Contacts of the helix formed by residues 187 - 197 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D GLU* 3.0 33.5 + - - +
82D SER* 2.8 17.8 + - - +
83D MET 3.7 14.7 + - - +
84D SER* 3.8 15.9 - - - -
87D GLY* 4.6 2.3 - - - -
158D LEU* 5.2 0.5 - - - +
185D VAL 3.2 0.9 + - - -
186D VAL* 1.3 71.5 - - - +
188D TRP* 1.3 58.3 + - - +
189D ASP* 3.2 23.5 + - - +
190D HIS* 3.4 18.1 + - - +
191D ALA* 3.1 25.0 + - - +
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Residues in contact with TRP 188 (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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87D GLY* 5.4 0.8 - - - -
88D GLY 3.3 18.4 + - - -
89D GLY 2.9 19.0 + - - -
90D GLU 3.6 12.7 - - - -
91D PRO* 3.6 27.4 - - + -
95D LEU* 4.1 5.2 - - + -
99D ILE* 4.2 10.5 - - + -
106D PHE* 3.6 25.6 - + - -
109D PHE* 3.9 24.2 - + - -
128D LEU* 4.9 2.2 - - + -
158D LEU* 3.5 26.5 - - + -
183D TRP* 4.3 3.6 - + - -
186D VAL* 3.4 30.3 + - + +
187D ASN* 1.3 70.9 + - - +
189D ASP* 1.3 62.1 + - - +
191D ALA* 3.7 13.6 - - + +
192D GLU* 2.8 51.1 + - - +
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Residues in contact with ASP 189 (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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86D ASN* 6.2 0.2 - - - +
187D ASN* 3.2 12.8 + - - +
188D TRP* 1.3 78.3 - - - +
190D HIS* 1.3 60.8 + - - +
192D GLU* 3.7 16.1 - - - +
193D ASN* 2.9 37.2 + - - +
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Residues in contact with HIS 190 (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 PHE* 3.3 34.8 + + - -
81D GLU* 3.2 51.9 + - + +
82D SER* 3.8 16.1 + - - -
157D ILE 3.5 13.7 - - - -
158D LEU* 5.0 0.9 - - + -
187D ASN* 3.4 16.3 + - - +
189D ASP* 1.3 76.3 - - - +
191D ALA* 1.3 57.6 + - + +
193D ASN* 3.3 9.6 + - - +
194D GLN* 2.9 61.7 + - - +
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Residues in contact with ALA 191 (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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95D LEU* 3.6 20.2 - - + -
157D ILE* 3.6 30.4 - - + +
158D LEU* 4.1 8.3 - - + -
187D ASN 3.1 14.4 + - - +
188D TRP* 3.7 15.7 - - + +
190D HIS* 1.3 79.8 - - + +
192D GLU* 1.3 55.4 + - - +
194D GLN* 3.2 3.5 + - - +
195D PHE* 2.9 30.0 + - - +
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Residues in contact with GLU 192 (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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91D PRO* 3.6 9.5 - - - +
92D SER* 3.3 39.3 + - - +
94D LYS 5.9 0.2 - - - +
95D LEU* 3.8 26.9 - - + +
188D TRP* 2.8 30.7 + - - +
189D ASP* 3.7 18.3 - - - +
191D ALA* 1.3 71.4 - - - +
193D ASN* 1.3 59.0 + - - +
195D PHE* 3.4 4.9 + - - +
196D THR* 3.0 37.3 + - + +
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Residues in contact with ASN 193 (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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189D ASP* 2.9 28.0 + - - +
190D HIS* 3.7 6.6 - - - +
192D GLU* 1.3 74.3 - - - +
194D GLN* 1.3 73.2 + - - +
196D THR* 3.5 7.8 + - - -
197D ARG 3.1 25.6 + - - -
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Residues in contact with GLN 194 (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 PHE* 3.7 18.7 - - + -
155D LYS* 3.0 26.6 + - + +
156D PRO 3.6 17.4 - - - +
157D ILE* 3.8 10.1 - - - +
190D HIS* 2.9 57.2 + - + +
191D ALA 3.6 6.3 - - - +
193D ASN* 1.3 84.9 - - - +
195D PHE* 1.3 59.0 - - - +
196D THR 3.5 0.2 + - - -
197D ARG* 3.6 12.5 + - - +
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Residues in contact with PHE 195 (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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94D LYS* 3.8 25.4 - - + -
95D LEU* 3.8 27.8 - - + -
98D ALA* 3.4 25.4 - - + -
130D GLN* 3.7 32.3 + - - +
135D LYS 4.7 2.2 - - - -
137D LEU* 4.0 22.0 - - + -
155D LYS* 3.0 17.3 + - - +
157D ILE* 3.7 10.0 - - + +
191D ALA 2.9 17.5 + - - +
192D GLU* 3.5 5.4 - - - +
193D ASN 3.3 0.2 - - - -
194D GLN* 1.3 76.1 - - - +
196D THR* 1.3 70.0 + - + +
197D ARG* 5.2 0.2 - - - +
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Residues in contact with THR 196 (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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94D LYS* 4.1 29.2 - - + +
192D GLU* 3.0 18.5 + - + +
193D ASN* 3.5 11.3 + - - -
195D PHE* 1.3 87.5 - - + +
197D ARG* 1.3 71.9 + - - +
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Residues in contact with ARG 197 (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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155D LYS* 4.0 19.1 + - - +
193D ASN 3.1 17.9 + - - -
194D GLN* 3.6 18.3 - - - +
195D PHE 5.2 0.2 - - - +
196D THR* 1.3 85.2 + - - +
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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