Contacts of the helix formed by residues 180 - 198 (chain A) in PDB entry 4R1Z
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 LEU 180 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A MET* 5.0 4.7 - - + +
169A VAL* 6.4 0.7 - - + -
170A LEU* 4.1 31.2 - - + -
178A VAL* 3.4 22.7 + - + -
179A ASP* 1.3 76.8 + - - +
181A GLY* 1.3 65.4 + - - +
182A PRO 3.6 0.4 - - - -
183A GLU* 3.5 5.7 + - + +
184A LEU* 2.9 43.4 + - + +
326A ILE* 4.3 28.0 - - + -
470A ILE* 6.1 3.8 - - + -
476A LEU* 4.8 10.3 - - + -
500A PHE 4.6 2.0 + - - -
502A VAL* 3.6 30.7 - - + +
504A ALA* 5.9 1.1 - - + -
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Residues in contact with GLY 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 3.0 15.4 + - - -
180A LEU* 1.3 78.6 - - - +
182A PRO* 1.3 68.2 - - - +
184A LEU* 3.5 2.7 - - - +
185A THR* 2.9 28.7 + - - -
323A LYS* 3.8 25.0 - - - -
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Residues in contact with PRO 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 3.4 27.6 - - + +
181A GLY* 1.3 89.4 - - - +
183A GLU* 1.3 59.5 + - + +
185A THR* 3.5 7.2 + - - -
186A ARG* 3.2 26.5 + - - +
208A PHE* 4.6 5.8 - - + -
212A LEU* 5.6 10.5 - - + -
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A MET* 3.4 25.2 - - + +
169A VAL* 3.7 28.7 - - + +
179A ASP 5.1 3.6 - - - +
180A LEU* 3.5 6.5 + - - +
181A GLY 3.2 0.6 - - - -
182A PRO* 1.3 82.1 - - + +
184A LEU* 1.3 62.1 + - - +
186A ARG* 2.7 42.9 + - - +
187A ALA* 3.4 17.7 + - - +
203A ARG* 2.8 38.2 + - - +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A MET* 3.4 27.1 - - + +
180A LEU* 2.9 36.7 + - + +
181A GLY* 3.5 3.1 - - - +
183A GLU* 1.3 76.6 - - - +
185A THR* 1.3 64.4 + - - +
187A ALA* 3.3 3.9 + - + +
188A VAL* 3.0 28.8 + - - +
319A THR* 4.8 4.9 - - + -
322A LEU* 4.3 33.9 - - + -
323A LYS* 4.8 12.3 - - + -
326A ILE* 4.2 23.8 - - + -
466A PHE* 5.2 6.1 - - + -
470A ILE* 4.9 11.7 - - + -
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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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181A GLY 2.9 17.9 + - - -
182A PRO* 3.6 8.2 - - - +
184A LEU* 1.3 76.3 - - - +
186A ARG* 1.3 54.5 + - - +
188A VAL* 3.4 3.1 + - - +
189A THR* 2.6 44.0 + - - +
208A PHE* 4.4 0.9 - - + -
212A LEU* 4.1 26.0 - - + -
315A VAL* 4.2 13.7 - - + -
319A THR* 3.2 27.1 + - + +
323A LYS* 3.8 8.8 + - - -
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Residues in contact with ARG 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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162A GLU* 5.3 2.6 + - - -
165A SER* 5.1 8.7 + - - -
169A VAL* 5.1 3.0 - - - +
182A PRO 3.2 12.3 + - - +
183A GLU* 2.7 34.7 + - - +
184A LEU 3.4 0.2 - - - -
185A THR* 1.3 79.8 - - - +
187A ALA* 1.3 57.4 + - - +
189A THR* 3.1 1.2 + - - -
190A ASN* 2.8 43.0 + - - +
201A TYR 3.0 23.7 + - - +
202A LYS* 3.7 16.7 - - - +
203A ARG* 3.4 36.3 - - - +
208A PHE* 3.4 39.2 - - + -
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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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162A GLU* 3.5 26.4 - - - +
166A MET* 3.9 22.4 - - + -
183A GLU 3.4 12.7 + - - +
184A LEU* 3.3 10.0 + - - +
186A ARG* 1.3 80.7 - - - +
188A VAL* 1.3 62.1 + - - +
190A ASN 3.3 9.2 + - - -
191A VAL* 3.4 16.1 + - - +
466A PHE* 3.9 16.6 - - + -
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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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184A LEU 3.0 16.8 + - - +
185A THR 3.7 1.1 - - - +
187A ALA* 1.3 75.8 - - - +
189A THR* 1.3 63.0 + - - +
191A VAL* 3.4 18.5 + - - +
192A VAL* 3.6 7.8 + - - +
314A GLY 3.2 24.6 - - - +
315A VAL* 3.9 4.9 - - - -
318A THR* 3.9 5.2 - - + -
319A THR* 3.1 31.9 - - - +
322A LEU* 3.9 27.1 - - + -
462A GLU* 3.7 20.8 - - - +
466A PHE* 4.4 7.9 - - + -
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Residues in contact with THR 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* 2.6 26.2 + - - +
186A ARG 3.1 5.1 + - - -
188A VAL* 1.3 73.6 - - - +
190A ASN* 1.3 52.2 + - - +
191A VAL 3.0 4.8 + - - -
192A VAL* 3.2 2.9 + - - +
193A CYS* 2.7 32.6 + - - +
201A TYR* 4.0 17.9 - - + -
208A PHE* 3.7 19.5 - - + -
211A MET* 3.4 28.1 - - + +
311A PHE* 4.3 3.6 - - + -
315A VAL* 3.2 29.0 - - + +
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Residues in contact with ASN 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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158A ILE* 4.1 3.1 - - - +
161A ARG* 4.3 3.8 + - - +
162A GLU* 3.2 40.4 + - - +
186A ARG* 2.8 28.6 + - - +
187A ALA 3.3 1.0 + - - +
189A THR* 1.3 75.0 - - - +
191A VAL* 1.3 58.0 + - - +
193A CYS* 3.8 5.2 - - - -
194A ALA* 3.1 27.2 + - - +
199A SER 4.0 2.4 - - - +
200A SER* 3.5 7.7 + - - +
201A TYR* 2.6 55.8 + - - +
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Residues in contact with VAL 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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155A ILE* 4.9 8.9 - - + +
158A ILE* 4.2 9.4 - - + +
159A ILE* 4.1 30.3 - - + -
162A GLU* 4.3 8.7 - - + -
187A ALA 3.5 15.3 - - - +
188A VAL 3.4 9.0 - - - +
189A THR 3.0 0.6 - - - -
190A ASN* 1.3 78.6 - - - +
192A VAL* 1.3 61.2 + - - +
194A ALA* 3.4 5.2 - - - +
195A LEU* 3.0 23.2 + - - +
458A LEU* 4.5 12.8 - - + -
462A GLU* 3.9 25.6 - - + +
466A PHE* 4.2 16.2 - - + -
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Residues in contact with VAL 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 3.9 6.5 - - - +
189A THR 3.5 9.0 - - - +
191A VAL* 1.3 79.7 - - + +
193A CYS* 1.3 62.9 + - - +
195A LEU* 3.6 9.6 - - + -
196A CYS* 3.0 29.6 + - - +
310A ILE* 3.2 41.7 - - + +
311A PHE* 4.1 13.6 - - + +
314A GLY* 4.1 14.4 - - - -
315A VAL* 3.8 25.8 - - + -
458A LEU* 5.2 9.0 - - + -
462A GLU* 5.5 1.8 - - - +
600A HEM 5.5 0.2 - - + -
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Residues in contact with CYS 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 THR 2.7 17.0 + - - +
190A ASN* 4.0 9.0 - - - +
192A VAL* 1.3 75.7 - - - +
194A ALA* 1.3 59.9 + - - +
197A PHE* 2.8 48.6 + - - +
198A ASN 3.3 4.5 + - - -
199A SER* 3.6 30.0 + - - +
200A SER* 4.5 0.2 - - - -
201A TYR* 3.4 36.1 - - + -
259A LYS* 4.6 1.1 - - - -
311A PHE* 4.5 10.3 - - + -
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Residues in contact with ALA 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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148A PHE* 2.9 22.5 - - + -
158A ILE* 3.9 28.5 - - + -
161A ARG* 5.8 1.6 - - - +
190A ASN 3.1 21.0 + - - +
191A VAL 3.4 5.8 - - - +
193A CYS* 1.3 76.6 - - - +
195A LEU* 1.3 60.7 + - - +
198A ASN* 3.1 16.4 + - - +
199A SER 3.2 18.6 + - - +
274A ASP* 4.1 0.2 - - - +
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Residues in contact with LEU 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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141A VAL* 5.5 4.3 - - + +
144A ALA* 4.9 1.9 - - + +
145A LEU* 4.0 33.0 - - + +
148A PHE* 3.9 25.6 - - + +
155A ILE* 3.5 29.2 - - + -
191A VAL 3.0 18.5 + - - +
192A VAL* 3.6 11.2 - - + +
193A CYS 3.3 0.6 - - - -
194A ALA* 1.3 76.3 - - - +
196A CYS* 1.3 58.8 + - - +
274A ASP* 3.7 3.6 - - - +
275A LEU* 3.2 28.2 + - + +
310A ILE* 4.5 19.3 - - + -
458A LEU* 4.5 13.5 - - + -
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Residues in contact with CYS 196 (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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192A VAL* 3.0 19.7 + - - +
195A LEU* 1.3 79.4 - - - +
197A PHE* 1.3 85.7 + - + +
274A ASP* 3.2 9.8 - - - -
275A LEU* 4.1 10.8 - - - -
276A LEU* 3.2 25.5 + - - +
307A VAL* 4.0 13.1 - - + +
310A ILE* 3.5 33.4 - - - -
311A PHE* 3.9 16.2 - - + -
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Residues in contact with PHE 197 (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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193A CYS* 2.8 25.1 + - - +
196A CYS* 1.3 82.8 - - + +
198A ASN* 1.3 68.7 + - - +
199A SER* 3.3 14.1 + - - +
201A TYR* 5.3 0.2 - - - -
255A LEU* 4.6 2.2 - - + -
256A LEU* 3.9 20.2 - - + -
259A LYS* 3.9 37.7 - - + -
263A HIS* 3.3 18.2 + - - +
274A ASP* 2.8 12.2 - - - +
276A LEU* 3.8 21.1 - - + -
307A VAL* 3.3 34.1 - - + -
311A PHE* 3.9 31.9 - + - -
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Residues in contact with ASN 198 (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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148A PHE* 3.9 14.7 - - - -
194A ALA* 3.1 18.0 + - - +
197A PHE* 1.3 80.6 - - - +
199A SER* 1.3 58.3 + - - +
263A HIS* 5.1 0.2 - - + -
273A ARG* 3.9 38.7 - - + +
274A ASP* 3.0 12.4 + - - +
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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