Contacts of the helix formed by residues 171 - 189 (chain A) in PDB entry 3SN5
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 MET 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A GLU 3.5 2.4 + - - -
170A GLY* 1.4 69.5 - - - -
172A TYR* 1.3 57.0 + - - +
174A PHE* 3.3 2.6 + - - +
175A CYS* 3.0 33.4 + - - -
295A PHE* 3.7 16.6 - - + +
298A LEU* 3.7 18.4 - - + -
299A PHE* 3.6 42.4 - - - -
302A ILE* 3.7 27.1 - - + -
469A LEU* 3.9 14.8 - - + -
494A ASP* 3.1 0.2 + - - -
495A ILE* 2.9 22.2 + - + +
497A PHE* 3.6 41.7 - - + -
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Residues in contact with TYR 172 (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 MET* 1.3 69.9 - - - +
173A SER* 1.3 60.1 + - - +
175A CYS* 3.3 3.7 + - - +
176A TYR* 2.9 61.4 + + - +
291A ILE* 3.8 10.1 - - + +
292A PRO* 3.7 36.7 - - + +
295A PHE* 3.5 30.8 - + + -
490A PRO* 3.6 18.1 - - + +
491A PRO* 3.6 26.0 - - + -
494A ASP* 2.8 28.4 + - + +
2491A UNX 4.5 7.6 - - - -
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Residues in contact with SER 173 (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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169A GLU* 3.4 13.3 + - - +
170A GLY* 3.4 14.1 - - - -
172A TYR* 1.3 78.4 - - - +
174A PHE* 1.4 54.6 + - - +
176A TYR* 3.5 7.2 - - - +
177A ARG* 3.1 32.4 + - - +
210A LYS* 4.9 11.8 + - - +
494A ASP* 3.1 13.4 + - - -
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Residues in contact with PHE 174 (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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153A MET* 5.4 3.6 - - + -
169A GLU* 3.4 17.0 + - - +
170A GLY 2.8 13.8 + - - +
171A MET 3.4 9.6 - - - +
172A TYR 3.2 0.2 - - - -
173A SER* 1.4 71.3 + - - +
175A CYS* 1.3 67.9 + - - +
177A ARG* 3.3 36.4 + - - +
178A VAL* 3.1 44.7 + - + +
298A LEU* 4.9 0.2 - - + -
457A PHE* 3.9 17.3 - + - -
461A MET* 3.6 35.7 - - + -
465A PHE* 4.8 9.0 - + - -
497A PHE* 3.8 18.8 - + + -
499A TYR* 3.6 29.2 - + - -
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Residues in contact with CYS 175 (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 MET* 3.0 21.7 + - - +
172A TYR* 3.8 4.9 - - - +
174A PHE* 1.3 76.6 - - - +
176A TYR* 1.3 53.7 + - - +
178A VAL* 4.8 0.2 - - - -
179A MET* 2.8 40.8 + - - +
291A ILE* 4.6 8.3 - - + +
294A THR* 4.2 7.4 - - + -
295A PHE* 3.9 33.4 - - + +
298A LEU* 3.8 26.7 - - - -
457A PHE* 3.8 20.4 - - - -
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Residues in contact with TYR 176 (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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172A TYR* 2.9 47.8 + + - +
173A SER* 3.5 7.0 - - - +
174A PHE 3.2 0.2 - - - -
175A CYS* 1.3 72.4 - - - +
177A ARG* 1.4 65.7 + - - +
180A PHE* 2.8 31.0 + + - +
206A LEU* 3.4 24.7 - - + -
209A PHE* 3.5 29.5 - + - -
210A LYS* 3.5 51.3 - - + +
213A ASP* 3.9 11.6 + - - -
291A ILE* 3.6 35.8 - - + +
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Residues in contact with ARG 177 (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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152A ILE* 5.1 7.8 + - - +
169A GLU* 3.0 36.0 + - - +
173A SER* 3.1 20.6 + - - +
174A PHE* 3.3 28.2 + - - +
176A TYR* 1.4 79.0 - - - +
178A VAL* 1.3 71.0 + - - +
180A PHE* 4.3 0.9 - - - +
181A GLU* 3.3 26.6 + - - +
206A LEU* 4.3 22.5 - - + +
210A LYS* 6.0 1.1 - - - +
499A TYR* 3.4 8.1 + - - -
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Residues in contact with VAL 178 (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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149A LEU* 3.7 23.3 - - + -
152A ILE* 4.3 17.7 - - + +
153A MET* 3.8 19.3 - - + -
174A PHE* 3.1 44.0 + - + +
177A ARG* 1.3 89.3 - - - +
179A MET* 1.3 65.5 + - - +
181A GLU* 4.1 1.2 - - - +
182A ALA* 3.1 26.0 + - - +
457A PHE* 3.7 21.1 - - + -
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Residues in contact with MET 179 (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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145A MET* 4.0 18.6 - - + +
149A LEU* 4.1 10.8 - - - -
175A CYS 2.8 25.2 + - - +
178A VAL* 1.3 73.5 - - - +
180A PHE* 1.3 55.4 + - - +
182A ALA* 4.1 1.3 - - - +
183A GLY* 2.9 27.9 + - - -
287A GLN* 3.5 6.8 - - - +
290A THR* 3.6 20.6 - - + -
291A ILE* 4.2 15.3 - - + -
294A THR* 3.6 37.7 - - + +
453A GLU* 4.0 23.7 - - + +
454A ILE 4.5 0.2 - - - +
457A PHE* 3.7 32.5 - - + -
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Residues in contact with PHE 180 (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 TYR* 2.8 24.8 + + + +
177A ARG 4.3 0.2 - - - +
179A MET* 1.3 76.8 - - - +
181A GLU* 1.3 56.3 + - + +
184A TYR* 2.8 64.6 + + + +
202A ILE 4.7 2.5 - - - -
205A ASN* 3.9 11.4 - - + -
206A LEU* 3.7 42.4 - - + -
209A PHE* 3.5 48.7 - + + -
238A LEU* 5.1 0.2 - - + -
283A LEU* 4.2 7.6 - - + -
287A GLN* 3.1 37.4 + - + +
291A ILE* 4.5 3.5 - - + +
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Residues in contact with GLU 181 (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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152A ILE* 3.6 35.2 - - + +
177A ARG 3.3 18.3 + - - +
178A VAL 4.2 0.7 - - - +
180A PHE* 1.3 83.3 - - + +
182A ALA* 1.3 63.0 + - - +
184A TYR* 3.4 3.5 + - - +
185A LEU* 3.1 42.5 + - + +
202A ILE* 4.5 25.9 - - + +
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Residues in contact with ALA 182 (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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145A MET* 3.6 23.3 - - + -
148A ASN* 4.0 5.1 - - + +
149A LEU* 3.7 23.1 - - + +
152A ILE* 3.4 16.7 - - + +
178A VAL 3.1 18.7 + - - +
179A MET 4.1 0.4 - - - +
181A GLU* 1.3 75.7 - - - +
183A GLY* 1.3 55.8 + - - +
185A LEU* 3.4 2.9 + - - +
186A THR* 2.7 37.8 + - - -
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Residues in contact with GLY 183 (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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145A MET* 3.9 12.9 - - - +
179A MET 2.9 19.0 + - - -
182A ALA* 1.3 74.3 - - - +
184A TYR* 1.3 61.8 + - - +
186A THR* 3.4 2.6 + - - -
187A ILE* 3.0 34.1 + - - +
286A SER* 5.6 1.3 - - - -
287A GLN* 3.5 12.6 - - - -
449A PHE* 5.8 1.8 - - - -
453A GLU* 5.0 4.5 - - - -
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Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A PHE* 2.8 39.2 + + + +
181A GLU* 3.7 6.1 - - - +
183A GLY* 1.3 73.2 - - - +
185A LEU* 1.3 57.2 + - + +
187A ILE* 5.1 0.2 - - - -
188A PHE* 2.8 47.9 + + + +
201A HIS* 5.1 1.6 - + - -
205A ASN* 3.0 33.6 + - + -
238A LEU* 5.4 0.7 - - + -
241A SER* 3.7 13.0 + - - -
242A LEU* 3.4 23.9 - - + +
250A ARG* 3.8 29.9 + - - -
283A LEU* 3.6 37.0 - - + -
287A GLN* 3.3 3.7 - - - +
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A SER* 4.8 0.5 + - - -
148A ASN* 3.8 26.8 + - + +
151A ARG* 6.2 3.1 - - + -
152A ILE* 4.3 12.1 - - + -
181A GLU* 3.1 37.5 + - + +
182A ALA 3.9 0.4 - - - +
184A TYR* 1.3 77.5 - - + +
186A THR* 1.4 60.4 + - - +
189A GLY* 2.9 43.1 + - - +
190A ARG* 3.8 21.9 - - + +
191A ASP 5.1 1.6 - - - +
250A ARG* 3.9 11.9 - - - +
252A SER* 4.1 2.9 - - - +
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Residues in contact with THR 186 (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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141A LEU* 3.5 40.5 - - + +
144A SER* 3.7 10.3 + - - +
145A MET* 3.3 25.6 - - - +
148A ASN* 2.8 17.2 + - - +
182A ALA 2.7 22.5 + - - -
183A GLY* 3.8 4.0 - - - -
185A LEU* 1.4 77.8 - - - +
187A ILE* 1.3 61.1 + - - +
252A SER 4.2 4.2 - - - +
254A SER* 3.5 19.5 + - - -
449A PHE* 4.0 11.2 - - + -
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Residues in contact with ILE 187 (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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141A LEU* 4.1 24.0 - - + -
183A GLY* 3.0 18.8 + - - +
186A THR* 1.3 77.2 - - - +
188A PHE* 1.4 83.9 - - + +
189A GLY 3.5 0.2 - - - -
253A ILE* 4.1 0.2 - - - +
254A SER* 2.8 31.2 + - - +
256A LEU* 4.6 15.7 - - + -
257A ILE* 3.4 26.1 - - + +
282A VAL* 4.3 9.6 - - + -
286A SER* 4.3 23.1 - - - +
449A PHE* 4.4 17.9 - - + -
601A HEM 4.7 4.7 - - + -
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Residues in contact with PHE 188 (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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184A TYR* 2.8 47.3 + + + +
187A ILE* 1.4 90.6 - - + +
189A GLY* 1.3 60.3 + - - +
242A LEU* 3.6 25.1 - - + -
247A LEU* 3.8 19.2 - - + +
250A ARG* 2.8 30.1 + - - +
253A ILE* 3.8 13.2 - - - +
257A ILE* 3.7 28.9 - - + -
279A HIS* 3.5 31.2 - - + -
283A LEU* 3.7 34.1 - - + -
286A SER* 5.3 0.2 - - - -
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Residues in contact with GLY 189 (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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185A LEU* 2.9 31.4 + - - +
187A ILE 3.5 2.6 + - - -
188A PHE* 1.3 79.5 - - - +
190A ARG* 1.4 55.6 + - - -
250A ARG* 2.7 26.1 + - - -
251A GLU 3.0 13.9 - - - -
252A SER* 3.4 15.6 + - - -
253A ILE* 3.9 2.0 - - - +
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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