Contacts of the helix formed by residues 184 - 194 (chain A) in PDB entry 4YET
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 ASN 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ASN* 3.3 22.5 + - - +
80A SER 2.8 20.6 + - - +
81A MET 3.8 15.8 + - - -
82A GLY* 5.0 0.6 - - - -
85A CYS* 4.0 20.2 - - - -
155A LEU* 3.6 6.6 - - - +
182A LEU 3.2 0.6 + - - -
183A VAL* 1.3 73.7 - - - +
185A TRP* 1.3 62.0 + - - +
186A ASP* 3.1 25.7 + - - +
187A PHE* 3.1 19.3 + - - +
188A ALA 3.5 6.8 + - - -
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Residues in contact with TRP 185 (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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85A CYS* 5.2 1.2 - - + +
86A GLY 3.4 15.5 + - - -
87A GLY 3.0 23.7 + - - -
88A GLU 3.3 16.1 + - - -
89A PRO* 3.4 20.0 - - + -
90A THR* 3.8 23.3 - - + +
93A ILE* 3.8 26.9 - - + -
97A ILE* 5.3 2.0 - - + -
104A PHE* 3.7 32.8 - + - -
107A PHE* 4.1 17.3 - + - -
126A LEU* 4.8 1.3 - - + -
155A LEU* 3.8 21.3 - - + -
180A TRP* 4.3 5.6 - + - -
183A VAL* 3.4 28.1 + - + -
184A ASN* 1.3 72.7 + - - +
186A ASP* 1.3 62.3 + - - +
188A ALA* 3.2 5.9 + - + +
189A ASN* 3.0 27.4 + - - -
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Residues in contact with ASP 186 (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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85A CYS* 6.0 0.9 - - - -
90A THR* 4.4 10.2 + - - -
184A ASN* 3.1 14.0 + - - +
185A TRP* 1.3 78.4 - - - +
187A PHE* 1.3 56.3 + - - +
189A ASN* 3.4 9.3 + - - +
190A LYS* 3.0 39.0 + - + +
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Residues in contact with PHE 187 (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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76A PHE* 3.6 38.8 - + - -
79A ASN* 3.2 58.3 - - + +
80A SER* 3.7 10.5 - - - -
154A LEU 3.8 4.9 - - - -
155A LEU* 4.3 0.4 - - + -
184A ASN* 3.1 16.3 + - + +
186A ASP* 1.3 76.8 - - - +
188A ALA* 1.3 64.5 + - - +
190A LYS* 3.2 19.9 + - + +
191A ASN* 2.9 55.2 + - - -
196A PHE* 3.7 25.8 - + - -
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Residues in contact with ALA 188 (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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93A ILE* 4.0 24.5 - - + -
154A LEU* 3.6 20.8 + - + +
155A LEU* 3.7 28.2 - - + +
184A ASN 3.5 2.4 + - - -
185A TRP* 3.2 11.5 + - - +
187A PHE* 1.3 77.0 - - - +
189A ASN* 1.3 59.8 + - - +
191A ASN* 3.2 4.9 + - - +
192A LEU* 3.0 30.5 + - - +
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Residues in contact with ASN 189 (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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90A THR* 3.0 29.9 + - - -
91A GLY* 3.8 4.2 - - - -
92A PRO* 3.4 19.6 - - + +
93A ILE* 2.8 33.4 + - - +
185A TRP 3.0 23.9 + - - +
186A ASP* 3.8 8.7 + - - +
187A PHE 3.2 0.2 - - - -
188A ALA* 1.3 72.7 - - - +
190A LYS* 1.3 63.4 + - - +
192A LEU* 3.2 16.4 + - - +
193A GLU* 3.2 13.2 + - - +
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Residues in contact with LYS 190 (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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186A ASP* 3.0 26.8 + - + +
187A PHE* 3.2 23.1 + - + +
189A ASN* 1.3 74.6 - - - +
191A ASN* 1.3 62.2 + - - +
193A GLU* 3.0 21.4 + - - +
194A ALA* 3.1 14.7 + - - +
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Residues in contact with ASN 191 (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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76A PHE* 3.4 8.6 - - - -
152A ARG* 2.9 30.8 + - - -
153A PRO 3.6 18.2 - - - +
154A LEU* 3.0 31.2 + - + -
187A PHE* 2.9 43.8 + - - -
188A ALA 3.6 5.8 - - - +
190A LYS* 1.3 75.1 - - - +
192A LEU* 1.3 60.5 + - - +
194A ALA 3.3 9.3 - - - +
196A PHE* 3.4 26.8 + - - +
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Residues in contact with LEU 192 (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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92A PRO* 3.8 19.3 - - + +
93A ILE* 3.6 40.2 - - + +
96A LYS* 4.1 26.2 - - + -
128A LEU* 4.1 17.7 - - + +
152A ARG* 3.0 15.5 + - - +
154A LEU* 3.8 26.0 - - + -
188A ALA 3.0 14.2 + - - +
189A ASN* 3.2 14.1 + - - +
191A ASN* 1.3 78.6 - - - +
193A GLU* 1.3 58.3 + - - +
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Residues in contact with GLU 193 (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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152A ARG* 4.2 1.6 + - - -
189A ASN 3.2 8.2 + - - +
190A LYS* 3.0 12.1 + - - +
192A LEU* 1.3 80.0 - - - +
194A ALA* 1.3 64.6 + - + +
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Residues in contact with ALA 194 (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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152A ARG* 4.0 2.2 - - - +
190A LYS 3.1 15.6 + - - +
191A ASN* 3.3 12.5 - - - +
192A LEU 3.3 1.0 - - - -
193A GLU* 1.3 82.6 - - + +
195A PRO* 1.3 80.0 - - + +
196A PHE 3.4 0.2 + - - -
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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