Contacts of the helix formed by residues 183 - 197 (chain B) in PDB entry 1RYF
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 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B LEU* 5.6 0.7 - - - +
175B GLU 3.8 14.9 - - - +
176B CYS* 3.7 5.0 - - - +
181B GLN 3.3 1.4 + - - -
182B ARG* 1.3 75.3 - - - +
184B LEU* 1.3 63.5 + - - +
185B LYS 3.6 1.3 - - - -
186B THR* 3.5 20.8 + - - -
187B VAL* 3.5 16.5 + - - +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.2 45.3 - - + +
22B SER* 3.5 26.5 - - - +
23B TYR* 3.6 28.9 - - + +
176B CYS* 4.1 8.1 - - - -
177B SER 4.5 1.6 - - - +
178B ALA* 4.5 8.1 - - - -
181B GLN* 3.3 35.9 + - + +
182B ARG 3.1 2.4 - - - -
183B GLY* 1.3 74.1 - - - +
185B LYS* 1.3 69.3 + - + +
186B THR 3.3 0.5 + - - -
187B VAL* 3.3 12.4 + - - +
188B PHE* 3.3 20.9 - - + -
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Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 4.1 29.1 + - + -
26B ASN* 3.8 21.7 + - - +
181B GLN* 4.8 3.5 + - - +
183B GLY 3.6 0.4 - - - -
184B LEU* 1.3 77.5 - - + +
186B THR* 1.3 58.2 + - - +
188B PHE* 3.1 5.7 + - - +
189B ASP* 3.0 38.0 + - - +
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Residues in contact with THR 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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174B LEU* 3.8 25.4 - - + -
183B GLY* 3.5 16.3 + - - -
184B LEU 3.2 0.8 - - - -
185B LYS* 1.3 74.6 - - - +
187B VAL* 1.3 68.2 + - - +
189B ASP* 4.3 9.1 + - + -
190B GLU* 2.8 37.3 + - + +
193B ARG* 5.9 1.3 - - - +
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.9 2.7 - - + -
98B LEU* 3.9 30.8 - - + +
130B ILE* 4.8 2.4 - - + +
132B VAL* 4.0 22.7 - - + -
174B LEU* 3.7 22.8 - - + +
176B CYS* 4.0 24.9 - - + -
183B GLY 3.5 14.5 + - - +
184B LEU 3.4 9.6 - - - +
186B THR* 1.3 78.1 - - - +
188B PHE* 1.3 68.8 + - + +
190B GLU* 3.9 1.9 - - - +
191B ALA* 3.0 25.5 + - - +
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B CYS* 5.3 0.4 - - - -
19B LEU* 3.9 16.4 - - + -
20B LEU* 3.9 18.6 - - + -
23B TYR* 3.4 58.6 - + + +
53B LEU* 3.9 10.0 - - + +
55B LEU* 3.6 33.4 - - + -
98B LEU* 3.8 16.6 - - + -
184B LEU* 3.3 28.5 - - + -
185B LYS 3.1 3.5 + - - +
187B VAL* 1.3 82.6 - - + +
189B ASP* 1.3 66.8 + - - +
190B GLU 3.2 1.3 - - - -
191B ALA* 3.3 7.4 + - + +
192B ILE* 3.0 30.4 + - - +
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Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 4.8 6.2 + - - -
44B VAL* 4.9 3.1 - - - +
45B MET 4.8 1.9 - - - +
46B VAL* 3.5 30.6 - - + +
185B LYS* 3.0 30.6 + - - +
186B THR* 3.9 7.9 + - + +
188B PHE* 1.3 75.3 - - - +
190B GLU* 1.3 58.4 + - + +
192B ILE* 3.3 3.5 + - - +
193B ARG* 2.9 50.6 + - - +
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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
----------------------------------------------------------
130B ILE* 4.1 7.2 - - + +
172B LYS* 4.1 34.5 + - + +
174B LEU* 3.7 22.9 - - + -
186B THR* 2.8 31.2 + - + +
187B VAL 4.0 0.2 - - - +
189B ASP* 1.3 72.9 - - - +
191B ALA* 1.3 61.7 + - - +
193B ARG* 3.0 41.5 + - - +
194B ALA* 2.9 30.7 + - - +
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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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6B CYS* 4.7 5.8 - - + -
53B LEU* 5.5 2.7 - - + -
96B VAL* 3.9 18.6 - - + +
98B LEU* 4.1 22.2 - - + -
130B ILE* 4.0 11.8 - - - +
187B VAL 3.0 18.6 + - - +
188B PHE* 3.3 10.5 + - + +
190B GLU* 1.3 78.5 - - - +
192B ILE* 1.3 64.2 + - + +
194B ALA* 3.4 9.0 + - - +
195B VAL* 3.4 17.5 - - - +
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Residues in contact with ILE 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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4B ILE* 4.0 14.6 - - + -
44B VAL* 3.5 32.5 - - + -
46B VAL* 3.7 21.8 - - + -
51B VAL* 3.9 18.2 - - + -
53B LEU* 4.1 28.5 - - + -
188B PHE 3.0 19.5 + - - +
189B ASP 3.5 6.3 - - - +
191B ALA* 1.3 75.9 - - - +
193B ARG* 1.3 57.3 + - - +
195B VAL* 2.9 6.8 + - - +
196B LEU* 2.9 50.9 + - + +
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Residues in contact with ARG 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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46B VAL* 4.0 12.9 - - + +
47B ASP* 2.8 42.5 + - - +
186B THR* 5.9 1.8 - - - +
189B ASP* 2.9 35.9 + - - +
190B GLU* 3.0 38.7 + - - +
192B ILE* 1.3 72.5 - - - +
194B ALA* 1.3 57.1 + - - +
196B LEU* 4.4 6.5 - - + +
197B CYS* 2.9 42.3 + - + +
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 4.5 1.6 - - + -
128B PRO* 3.9 25.1 - - + +
130B ILE* 4.3 5.2 - - + -
171B VAL* 3.9 27.8 - - + -
190B GLU 2.9 16.1 + - - +
191B ALA 3.6 7.9 - - - +
192B ILE 3.2 0.2 - - - -
193B ARG* 1.3 77.0 - - - +
195B VAL* 1.3 60.0 + - - +
197B CYS 4.4 4.0 - - - -
198B PRO* 4.0 19.6 - - - +
199B PRO* 5.2 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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4B ILE* 4.1 22.7 - - + -
95B ASP* 3.6 44.0 - - + +
96B VAL* 3.7 15.7 - - + -
128B PRO* 5.2 0.7 - - - -
191B ALA 3.4 15.9 - - - +
192B ILE 2.9 5.3 + - - +
194B ALA* 1.3 79.8 - - - +
196B LEU* 1.3 67.4 + - + +
197B CYS 3.3 1.5 + - - -
198B PRO* 3.6 12.7 - - - +
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Residues in contact with LEU 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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2B GLN* 3.7 32.3 - - + +
4B ILE* 3.9 18.6 - - + -
46B VAL* 4.5 6.7 - - + +
47B ASP* 5.9 2.2 - - + +
49B LYS* 3.3 48.7 + - + +
51B VAL* 4.2 4.0 - - + -
192B ILE* 2.9 38.3 + - + +
193B ARG* 4.4 3.4 - - - +
195B VAL* 1.3 80.6 - - + +
197B CYS* 1.3 67.2 + - - +
198B PRO* 3.6 5.6 - - - +
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Residues in contact with CYS 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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47B ASP* 5.6 3.8 - - - -
193B ARG* 2.9 27.5 + - + +
194B ALA* 4.2 3.8 - - - +
196B LEU* 1.3 89.5 - - - +
198B PRO* 1.3 66.8 - - - +
199B PRO* 3.8 3.6 - - - +
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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