Contacts of the helix formed by residues 187 - 197 (chain A) in PDB entry 3ESF
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLU* 3.0 33.8 + - - +
82A SER 2.9 16.2 + - - -
83A MET 3.7 15.6 + - - +
84A SER* 3.8 17.2 - - - -
87A GLY* 4.6 1.5 - - - -
158A LEU* 3.6 11.9 - - - +
185A VAL 3.1 0.6 + - - -
186A VAL* 1.3 71.0 - - - +
188A TRP* 1.3 57.0 + - - +
189A ASP* 3.3 25.8 + - - +
190A HIS* 3.5 12.8 - - - +
191A ALA 3.2 20.1 + - - -
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Residues in contact with TRP 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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87A GLY* 5.5 0.8 - - - -
88A GLY 3.3 19.0 + - - -
89A GLY 2.9 20.2 + - - -
90A GLU 3.6 12.8 - - - -
91A PRO* 3.6 36.5 - - + +
95A LEU* 3.9 13.4 - - + +
99A ILE* 4.2 10.8 - - + -
106A PHE* 3.5 35.7 - + - -
109A PHE* 3.8 15.7 - + - -
128A LEU* 4.8 1.3 - - + -
158A LEU* 3.5 26.0 - - + -
183A TRP* 4.3 2.9 - + - -
186A VAL* 3.5 30.8 + - + +
187A ASN* 1.3 68.8 + - - +
189A ASP* 1.3 64.0 + - - +
191A ALA* 3.8 6.5 - - + +
192A GLU* 2.9 32.4 + - - +
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Residues in contact with ASP 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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187A ASN* 3.3 13.8 + - - +
188A TRP* 1.3 80.0 + - - +
190A HIS* 1.3 61.4 + - - +
192A GLU* 3.7 7.2 - - - +
193A ASN* 3.1 33.2 + - - +
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Residues in contact with HIS 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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78A PHE* 3.6 39.8 - + - -
81A GLU* 3.2 57.1 + - + +
82A SER* 4.0 10.5 + - - -
157A ILE 3.7 8.3 + - - -
158A LEU* 4.5 1.2 - - - +
187A ASN* 3.5 15.1 + - - +
188A TRP 3.4 0.2 - - - -
189A ASP* 1.3 75.3 - - - +
191A ALA* 1.3 60.2 + - - +
193A ASN* 3.4 5.9 + - - +
194A GLN* 3.0 63.8 + - + +
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Residues in contact with ALA 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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95A LEU* 3.6 21.1 - - + -
157A ILE* 3.6 28.0 - - + +
158A LEU* 3.7 16.2 - - + -
187A ASN 3.2 15.1 + - - +
188A TRP* 3.8 9.6 - - + +
190A HIS* 1.3 79.7 - - - +
192A GLU* 1.3 56.4 + - - +
194A GLN* 3.3 3.1 + - - +
195A PHE* 2.9 30.0 + - - +
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Residues in contact with GLU 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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91A PRO* 6.5 0.2 - - + -
92A SER* 3.4 25.5 + - - +
93A GLY* 4.5 1.6 - - - -
94A LYS* 4.4 12.8 + - + +
95A LEU* 3.8 21.4 - - + +
188A TRP 2.9 21.6 + - - +
189A ASP* 3.7 7.5 - - - +
191A ALA* 1.3 74.4 - - - +
193A ASN* 1.3 63.8 + - - +
195A PHE* 3.3 5.8 + - + +
196A THR* 3.0 38.3 + - - +
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Residues in contact with ASN 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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189A ASP* 3.1 19.7 + - - +
190A HIS* 3.8 5.9 - - - +
191A ALA 3.4 0.2 - - - -
192A GLU* 1.3 83.3 - - - +
194A GLN* 1.3 74.8 + - - +
196A THR* 4.0 10.4 - - - +
197A ARG 3.0 25.8 + - - -
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Residues in contact with GLN 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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78A PHE* 3.8 14.9 - - + -
155A LYS* 3.0 26.4 + - + +
156A PRO 3.7 15.9 - - - +
157A ILE* 3.7 14.8 - - + +
190A HIS* 3.0 57.9 + - + +
191A ALA 3.5 6.5 - - - +
193A ASN* 1.3 82.7 - - - +
195A PHE* 1.3 58.5 + - - +
196A THR 3.4 0.2 + - - -
197A ARG 3.5 13.1 + - - +
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Residues in contact with PHE 195 (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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94A LYS* 3.7 30.3 - - + -
95A LEU* 3.7 27.4 - - + -
98A ALA* 3.3 28.3 - - + -
130A GLN* 3.6 29.6 + - - +
135A LYS 4.9 2.2 - - - -
137A LEU* 3.9 22.2 - - + -
155A LYS* 2.9 18.3 + - - +
157A ILE* 3.5 10.5 - - + +
191A ALA 2.9 17.0 + - - +
192A GLU* 3.5 6.5 - - + +
193A ASN 3.3 0.2 - - - -
194A GLN* 1.3 77.0 - - - +
196A THR* 1.3 61.7 + - - +
197A ARG* 4.3 0.7 + - - -
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Residues in contact with THR 196 (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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94A LYS* 3.9 24.1 + - - +
192A GLU* 3.0 21.1 + - - +
193A ASN* 4.0 11.0 - - - +
195A PHE* 1.3 81.8 - - - +
197A ARG* 1.3 74.1 + - + +
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Residues in contact with ARG 197 (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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135A LYS* 5.0 11.3 - - - +
155A LYS* 2.9 39.1 + - - +
193A ASN 3.0 18.8 + - - -
194A GLN* 3.7 15.5 - - - +
195A PHE 3.5 0.8 + - - -
196A THR* 1.3 89.5 + - + +
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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