Contacts of the strand formed by residues 173 - 182 (chain N) in PDB entry 2NX5
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 PHE 173 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143N ASP* 4.4 4.9 - - - -
166N LEU* 5.6 0.4 - - + -
167N ASP* 3.6 1.4 - - - -
168N MET* 2.8 60.7 + - + +
171N MET* 3.1 30.4 - - + +
172N ASP* 1.3 77.6 - - - +
174N LYS* 1.3 81.5 + - - +
175N SER* 4.2 7.9 - - - -
143P LYS* 3.8 30.1 - - + -
198P ARG* 3.3 29.6 - - - -
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Residues in contact with LYS 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N GLU* 4.0 17.3 + - - +
82N MET* 3.7 28.0 - - + -
116N PRO* 4.2 27.8 - - + -
117N TYR 6.1 1.6 - - - +
118N ILE* 4.7 11.4 - - + +
165N VAL* 4.8 3.4 - - + -
166N LEU 3.3 11.0 - - - +
167N ASP* 3.2 31.8 + - + +
172N ASP* 4.2 18.8 + - - +
173N PHE* 1.3 92.2 - - - +
175N SER* 1.3 62.9 + - - +
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Residues in contact with SER 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116N PRO* 5.6 0.9 - - - -
118N ILE* 4.9 9.6 - - - -
142N THR* 4.1 2.4 + - - -
143N ASP* 3.4 25.6 + - - -
165N VAL* 3.6 6.7 - - - +
166N LEU* 3.2 50.9 + - - +
173N PHE* 4.2 4.0 - - - -
174N LYS* 1.3 78.3 - - - +
176N ASN* 1.3 68.3 + - - +
198P ARG* 3.2 16.2 + - - -
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Residues in contact with ASN 176 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N PRO* 4.1 4.0 - - - +
118N ILE* 3.5 8.7 - - - +
142N THR* 3.2 3.6 + - - -
143N ASP 2.9 24.5 + - - -
144N PHE* 3.2 44.4 + - + +
145N ASP 3.2 23.8 + - - -
146N SER* 3.2 11.8 + - - +
163N LYS* 4.1 15.5 + - + +
164N CYS 3.5 4.0 - - - +
165N VAL* 3.2 27.2 - - - +
175N SER* 1.3 76.9 + - - +
177N SER* 1.3 63.0 + - - +
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Residues in contact with SER 177 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140N LEU* 3.8 21.3 - - - -
141N PHE 3.3 7.0 - - - -
142N THR* 3.9 9.2 - - - -
144N PHE* 4.5 4.0 - - - -
164N CYS 3.0 29.9 + - - +
166N LEU* 3.7 16.7 - - - +
176N ASN* 1.3 78.0 - - - +
178N ALA* 1.3 60.4 + - - +
145P THR* 6.0 0.9 - - - -
196P ARG* 3.1 33.2 + - - +
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Residues in contact with ALA 178 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140N LEU* 3.4 9.0 - - - +
141N PHE* 2.8 41.6 + - + +
144N PHE* 4.3 2.0 - - + -
150N VAL* 4.2 24.9 - - + -
160N ILE* 4.9 0.2 - - + -
161N THR 3.9 18.2 - - - +
162N ASP 4.1 5.2 - - - +
163N LYS* 4.8 0.2 - - - -
177N SER* 1.3 74.5 - - - +
179N VAL* 1.3 63.4 + - - +
193N PHE* 4.6 5.2 - - + -
196P ARG* 3.6 7.2 - - - +
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Residues in contact with VAL 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138N VAL* 3.7 22.4 - - + -
139N CYS 3.5 3.1 - - - -
140N LEU* 4.2 4.9 - - + -
159N TYR 3.8 0.3 - - - +
160N ILE* 3.4 4.2 - - - +
161N THR* 2.9 40.8 + - - +
178N ALA* 1.3 77.3 - - - +
180N ALA* 1.3 64.3 + - - +
181N TRP* 3.8 23.3 - - + -
193N PHE* 5.1 0.9 - - - -
147P VAL* 3.8 31.4 - - + -
149P LEU* 4.8 0.4 - - + -
194P SER* 3.9 11.2 - - - +
196P ARG* 3.3 26.0 - - - +
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Residues in contact with ALA 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138N VAL* 3.5 0.7 - - - -
139N CYS* 2.6 55.1 + - + +
158N VAL* 5.6 0.4 - - + -
159N TYR 3.0 12.6 - - - +
160N ILE* 3.8 16.2 - - + -
179N VAL* 1.3 76.6 - - - +
181N TRP* 1.3 62.7 + - - +
187N PHE* 4.4 8.5 - - + -
192N ALA* 5.0 4.9 - - + -
193N PHE* 4.0 16.6 - - + -
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Residues in contact with TRP 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N ASP* 4.6 7.6 - - - +
137N SER 3.8 7.2 - - - +
138N VAL* 3.6 18.8 - - + -
159N TYR* 2.9 70.5 + + + -
161N THR* 3.7 25.1 - - + -
179N VAL* 3.8 15.9 - - + -
180N ALA* 1.3 74.8 - - - +
182N SER* 1.3 64.1 + - - +
183N ASN* 4.1 15.0 + - - -
187N PHE* 4.0 8.7 - - - -
149P LEU* 3.6 38.0 - - + +
151P THR* 4.5 7.3 - - + +
180P LEU* 3.7 23.3 - - + -
182P GLU* 5.2 2.9 + - + -
192P ALA* 3.6 26.7 - - + -
193P LEU 4.9 0.2 - - - -
194P SER* 4.5 0.7 - - - -
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Residues in contact with SER 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N ASP* 4.9 5.5 - - - +
136N LYS* 5.6 5.0 - - - +
137N SER 4.8 2.9 + - - +
157N ASP 2.6 24.2 + - - -
158N VAL* 3.5 13.4 - - - +
159N TYR* 4.8 0.7 - - - -
181N TRP* 1.3 79.6 - - - +
183N ASN* 1.3 63.9 + - - +
184N LYS* 3.3 23.6 + - - +
187N PHE* 3.5 40.3 - - - -
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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