Contacts of the helix formed by residues 177 - 191 (chain B) in PDB entry 4ZZ7
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 ASP 177 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU 5.8 0.2 - - - +
86B ILE* 5.4 0.7 - - - +
89B GLU* 3.1 28.0 - - + +
90B HIS* 3.7 21.3 - - + +
148B PHE* 2.5 41.8 - - - +
151B PRO* 3.4 35.2 - - + +
174B SER* 3.5 9.7 + - - +
175B GLU 3.4 0.4 - - - -
176B ARG* 1.3 80.8 - - - +
178B PRO* 1.3 63.6 - - - +
180B SER* 3.6 6.3 + - - +
181B THR* 3.6 1.6 + - - -
324B ILE* 5.0 0.7 - - + -
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Residues in contact with PRO 178 (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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4B ILE* 3.9 11.9 - - + -
22B VAL* 4.0 7.2 - - + -
34B LEU* 3.5 31.4 - - + -
89B GLU* 3.5 9.0 - - - +
173B PRO* 4.9 2.4 - - + +
174B SER 3.9 9.2 - - - +
175B GLU 3.9 4.7 - - - +
176B ARG 3.9 3.4 - - - -
177B ASP* 1.3 89.9 - - - +
179B SER* 1.3 66.3 + - - +
180B SER 3.4 0.4 - - - -
181B THR* 3.3 10.2 + - - +
182B LEU* 3.0 24.8 + - - +
202B ASN* 3.4 28.2 + - - +
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.3 13.6 - - - +
32B LYS* 3.0 22.1 + - - -
85B LEU* 3.6 24.5 - - - +
89B GLU* 2.6 30.4 + - - -
178B PRO* 1.3 79.2 - - - +
180B SER* 1.3 57.0 + - - +
182B LEU* 3.4 5.7 + - - +
183B TYR* 2.9 31.1 + - - +
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Residues in contact with SER 180 (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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82B ILE* 4.3 3.1 - - - -
85B LEU* 3.9 11.5 - - - +
86B ILE* 3.6 39.1 - - - +
89B GLU* 4.1 1.9 + - - -
151B PRO* 3.5 26.3 - - - +
152B VAL* 4.0 8.0 - - - +
177B ASP* 3.6 5.7 + - - +
179B SER* 1.3 78.1 - - - +
181B THR* 1.3 63.9 + - - +
183B TYR* 3.4 6.0 + - - +
184B ILE* 3.2 28.1 + - - +
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Residues in contact with THR 181 (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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151B PRO* 2.8 28.6 + - - +
155B PRO* 3.8 11.4 - - + -
171B LEU* 3.8 29.3 - - + +
173B PRO* 3.8 22.7 - - + +
177B ASP 3.6 16.5 + - - -
178B PRO* 3.6 7.8 + - - +
179B SER 3.3 0.4 - - - -
180B SER* 1.3 78.0 + - - +
182B LEU* 1.3 61.3 + - - +
184B ILE* 3.2 23.7 - - + +
185B ALA* 3.2 10.2 + - - +
200B VAL* 4.7 1.6 - - + +
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Residues in contact with LEU 182 (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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4B ILE* 3.9 24.9 - - + -
5B GLY 3.9 13.5 - - - +
6B HIS 4.4 0.2 - - - -
7B LEU* 3.6 36.3 - - + +
12B LEU* 4.0 19.5 - - + -
178B PRO 3.0 17.5 + - - +
179B SER* 3.9 4.0 - - - +
181B THR* 1.3 76.5 - - - +
183B TYR* 1.3 62.4 + - - +
185B ALA* 3.3 3.4 + - - -
186B GLN* 3.0 33.7 + - + +
200B VAL* 3.8 22.8 - - + +
202B ASN* 4.8 2.9 - - - +
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Residues in contact with TYR 183 (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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78B HIS* 2.8 38.4 + + + +
81B GLU* 3.6 21.0 + - + +
82B ILE* 3.6 31.9 - - + -
85B LEU* 3.7 23.8 - - + -
179B SER 2.9 18.6 + - - +
180B SER* 3.5 6.1 - - - +
182B LEU* 1.3 77.1 - - - +
184B ILE* 1.3 60.7 + - - +
186B GLN* 3.3 25.8 + - + +
187B LEU* 3.5 25.5 + - + +
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Residues in contact with ILE 184 (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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71B PHE* 3.3 24.9 - - + -
75B LEU* 3.9 22.9 - - + -
82B ILE* 4.0 30.7 - - + -
152B VAL* 4.1 33.9 - - + +
155B PRO* 5.0 2.9 - - + -
156B LEU* 4.2 18.2 - - + -
159B PHE* 4.2 16.2 - - + -
180B SER 3.2 12.3 + - - +
181B THR* 3.2 16.4 - - - +
183B TYR* 1.3 73.3 - - - +
185B ALA* 1.3 68.0 + - - +
186B GLN 3.2 0.4 - - - -
187B LEU* 3.3 12.5 + - - +
188B LEU 3.8 0.5 + - - -
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Residues in contact with ALA 185 (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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7B LEU* 3.4 12.4 - - + +
159B PHE* 5.0 3.6 - - + -
171B LEU* 5.8 0.2 - - + -
181B THR 3.2 8.1 + - - +
182B LEU 3.3 4.0 + - - +
184B ILE* 1.3 82.5 - - + +
186B GLN* 1.3 61.8 + - - +
188B LEU* 3.3 18.1 - - - +
189B GLN* 3.2 15.6 - - - +
198B MET* 4.3 16.9 - - + +
200B VAL* 3.5 32.8 - - + -
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Residues in contact with GLN 186 (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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7B LEU* 4.5 17.9 - - + +
12B LEU* 3.1 41.3 - - + +
182B LEU* 3.0 28.2 + - + +
183B TYR* 3.6 21.8 - - - +
184B ILE 3.2 0.6 - - - -
185B ALA* 1.3 75.2 - - - +
187B LEU* 1.3 61.9 + - + +
188B LEU 3.1 5.4 + - - -
189B GLN* 3.5 21.0 + - - +
190B GLU* 4.1 3.8 + - - +
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Residues in contact with LEU 187 (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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71B PHE* 3.9 9.2 - - + -
74B LEU* 3.4 24.3 - - + +
75B LEU* 4.1 18.4 - - + -
78B HIS* 3.7 41.1 - - + +
82B ILE* 4.5 1.6 - - + -
183B TYR* 3.5 30.5 - - + +
184B ILE* 3.3 22.7 - - - +
186B GLN* 1.3 76.3 - - + +
188B LEU* 1.3 63.0 + - - +
189B GLN 3.3 0.2 - - - -
190B GLU* 3.3 18.3 + - - +
191B ALA* 3.1 17.0 + - - +
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Residues in contact with LEU 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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67B VAL* 4.5 10.8 - - + -
68B MET* 4.7 6.1 - - - -
71B PHE* 3.3 44.4 - - + -
159B PHE* 3.8 18.2 - - + -
163B ILE* 4.1 6.7 - - + -
184B ILE 3.8 2.6 + - - +
185B ALA* 3.3 15.3 - - - +
186B GLN 3.1 0.4 - - - -
187B LEU* 1.3 77.4 - - - +
189B GLN* 1.3 67.3 + - - +
191B ALA* 3.3 11.2 + - + +
193B LEU* 3.1 54.5 + - + +
198B MET* 3.7 22.7 - - + -
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Residues in contact with GLN 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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7B LEU* 3.8 11.5 - - - +
10B GLY* 3.8 29.1 - - - +
185B ALA 3.2 18.5 - - - +
186B GLN* 3.5 9.7 + - - +
187B LEU 3.3 0.6 - - - -
188B LEU* 1.3 76.7 - - - +
190B GLU* 1.3 58.7 + - - +
192B GLY* 2.9 22.3 + - - -
193B LEU* 3.7 17.6 + - - +
194B PRO 4.0 17.4 + - - -
195B ASP* 3.9 18.8 - - - +
198B MET* 4.2 17.2 + - - +
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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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70B ARG* 5.2 2.3 - - - -
74B LEU* 3.8 24.7 - - + +
77B GLN* 5.5 0.5 - - - +
78B HIS* 4.8 4.8 + - - -
186B GLN 4.1 3.0 + - - +
187B LEU* 3.3 29.1 + - - +
189B GLN* 1.3 80.0 - - - +
191B ALA* 1.3 57.6 - - - +
192B GLY* 3.1 1.7 + - - -
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Residues in contact with ALA 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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67B VAL* 3.7 27.3 - - + +
70B ARG* 2.6 47.3 + - + +
71B PHE* 3.9 16.6 - - + +
74B LEU* 4.0 6.9 - - + +
187B LEU 3.1 11.2 + - - +
188B LEU* 3.4 15.0 - - - +
189B GLN 3.1 1.0 - - - -
190B GLU* 1.3 76.4 - - - +
192B GLY* 1.3 52.3 + - - +
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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