Contacts of the strand formed by residues 171 - 180 (chain A) in PDB entry 2HNK
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 LEU 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A SER* 3.4 8.6 - - - -
148A ILE 3.3 15.5 - - - +
149A ASP 3.5 21.5 - - - +
151A PHE* 3.6 21.8 - - + -
167A ILE* 2.8 41.0 + - + +
168A LEU* 4.7 6.3 - - + -
169A LYS 3.4 0.4 - - - -
170A LEU* 1.3 74.0 - - - +
172A LYS* 1.3 62.4 + - - +
175A GLY 4.0 9.9 - - - +
176A LEU 3.7 25.8 - - - +
177A LEU* 4.0 4.9 - - + +
228A VAL 4.9 1.1 - - - +
230A LYS* 2.7 46.4 + - + +
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Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ARG* 6.1 1.2 - - - +
146A SER* 3.4 24.5 - - - +
147A SER* 4.0 17.3 - - - +
148A ILE 2.9 17.3 + - - +
149A ASP* 2.9 28.8 + - - +
170A LEU 3.6 0.4 + - - -
171A LEU* 1.3 76.3 - - - +
173A PRO* 1.4 80.3 - - + +
174A GLY 3.4 0.2 + - - -
175A GLY* 3.0 17.6 + - - +
230A LYS* 3.4 8.7 - - - +
3001A PEG 3.5 28.9 + - - -
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Residues in contact with PRO 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A SER* 3.4 15.3 - - - +
171A LEU 4.5 0.4 - - - +
172A LYS* 1.4 92.4 - - + +
174A GLY* 1.3 60.2 - - - +
175A GLY 3.4 0.2 + - - -
230A LYS* 4.2 9.8 - - + +
231A ARG 4.0 16.2 - - - +
232A LEU* 3.8 23.5 - - + +
233A GLU* 4.0 27.6 - - + +
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Residues in contact with GLY 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PRO* 1.3 71.8 - - - +
175A GLY* 1.3 63.5 + - - +
176A LEU* 5.2 1.4 - - - +
229A ARG* 3.8 33.0 + - - +
230A LYS 2.6 21.5 + - - -
231A ARG 4.2 0.2 + - - -
232A LEU* 3.8 8.2 - - - +
58C ILE* 5.7 2.9 - - - +
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ILE 4.8 0.2 - - - -
149A ASP* 3.3 17.0 - - - -
171A LEU* 4.0 11.3 - - - +
172A LYS* 3.0 20.0 + - - +
173A PRO 3.2 1.8 + - - -
174A GLY* 1.3 80.8 - - - +
176A LEU* 1.3 60.1 + - - -
228A VAL 4.1 0.2 - - - +
229A ARG* 3.5 2.8 - - - -
230A LYS* 2.9 26.9 + - - +
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 4.8 9.2 - - + -
59A SER* 4.7 7.9 - - - -
149A ASP 2.9 12.4 + - - +
150A LEU* 3.1 19.8 - - + +
151A PHE 2.8 24.8 + - - +
171A LEU* 3.7 6.3 - - - +
174A GLY 5.2 1.8 - - - +
175A GLY* 1.3 73.3 - - - -
177A LEU* 1.3 73.6 + - - +
178A ILE* 3.9 28.9 - - + -
227A LEU* 4.2 7.9 - - + -
228A VAL 3.6 20.4 - - - +
229A ARG* 4.3 2.9 - - + +
58C ILE* 3.8 45.8 - - + -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A PHE* 3.6 18.6 - - + -
153A LEU* 3.8 20.2 - - + -
164A TYR* 4.2 15.9 - - + -
167A ILE* 4.0 26.0 - - + -
168A LEU* 5.9 1.1 - - + -
171A LEU* 4.0 4.6 - - + +
176A LEU* 1.3 74.4 - - - +
178A ILE* 1.3 82.7 + - - +
179A ALA* 4.3 2.2 - - + +
204A PHE* 3.8 33.2 - - + -
226A SER 3.4 2.6 - - - +
227A LEU* 3.6 1.9 - - - -
228A VAL* 2.6 58.1 + - + +
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Residues in contact with ILE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.7 27.4 - - + +
55A LEU* 3.9 27.6 - - + -
78A PHE* 4.6 4.9 - - + -
150A LEU* 4.1 19.5 - - + -
151A PHE 2.7 14.1 + - - +
152A PHE* 3.3 14.2 - - + -
153A LEU 2.8 25.6 + - - -
176A LEU* 3.9 24.2 - - + -
177A LEU* 1.3 76.8 - - - +
179A ALA* 1.3 58.0 + - - +
225A VAL* 3.5 28.3 - - + -
226A SER 3.4 2.7 - - - -
227A LEU* 3.9 10.3 - - + -
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.8 15.9 - - + -
160A TYR* 4.7 2.2 - - + -
177A LEU* 4.0 5.1 - - + -
178A ILE* 1.3 74.1 - - - +
180A ASP* 1.3 62.3 + - - +
182A VAL* 3.6 10.1 - - + +
204A PHE* 3.6 36.6 - - + -
225A VAL* 3.3 8.0 - - - -
226A SER* 2.8 41.3 + - - +
228A VAL* 5.3 0.2 - - + -
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ILE* 4.1 10.6 - - - +
48A GLU* 2.6 32.7 - - - +
152A PHE* 3.9 11.7 - - + -
153A LEU 2.9 12.8 + - - +
154A ASP* 3.2 27.2 - - - +
160A TYR* 2.7 29.1 + - - -
178A ILE 4.1 0.8 + - - -
179A ALA* 1.3 72.6 - - - +
181A ASN* 1.3 85.5 + - - +
182A VAL 3.3 1.5 + - - -
222A ALA* 4.9 2.4 - - - +
223A ASP* 5.4 0.8 + - - -
224A GLY 3.9 1.6 - - - +
225A VAL* 3.8 8.9 - - - +
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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