Contacts of the helix formed by residues 190 - 200 (chain A) in PDB entry 1TW2
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 GLY 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ASP* 5.3 0.2 - - - -
187A GLY 3.2 9.0 + - - -
188A GLY 3.1 6.3 + - - -
189A LYS* 1.3 78.7 - - - +
191A GLY* 1.3 59.3 + - - +
192A PHE 3.3 2.9 - - - -
193A ALA* 3.1 7.3 + - - +
194A ALA* 2.9 26.7 + - - +
207A VAL* 4.2 22.4 - - - -
220A TYR* 4.5 3.6 - - - -
221A LEU* 3.9 10.0 - - - +
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Residues in contact with GLY 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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163A GLN* 4.0 26.7 - - - +
167A PHE* 3.4 19.2 - - - -
187A GLY 4.2 2.6 + - - -
189A LYS 3.6 3.6 + - - +
190A GLY* 1.3 76.4 - - - +
192A PHE* 1.3 56.8 + - - +
194A ALA* 3.5 3.1 + - - +
195A ALA* 3.1 27.2 + - - +
198A ARG* 4.9 0.9 + - - -
220A TYR* 4.2 10.3 - - - -
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Residues in contact with PHE 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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167A PHE* 3.4 47.5 - + + -
170A PRO* 3.9 22.2 - - + -
171A ALA* 4.4 5.6 - - - -
176A TRP* 5.4 0.2 - + - -
184A ASP* 3.5 13.9 + - - +
187A GLY 5.1 1.9 + - - +
190A GLY 3.3 0.6 - - - -
191A GLY* 1.3 72.8 - - - +
193A ALA* 1.3 67.1 + - - +
195A ALA* 3.1 1.6 + - + -
196A ILE* 3.1 46.2 + - + +
249A ILE* 3.5 29.4 - - + -
251A SER* 3.5 24.9 - - - -
280A LEU* 5.0 9.6 - - + -
282A HIS* 3.8 18.2 - + + -
345A LEU* 5.3 1.6 - - + -
635A SAH 5.8 0.7 - - - +
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Residues in contact with ALA 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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182A VAL* 5.7 1.3 - - + -
184A ASP* 3.8 13.6 + - + +
190A GLY 3.1 9.7 + - - +
192A PHE* 1.3 79.4 - - - +
194A ALA* 1.3 61.3 + - - +
196A ILE* 3.4 9.8 + - - +
197A ALA* 3.0 23.1 + - - +
205A ALA* 4.2 16.1 - - + +
207A VAL* 3.9 25.4 - - + -
230A VAL* 4.1 18.5 - - + +
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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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190A GLY 2.9 16.5 + - - +
191A GLY 3.7 6.1 - - - +
192A PHE 3.2 0.2 - - - -
193A ALA* 1.3 77.5 - - - +
195A ALA* 1.3 60.4 + - - +
197A ALA* 3.4 2.9 + - - +
198A ARG* 3.2 45.9 + - - +
220A TYR* 4.1 19.5 - - + +
221A LEU* 4.3 4.4 - - + +
224A GLU* 4.8 0.4 - - + -
226A LEU* 3.7 24.7 - - + +
230A VAL* 5.5 0.2 - - - -
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Residues in contact with ALA 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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163A GLN 5.8 0.4 - - - +
167A PHE* 3.8 28.7 - - + +
168A ASP* 3.9 18.6 - - - +
171A ALA* 4.2 4.1 - - + +
191A GLY 3.1 16.8 + - - +
192A PHE 3.1 4.4 + - - +
194A ALA* 1.3 73.8 - - - +
196A ILE* 1.3 65.2 + - - +
198A ARG* 3.7 15.6 + - - +
199A ARG* 3.1 24.9 + - - +
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Residues in contact with ILE 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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171A ALA* 4.1 6.5 - - + -
176A TRP* 3.5 57.4 - - + -
182A VAL* 4.1 15.7 - - + -
192A PHE* 3.1 41.1 + - + +
193A ALA* 3.7 6.5 - - - +
195A ALA* 1.3 74.8 - - - +
197A ALA* 1.3 58.2 + - - +
199A ARG* 3.4 5.8 + - - +
200A ALA* 2.9 28.2 + - - +
203A VAL* 4.2 18.4 - - + -
249A ILE* 3.9 15.3 - - + -
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Residues in contact with ALA 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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193A ALA 3.0 17.8 + - - +
194A ALA* 3.5 8.1 - - - +
195A ALA 3.2 0.4 - - - -
196A ILE* 1.3 78.9 - - - +
198A ARG* 1.3 62.0 + - - +
200A ALA 3.2 13.0 + - - +
201A PRO* 3.7 1.9 - - - +
203A VAL* 5.3 4.9 - - + +
205A ALA* 6.3 0.7 - - + -
226A LEU* 4.2 14.1 - - + -
229A ARG* 3.2 43.6 + - - +
230A VAL* 4.7 10.1 - - + -
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Residues in contact with ARG 198 (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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163A GLN 4.7 3.2 + - - -
164A ASP* 3.2 32.1 + - - +
168A ASP* 3.5 16.4 + - - -
191A GLY 4.9 0.4 + - - -
194A ALA* 3.2 36.5 + - - +
195A ALA* 3.9 14.9 - - - +
197A ALA* 1.3 78.9 - - - +
199A ARG* 1.3 60.5 + - - +
200A ALA 3.5 0.4 - - - -
201A PRO* 5.2 3.4 - - - +
220A TYR* 4.1 3.6 + - - -
224A GLU* 3.6 20.8 + - - +
226A LEU* 4.9 9.5 - - + +
229A ARG* 5.0 2.7 - - - +
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Residues in contact with ARG 199 (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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168A ASP 5.8 0.4 - - - -
171A ALA* 4.0 20.5 + - + +
172A ALA* 3.6 34.4 + - - +
174A TYR 5.5 1.2 + - - -
176A TRP* 4.3 12.2 - - + -
195A ALA 3.1 20.3 + - - +
196A ILE* 3.5 7.0 - - - +
198A ARG* 1.3 80.1 - - - +
200A ALA* 1.3 55.7 + - - +
201A PRO* 4.0 5.6 - - - +
3B GLU 4.6 7.0 + - - -
4B PRO* 4.8 3.0 - - - +
5B THR* 3.3 33.7 + - - +
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Residues in contact with ALA 200 (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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176A TRP* 3.7 34.1 - - + -
196A ILE 2.9 13.0 + - - +
197A ALA 3.2 8.7 - - - +
199A ARG* 1.3 79.6 - - - +
201A PRO* 1.3 68.5 - - - +
202A HIS* 3.2 11.2 + - + -
203A VAL* 3.4 20.1 + - + +
229A ARG* 3.2 6.9 + - - -
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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