Contacts of the helix formed by residues 164 - 173 (chain B) in PDB entry 1T8U
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 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B GLY* 1.3 79.3 - - - +
165B THR* 1.3 65.3 + - - +
166B ARG 3.4 2.2 - - - -
167B ALA* 3.6 3.2 + - - -
168B LEU* 3.2 20.3 + - - +
241B VAL* 4.0 5.9 - - - +
315B LEU* 3.5 13.0 - - - +
603B A3P 3.1 38.0 + - - -
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Residues in contact with THR 165 (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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157B ILE* 3.9 15.0 - - + +
159B GLY* 3.5 24.7 - - - +
160B VAL 3.5 23.1 - - - +
164B GLY* 1.3 75.8 - - - +
166B ARG* 1.3 61.6 + - - +
168B LEU* 3.6 1.9 + - - +
169B LEU* 3.2 23.7 + - - +
215B LYS* 3.1 34.6 + - + +
217B PRO* 3.4 12.8 - - + +
241B VAL* 4.4 9.9 - - + -
603B A3P 2.6 19.3 + - - -
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Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B THR* 1.3 78.2 + - - +
167B ALA* 1.3 67.5 + - - +
169B LEU* 3.2 17.5 + - - +
170B GLU* 2.9 57.3 + - + +
173B ARG* 4.5 1.6 - - - +
182B GLY 3.0 29.0 + - - -
183B ALA* 4.4 3.4 - - - +
184B GLU* 4.3 9.7 - - - +
215B LYS* 3.5 19.5 - - - +
364B LEU* 4.2 13.2 - - + -
368B LYS* 3.7 15.5 - - + -
603B A3P 3.2 16.1 + - - +
4C UAP 2.5 39.9 + - - +
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Residues in contact with ALA 167 (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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164B GLY* 3.6 9.7 + - - +
166B ARG* 1.3 80.2 - - - +
168B LEU* 1.3 63.2 + - - +
170B GLU* 3.3 1.0 + - - -
171B PHE* 3.0 44.7 + - + -
315B LEU* 4.2 2.2 - - + -
364B LEU* 3.7 23.8 - - + +
603B A3P 3.5 34.2 + - + +
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Residues in contact with LEU 168 (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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157B ILE* 3.7 15.9 - - + -
164B GLY 3.2 15.7 + - - +
165B THR 3.9 4.0 - - - +
167B ALA* 1.3 79.7 - - - +
169B LEU* 1.3 57.6 + - - +
171B PHE* 3.3 4.3 + - - +
172B LEU* 2.9 38.0 + - + +
239B ILE* 3.7 26.7 - - + -
241B VAL* 3.4 26.5 - - + -
310B VAL* 4.3 9.4 - - + -
315B LEU* 4.0 13.6 - - + +
323B LEU* 4.3 16.2 - - + -
326B VAL* 4.1 21.3 - - + -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 4.1 19.9 - - + +
165B THR 3.2 15.4 + - - +
166B ARG* 3.8 22.9 - - - +
168B LEU* 1.3 79.1 - - - +
170B GLU* 1.3 65.0 + - - +
172B LEU* 3.2 8.3 + - + +
173B ARG* 3.0 37.4 + - + +
178B VAL* 5.6 0.4 - - + -
180B ALA* 3.8 22.4 - - + -
181B VAL 3.9 18.2 - - - +
182B GLY 4.9 0.2 - - - +
183B ALA 6.0 0.4 - - - +
213B MET* 4.6 17.0 - - + -
214B GLU 5.0 1.8 - - - -
215B LYS* 3.6 29.2 - - + +
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ARG* 2.9 52.7 + - + +
167B ALA 3.8 2.9 - - - +
169B LEU* 1.3 76.2 - - - +
171B PHE* 1.3 68.1 + - + +
173B ARG* 3.1 47.8 + - - +
174B VAL* 3.9 3.5 - - - +
352B LEU* 3.6 18.6 - - + +
355B ALA* 5.9 1.6 - - - +
356B GLU* 5.4 3.3 + - - +
362B HIS* 4.7 15.0 + - + +
364B LEU* 4.2 17.5 - - + -
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Residues in contact with PHE 171 (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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167B ALA* 3.0 38.6 + - + +
168B LEU* 3.6 3.6 - - - +
170B GLU* 1.3 77.4 - - + +
172B LEU* 1.3 67.2 + - - +
174B VAL* 3.2 13.5 + - - +
315B LEU* 4.0 28.5 - - + -
319B PRO* 4.2 6.3 - - + -
323B LEU* 4.1 14.8 - - + -
336B ILE* 3.0 18.3 - - - +
341B PHE* 3.6 41.1 - + + -
350B PRO* 4.7 5.2 - - + -
351B CYS* 5.1 1.6 - - - -
352B LEU* 3.7 28.5 - - + -
362B HIS 6.0 0.2 - - - -
364B LEU* 5.6 5.6 - - + -
603B A3P 3.8 25.8 - - - -
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Residues in contact with LEU 172 (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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157B ILE* 4.5 4.7 - - + -
168B LEU* 2.9 31.3 + - + +
169B LEU* 3.6 7.4 - - + +
171B PHE* 1.3 78.1 - - - +
173B ARG* 1.3 56.5 + - - +
174B VAL 3.0 0.2 - - - -
175B HIS* 2.9 30.5 + - + +
178B VAL* 3.6 15.4 - - + +
213B MET* 3.7 33.7 - - + -
239B ILE* 4.8 0.9 - - + -
323B LEU* 3.7 20.8 - - + +
326B VAL* 3.8 27.1 - - + -
327B GLN* 4.8 8.3 - - + -
330B LEU* 4.1 9.2 - - + -
332B LEU* 4.9 6.7 - - + -
336B ILE* 3.8 6.7 - - + -
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Residues in contact with ARG 173 (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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354A LYS* 2.7 27.2 + - - -
359A SER* 5.3 4.2 - - - -
166B ARG* 4.5 2.0 - - - +
169B LEU* 3.0 30.6 + - + +
170B GLU* 3.1 41.3 + - - +
171B PHE 3.2 0.8 - - - -
172B LEU* 1.3 75.3 - - - +
174B VAL* 1.3 56.3 + - - +
175B HIS 3.1 0.2 - - - -
178B VAL* 4.2 9.4 - - + +
179B ARG* 5.3 3.0 - - - +
180B ALA* 3.9 38.5 + - + +
181B VAL 4.6 1.0 + - - -
182B GLY* 3.8 24.4 - - - +
356B GLU* 2.8 47.9 + - + +
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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