170D ARG* 2.5 38.1 - - - +
171D CYS 3.7 0.9 - - - -
172D ASP* 2.5 35.5 + - - +
174D LYS* 5.5 1.7 + - - -
145F LYS* 3.3 35.1 - - + +
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Residues in contact with THR 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D KZ4 4.1 14.0 + - + -
139D TRP* 3.6 24.4 - - + -
140D GLU* 4.0 9.2 + - - +
141D PRO 4.3 3.5 + - - -
142D SER* 3.7 26.9 - - - -
157D VAL* 4.3 3.4 - - - +
158D ASN* 1.3 75.3 - - - +
160D ALA* 1.3 76.3 + - - +
170D ARG* 3.1 9.8 + - - -
171D CYS 2.9 33.9 + - - +
173D PHE* 4.0 15.7 - - + -
145F LYS* 5.4 4.0 - - - -
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D TRP* 3.5 11.8 - - - -
140D GLU* 3.0 31.8 + - + +
159D THR* 1.3 85.9 + - - +
161D LEU* 1.3 58.4 + - - +
168D HIS* 4.0 27.1 - - + -
169D TYR 3.3 13.0 - - - +
170D ARG* 4.2 11.2 - - - +
147F TYR* 6.0 4.7 - - + -
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Residues in contact with LEU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ASP* 3.5 27.4 - - + +
56D ILE* 4.9 4.7 - - + -
95D TYR* 4.1 8.5 - - + +
136D THR* 4.0 19.7 - - + -
138D LYS 3.4 7.9 - - - +
139D TRP* 3.4 64.1 - - + +
160D ALA* 1.3 73.2 - - - +
162D SER* 1.3 67.1 + - - +
163D LEU* 5.1 0.2 - - + -
168D HIS* 3.3 6.8 - - - -
169D TYR* 2.8 58.7 + - + +
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Residues in contact with SER 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D THR* 3.6 4.5 - - - -
137D VAL* 2.7 53.0 + - - +
138D LYS* 2.8 22.5 + - - +
140D GLU* 3.8 21.7 - - - +
160D ALA 4.2 0.4 + - - -
161D LEU* 1.3 74.9 - - - +
163D LEU* 1.3 57.2 + - - +
167D GLY 3.8 1.6 - - - -
168D HIS* 3.7 14.1 - - - -
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Residues in contact with LEU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PRO* 3.8 24.9 - - + -
135D ARG* 3.4 24.9 - - + +
136D THR* 4.2 8.3 - - + -
137D VAL* 3.7 5.7 - - - +
161D LEU 4.3 1.1 - - - +
162D SER* 1.3 82.1 - - - +
164D GLU* 1.3 60.7 + - - +
165D GLY 2.9 10.9 + - - +
166D GLY* 3.0 31.7 + - - +
167D GLY 3.1 10.0 + - - +
168D HIS 4.2 10.5 - - - +
169D TYR* 3.7 33.4 - - + +
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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