Contacts of the helix formed by residues 187 - 199 (chain B) in PDB entry 1NTZ
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 THR 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B LYS 3.5 14.1 - - - +
186B VAL* 1.3 74.8 - - - +
188B PRO* 1.3 73.8 - - + +
189B VAL* 3.4 17.4 - - + +
190B GLU* 3.0 46.6 + - - +
191B LEU* 3.2 16.8 + - - +
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Residues in contact with PRO 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE* 3.5 30.3 - - + +
134B ARG* 4.6 24.7 - - + +
137B VAL* 4.1 19.3 - - + -
186B VAL 4.3 0.9 - - - +
187B THR* 1.3 86.2 - - + +
189B VAL* 1.3 66.9 + - + +
191B LEU* 3.3 8.4 + - + +
192B HIS* 3.0 31.4 + - + -
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B THR* 3.4 21.5 - - + +
188B PRO* 1.3 77.7 - - + +
190B GLU* 1.4 52.8 + - + +
192B HIS* 3.3 10.9 + - - +
193B ASP* 2.8 50.5 + - - +
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASN 3.5 14.4 - - - +
62B ASN* 4.1 12.6 + - + +
65B THR* 3.6 16.6 - - + +
182B ARG* 2.7 38.2 + - - -
185B LYS 4.0 0.7 - - - +
186B VAL* 3.3 2.1 - - + +
187B THR* 3.0 44.0 + - - +
189B VAL* 1.4 75.8 - - + +
191B LEU* 1.3 59.9 + - - +
193B ASP* 3.9 7.9 - - - +
194B TYR* 3.0 28.8 + - - +
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B THR* 3.7 32.3 - - + +
68B LEU* 4.1 23.1 - - + -
69B LEU* 3.8 26.9 - - + +
72B ALA* 5.3 3.8 - - + -
132B PHE* 3.7 35.7 - - + -
137B VAL* 3.9 23.3 - - + -
140B LEU* 6.2 0.2 - - + -
186B VAL* 4.4 3.6 - - + -
187B THR 3.2 11.5 + - - +
188B PRO* 3.3 6.5 + - + +
190B GLU* 1.3 72.3 - - - +
192B HIS* 1.3 67.2 + - - +
194B TYR* 3.1 3.1 + - - +
195B VAL* 3.0 27.5 + - - +
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Residues in contact with HIS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PRO 3.8 10.4 + - - -
131B GLU* 3.0 32.6 + - - -
132B PHE* 3.6 23.9 + + + +
188B PRO* 3.0 30.4 + - + -
189B VAL* 3.5 10.5 - - - +
191B LEU* 1.3 77.4 - - - +
193B ASP* 1.3 64.4 + - - +
195B VAL* 3.2 2.8 + - - +
196B GLN* 2.9 45.1 + - - +
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B VAL* 2.8 39.3 + - - +
190B GLU* 3.9 7.9 - - - +
192B HIS* 1.3 73.8 - - - +
194B TYR* 1.3 57.7 + - - +
196B GLN* 3.9 9.7 + - - +
197B ASN* 2.8 42.6 + - - +
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Residues in contact with TYR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ALA* 2.5 34.2 + - + -
54B GLY 2.8 15.1 + - - -
57B TYR* 3.8 10.2 - - - +
58B GLU* 3.9 21.2 - - + +
62B ASN* 4.0 18.4 - - - -
65B THR* 4.1 14.1 - - + -
66B SER* 3.5 15.5 + - - -
69B LEU* 3.8 19.7 - - + -
105B MET* 3.6 13.0 - - + -
190B GLU 3.0 18.7 + - - +
191B LEU* 3.1 5.1 + - - +
193B ASP* 1.3 76.5 - - - +
195B VAL* 1.3 60.6 - - - +
197B ASN* 4.0 1.1 - - - +
198B HIS* 2.8 58.8 + + - +
199B PHE* 4.1 2.0 - + - -
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 4.3 18.6 - - + -
127B THR 4.1 12.8 - - - +
128B THR* 5.5 1.1 - - - -
130B PRO* 4.7 14.6 - - + -
132B PHE* 3.7 26.0 - - + -
191B LEU 3.0 13.7 + - - +
192B HIS* 3.7 6.5 - - - +
194B TYR* 1.3 76.0 - - - +
196B GLN* 1.3 64.3 + - + +
199B PHE* 2.9 56.8 + - + +
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Residues in contact with GLN 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B HIS* 2.9 40.1 + - - +
193B ASP* 4.1 9.7 + - - +
195B VAL* 1.3 81.5 - - + +
197B ASN* 1.3 63.3 + - + +
199B PHE 5.2 0.2 - - - +
200B THR* 3.5 17.2 - - - +
226B ILE* 5.6 3.9 - - - +
228B GLY 4.4 3.3 - - - +
229B GLY* 3.9 4.9 + - - -
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Residues in contact with ASN 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ASP* 2.8 28.2 + - - +
194B TYR* 4.0 0.2 - - - +
196B GLN* 1.3 82.3 - - + +
198B HIS* 1.3 90.5 + - - +
200B THR* 4.2 0.9 - - - -
203B ARG* 3.9 4.2 - - - -
228B GLY 4.9 2.0 - - - +
229B GLY* 3.4 16.1 - - - -
230B LEU* 3.0 36.0 + - + +
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Residues in contact with HIS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ILE* 3.4 12.1 - - - +
52B LYS 4.1 0.2 - - - +
53B ALA* 3.9 19.7 - - + -
57B TYR* 3.5 25.7 + + + +
62B ASN* 5.9 0.4 - - - -
194B TYR* 2.8 59.7 + + - +
197B ASN* 1.3 97.0 + - - +
199B PHE* 1.3 60.7 + - + +
200B THR 3.0 11.2 + - - -
203B ARG* 3.2 42.4 + - - +
230B LEU* 3.6 22.1 - - + +
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Residues in contact with PHE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ILE* 3.3 37.0 - - + -
53B ALA* 3.8 19.3 - - + -
69B LEU* 3.6 32.5 - - + -
105B MET* 4.2 5.6 - - + -
107B TYR* 3.6 25.6 - + - -
126B VAL 5.5 0.7 - - - -
127B THR* 3.5 30.5 - - - +
128B THR* 6.0 0.7 - - - +
194B TYR* 4.1 4.5 - + - -
195B VAL* 2.9 42.6 + - + +
198B HIS* 1.3 79.4 - - + +
200B THR* 1.3 60.4 + - - +
204B MET* 3.7 14.8 - - - +
226B ILE* 3.9 16.6 - - - +
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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