Contacts of the helix formed by residues 181 - 195 (chain A) in PDB entry 1R37
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLY 3.3 7.8 + - - -
179A ALA 3.4 0.4 - - - -
180A GLY* 1.3 78.8 - - - +
182A GLY* 1.3 62.4 + - - -
183A LEU 3.5 2.0 - - - -
184A GLY 3.8 1.3 - - - -
185A THR* 2.8 30.0 + - - +
339A ALA 5.3 0.4 - - - -
340A ILE* 4.9 2.5 - - - -
341A GLY* 3.5 7.6 - - - -
403A NAD 3.2 30.9 + - - -
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Residues in contact with GLY 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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155A SER* 4.1 7.6 + - - -
181A GLY* 1.3 71.2 - - - -
183A LEU* 1.3 61.4 + - - +
185A THR* 3.1 15.6 + - - -
186A MET* 3.6 10.2 + - - +
341A GLY 3.1 20.4 + - - -
342A ARG* 3.6 25.5 - - - +
403A NAD 2.8 14.8 + - - -
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Residues in contact with LEU 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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155A SER* 3.7 15.3 - - - -
158A THR* 3.9 10.5 - - + -
159A THR* 3.4 14.9 - - + +
182A GLY* 1.3 71.2 - - - -
184A GLY* 1.3 56.9 + - - +
186A MET* 2.9 5.1 + - - +
187A ALA* 2.7 33.1 + - - +
247A LEU* 3.6 18.2 - - + -
270A VAL* 3.7 25.8 - - + -
342A ARG* 3.7 17.9 - - - +
403A NAD 2.9 70.9 + - + +
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Residues in contact with GLY 184 (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 VAL* 4.0 1.0 - - - +
178A GLY 3.4 17.1 + - - -
179A ALA* 3.2 12.1 - - - -
181A GLY 3.5 3.8 + - - -
182A GLY 3.4 0.6 - - - -
183A LEU* 1.3 78.2 - - - +
185A THR* 1.3 61.7 + - - +
187A ALA* 3.3 1.4 + - - +
188A VAL* 3.1 29.3 + - - +
247A LEU* 3.2 23.5 - - - +
403A NAD 4.4 0.8 + - - -
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Residues in contact with THR 185 (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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179A ALA 3.3 12.8 + - - +
180A GLY* 3.7 14.4 - - - +
181A GLY 2.8 24.6 + - - +
182A GLY 3.1 10.2 + - - -
184A GLY* 1.3 73.6 - - - +
186A MET* 1.3 58.7 + - - +
189A GLN* 3.0 33.2 + - - +
211A ALA* 4.2 8.3 - - + +
215A ALA* 3.6 9.0 - - - +
317A MET* 3.8 44.1 + - + +
341A GLY* 4.0 11.0 - - - -
342A ARG* 5.9 0.5 - - - +
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Residues in contact with MET 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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152A LEU* 4.5 6.3 - - + -
155A SER* 3.6 17.3 - - - +
156A GLY* 3.7 10.3 - - - -
159A THR* 3.5 17.0 - - - +
182A GLY 3.7 11.2 - - - +
183A LEU 2.9 8.4 + - - +
185A THR* 1.3 79.5 + - - +
187A ALA* 1.3 65.7 + - - +
188A VAL 3.2 0.2 - - - -
189A GLN* 3.1 9.7 + - + +
190A ILE* 3.0 45.7 + - + +
305A ILE* 4.1 6.5 - - + -
314A VAL* 3.6 38.4 - - + -
315A LYS 4.5 2.5 - - - +
316A PRO* 4.2 31.0 - - - -
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Residues in contact with ALA 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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159A THR* 3.8 22.6 + - + -
163A VAL* 3.9 7.1 - - - +
174A LEU* 4.8 0.2 - - - +
176A VAL* 4.1 22.7 - - + -
183A LEU 2.7 19.5 + - - +
184A GLY 3.8 4.0 - - - +
186A MET* 1.3 72.5 - - - +
188A VAL* 1.3 63.5 + - - +
190A ILE* 4.9 0.2 - - - -
191A ALA* 3.1 27.4 + - - +
245A ILE* 4.6 16.4 - - + -
247A LEU* 4.6 3.6 - - + -
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Residues in contact with VAL 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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176A VAL* 3.9 21.3 - - + -
179A ALA* 4.0 19.5 - - + +
184A GLY 3.1 18.0 + - - +
185A THR 4.0 0.2 - - - +
187A ALA* 1.3 77.6 - - - +
189A GLN* 1.3 55.9 + - - +
191A ALA* 4.7 2.7 - - - -
192A LYS* 3.1 26.7 + - - +
199A ILE* 3.7 13.9 - - + +
201A GLY* 5.2 0.4 - - - -
212A ALA 4.1 1.6 - - - +
215A ALA* 3.6 24.9 - - + +
216A GLY 3.8 1.6 - - - -
217A ALA* 3.4 38.8 - - + +
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Residues in contact with GLN 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 THR 3.0 24.0 + - - +
186A MET* 3.1 15.7 + - + +
188A VAL* 1.3 74.9 - - - +
190A ILE* 1.3 60.4 + - - +
192A LYS* 3.1 5.2 + - - +
193A ALA* 2.8 29.6 + - - +
215A ALA* 3.6 23.1 - - + +
313A LYS 4.8 0.9 - - - +
314A VAL* 3.6 16.0 - - + +
315A LYS* 2.8 48.8 + - - +
317A MET* 3.7 21.7 - - - +
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Residues in contact with ILE 190 (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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156A GLY 3.7 6.1 - - - +
159A THR* 3.5 26.2 - - - +
160A TYR* 3.7 19.7 - - + +
163A VAL* 4.3 18.8 - - + -
186A MET* 3.0 26.1 + - + +
187A ALA 4.1 2.7 - - - +
189A GLN* 1.3 74.6 - - - +
191A ALA* 1.3 58.0 + - - +
193A ALA* 3.6 1.2 - - - -
194A VAL* 2.9 44.5 + - + +
305A ILE* 3.5 28.3 - - + -
308A LEU* 4.2 9.6 - - + -
314A VAL* 4.0 11.0 - - + -
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Residues in contact with ALA 191 (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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163A VAL* 4.2 13.4 - - + +
168A LEU* 4.4 0.4 - - + -
174A LEU* 3.5 29.4 - - + -
187A ALA 3.1 18.6 + - - +
188A VAL* 3.9 1.1 - - - +
190A ILE* 1.3 76.7 - - - +
192A LYS* 1.3 61.5 + - - +
195A SER* 2.5 35.3 + - - +
196A GLY 4.0 2.6 + - - -
197A ALA 4.6 1.4 - - - +
199A ILE* 3.7 16.2 - - + +
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Residues in contact with LYS 192 (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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188A VAL 3.1 18.7 + - - +
189A GLN* 3.4 7.6 - - - +
190A ILE 3.1 0.2 - - - -
191A ALA* 1.3 80.8 - - - +
193A ALA* 1.3 59.9 + - - +
195A SER 4.8 1.4 + - - -
196A GLY* 4.9 4.3 + - - -
197A ALA 5.6 1.8 - - - +
199A ILE* 3.5 11.6 - - + +
215A ALA 4.8 3.1 - - - +
216A GLY* 3.2 31.3 + - - +
218A ASP* 2.8 30.9 + - - +
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Residues in contact with ALA 193 (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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189A GLN 2.8 16.3 + - - +
190A ILE* 3.1 4.2 + - - +
192A LYS* 1.3 79.5 - - - +
194A VAL* 1.3 69.9 + - + +
308A LEU* 4.4 1.2 - - + +
313A LYS* 3.7 34.8 - - + +
314A VAL* 3.8 9.6 - - + -
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Residues in contact with VAL 194 (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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160A TYR* 5.7 6.5 - - + -
163A VAL* 5.0 6.7 - - + -
190A ILE* 2.9 32.4 + - + +
193A ALA* 1.3 86.1 - - + +
195A SER* 1.3 61.9 + - - +
196A GLY 3.8 1.1 - - - -
308A LEU* 3.7 29.2 - - + -
313A LYS* 5.8 0.7 - - + -
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Residues in contact with SER 195 (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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163A VAL* 4.9 6.1 - - - -
168A LEU* 3.6 35.2 - - - +
169A ASP* 3.7 5.5 - - - -
170A PRO* 3.6 19.4 - - - +
191A ALA* 2.5 32.1 + - - +
194A VAL* 1.3 80.8 - - - +
196A GLY* 1.3 59.0 + - - +
197A ALA* 3.0 19.4 + - - +
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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