Contacts of the helix formed by residues 169 - 180 (chain B) in PDB entry 1B70
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 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 4.3 1.1 - - - -
166B ASP 3.5 6.5 + - - +
167B ALA 2.9 6.7 - - - +
168B LEU* 1.3 82.1 - - - +
170B LEU* 1.3 61.6 + - - -
171B LEU 3.1 2.9 - - - -
172B GLY* 2.8 22.2 + - - -
173B LEU* 3.4 5.0 + - - +
254B LEU 3.2 5.2 - - - -
255B GLU 3.1 15.7 - - - -
256B ARG* 4.0 0.4 - - - -
257B ALA* 3.9 11.7 - - - +
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Residues in contact with LEU 170 (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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1B MET* 3.7 21.5 - - + +
2B ARG 4.4 5.8 - - - +
3B VAL* 4.0 16.8 - - + -
4B PRO* 4.3 7.6 - - + -
7B TRP* 3.5 52.9 - - + -
8B LEU* 3.8 17.5 - - + +
11B TYR* 3.9 14.4 - - + -
169B GLY* 1.3 71.4 - - - -
171B LEU* 1.3 57.1 + - - +
173B LEU* 3.2 20.5 + - + +
174B ALA* 2.9 27.5 + - - +
254B LEU* 2.9 19.1 + - + +
255B GLU* 4.4 2.5 - - - +
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Residues in contact with LEU 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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11B TYR* 4.1 23.8 - - + -
170B LEU* 1.3 76.4 - - - +
172B GLY* 1.3 64.0 + - - +
174B ALA* 3.8 16.6 - - + -
175B ARG* 3.2 42.9 + - - +
184B LEU* 4.3 11.2 - - + -
186B GLU* 4.1 25.4 - - + +
187B PRO* 4.1 8.1 - - + -
255B GLU* 2.9 30.1 + - + +
256B ARG* 4.3 24.0 - - + +
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Residues in contact with GLY 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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164B ARG* 5.7 0.9 - - - -
166B ASP* 3.3 35.0 + - - +
167B ALA* 4.9 1.8 - - - -
169B GLY 2.8 7.4 + - - -
171B LEU* 1.3 78.8 - - - +
173B LEU* 1.3 61.5 + - - +
175B ARG* 3.1 33.7 - - - +
176B ASP* 3.4 8.8 + - - +
255B GLU 4.1 0.4 + - - -
256B ARG* 5.6 0.8 - - - +
449B HIS* 6.0 0.4 - - - -
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Residues in contact with LEU 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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1B MET* 4.9 2.0 - - - -
3B VAL* 4.6 17.3 - - + -
8B LEU* 4.6 10.8 - - + -
25B LEU* 4.9 9.9 - - + -
30B PHE* 4.7 17.0 - - + -
158B LEU* 4.0 22.9 - - + -
160B VAL* 5.7 0.9 - - + -
166B ASP 4.7 0.2 + - - -
167B ALA* 4.1 29.5 - - + +
169B GLY 3.4 4.9 + - - +
170B LEU* 3.5 37.9 - - + +
172B GLY* 1.3 71.4 - - - +
174B ALA* 1.3 67.9 + - - +
175B ARG 3.0 1.8 - - - -
176B ASP* 2.7 20.1 + - + +
177B LEU* 3.0 20.7 + - + +
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Residues in contact with ALA 174 (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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8B LEU* 4.1 2.0 - - + +
11B TYR* 3.5 22.4 - - + -
12B VAL* 3.6 18.3 - - + +
170B LEU 2.9 15.6 + - - +
171B LEU* 3.7 8.1 - - + +
173B LEU* 1.3 76.4 - - - +
175B ARG* 1.3 62.8 + - - +
177B LEU* 3.1 4.6 + - - +
178B HIS* 2.9 24.4 + - - +
184B LEU* 3.2 26.0 - - + +
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Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ASP* 5.5 1.6 + - - +
171B LEU* 3.2 34.1 + - - +
172B GLY* 3.1 24.1 + - - +
173B LEU 3.0 0.4 - - - -
174B ALA* 1.3 79.3 - - - +
176B ASP* 1.3 61.8 + - - +
178B HIS* 3.3 12.3 + - + +
179B ALA* 3.2 18.2 + - - +
184B LEU* 4.0 13.6 - - + +
186B GLU* 3.3 25.7 + - - -
256B ARG* 5.9 5.1 - - - +
430B ARG 4.6 6.8 - - - +
431B LEU* 4.6 14.6 - - + +
432B GLY* 6.3 0.7 - - - -
449B HIS* 3.7 45.4 + - + +
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Residues in contact with ASP 176 (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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28B LEU* 3.6 21.2 - - + +
30B PHE* 4.1 7.3 - - + -
164B ARG* 3.2 23.8 + - - -
172B GLY 3.4 5.4 + - - +
173B LEU* 2.7 20.7 + - + +
175B ARG* 1.3 73.5 - - - +
177B LEU* 1.3 60.2 + - - +
178B HIS 3.0 1.8 - - - -
179B ALA* 2.9 27.2 + - - +
180B LEU* 3.3 8.8 + - - +
431B LEU* 3.9 15.0 - - - +
450B ARG* 4.3 1.2 + - - -
465B ARG* 2.2 37.1 + - - -
466B ILE* 4.3 1.1 - - - +
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Residues in contact with LEU 177 (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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8B LEU* 4.0 22.4 - - + -
12B VAL* 3.7 33.4 - - + -
15B LEU* 4.7 6.5 - - + -
21B LEU* 4.3 6.5 - - + -
24B ARG* 4.3 18.4 - - + -
25B LEU* 4.1 23.3 - - + -
28B LEU* 4.1 11.0 - - + -
173B LEU* 3.0 15.4 + - + +
174B ALA* 3.6 5.6 - - - +
176B ASP* 1.3 74.2 - - - +
178B HIS* 1.3 58.9 + - - +
180B LEU* 2.8 30.7 + - + +
182B TYR* 3.3 29.6 + - + -
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Residues in contact with HIS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 5.3 0.6 - - + +
174B ALA 2.9 12.9 + - - +
175B ARG* 3.3 13.9 + - - +
177B LEU* 1.3 78.1 - - - +
179B ALA* 1.3 55.5 + - - +
181B GLY 2.8 8.0 + - - -
182B TYR* 2.9 32.3 - - - +
183B ALA* 4.3 1.7 - - - -
184B LEU* 3.3 39.1 + - + +
430B ARG* 2.3 82.7 + - + -
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Residues in contact with ALA 179 (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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175B ARG 3.2 3.3 + - - +
176B ASP 2.9 14.7 + - - +
178B HIS* 1.3 82.0 - - - +
180B LEU* 1.3 57.6 + - - +
181B GLY 3.3 0.5 + - - -
427B ILE* 5.2 3.1 - - + +
430B ARG* 3.9 25.1 - - + +
431B LEU* 3.5 31.2 - - + -
466B ILE* 3.4 35.7 - - + +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 4.2 31.6 - - + +
28B LEU* 3.9 32.1 - - + -
176B ASP 3.3 6.0 + - - +
177B LEU* 2.8 18.2 + - + +
179B ALA* 1.3 76.7 - - - +
181B GLY* 1.3 56.5 + - - +
182B TYR* 3.7 10.7 - - + -
465B ARG 4.8 1.8 - - - +
466B ILE* 3.8 35.0 - - + +
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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