Contacts of the helix formed by residues 185 - 202 (chain A) in PDB entry 5IVI
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 ASN 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A GLY 4.3 2.6 + - - -
172A PHE* 3.9 17.5 + - - +
173A LEU 4.5 0.8 + - - -
184A GLY* 1.3 71.4 - - - +
186A ALA* 1.3 66.2 + - - +
187A GLY 3.1 2.9 - - - -
188A LEU* 2.9 29.7 + - + +
189A LYS* 3.0 15.9 + - - +
313A PRO* 3.1 10.7 - - - +
314A THR* 2.8 50.0 + - - +
316A GLU* 3.1 29.0 + - - +
324A VAL* 4.7 1.3 - - + -
325A LEU* 3.5 12.1 - - - +
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Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE 3.6 23.6 - - - +
74A LYS 3.8 5.2 - - - +
75A ALA* 4.7 0.9 - - - +
166A ARG* 3.7 24.2 + - - +
170A LEU 4.7 0.4 - - - +
171A GLY* 3.1 15.0 + - - +
173A LEU 6.0 0.9 - - - +
184A GLY 3.1 5.5 + - - +
185A ASN* 1.3 75.3 - - - +
187A GLY* 1.3 59.0 + - - +
189A LYS* 3.0 16.0 + - - +
190A ASP* 2.8 32.8 + - - +
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Residues in contact with GLY 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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165A TYR* 3.6 5.2 - - - +
166A ARG* 3.8 22.4 - - - -
171A GLY* 2.9 13.6 + - - -
172A PHE* 3.9 8.9 - - - -
185A ASN 3.1 0.4 - - - -
186A ALA* 1.3 75.4 - - - +
188A LEU* 1.3 61.2 + - - +
190A ASP* 3.2 16.7 - - - +
191A GLN* 3.2 24.9 + - - +
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Residues in contact with LEU 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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138A PHE* 4.2 12.1 - - + -
172A PHE* 3.8 22.1 - - + -
185A ASN* 2.9 18.6 + - + +
187A GLY* 1.3 74.1 - - - +
189A LYS* 1.3 61.0 + - - +
191A GLN* 3.0 32.1 + - - +
192A VAL* 2.9 29.6 + - - +
223A SER* 4.4 0.7 - - - +
226A TYR* 4.0 24.0 - - + -
227A MET* 3.7 4.9 - - + +
313A PRO* 4.1 5.2 - - + -
324A VAL* 4.1 23.1 - - + -
325A LEU* 3.8 28.7 - - + -
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 4.1 20.2 - - + +
76A PRO* 3.4 24.6 - - + +
183A PRO* 3.4 14.8 - - - +
184A GLY 2.8 22.4 + - - +
185A ASN 3.0 15.0 + - - +
186A ALA* 3.3 10.3 - - - +
188A LEU* 1.3 75.8 - - - +
190A ASP* 1.3 61.1 + - - +
192A VAL* 3.4 7.3 + - + +
193A MET* 3.0 18.4 + - - +
316A GLU* 2.7 35.3 + - - -
320A THR* 4.7 2.8 + - - -
322A ASP* 3.3 27.1 - - + +
323A CYS* 4.6 1.4 - - - +
324A VAL* 3.5 17.9 - - + -
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 3.1 28.3 - - + +
76A PRO* 3.3 16.3 - - - +
112A LEU* 3.5 11.0 - - - +
165A TYR* 3.9 5.4 - - + -
166A ARG* 2.8 64.3 + - - +
186A ALA 2.8 13.1 + - - -
187A GLY* 3.2 11.0 - - - +
189A LYS* 1.3 73.8 - - - +
191A GLN* 1.3 59.8 + - - +
193A MET 3.2 2.1 + - - -
194A ALA* 2.9 24.9 + - - +
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Residues in contact with GLN 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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63A TYR* 5.0 0.2 - - - -
133A ILE* 3.8 11.6 - - + +
138A PHE* 4.7 0.2 - - - -
163A ILE* 4.2 20.8 - - + +
165A TYR* 3.6 41.2 - - + -
187A GLY 3.3 11.4 + - - +
188A LEU* 3.0 19.3 + - - +
190A ASP* 1.3 75.9 - - - +
192A VAL* 1.3 56.6 + - - +
194A ALA* 3.2 2.1 + - - +
195A LEU* 2.8 33.4 + - + +
223A SER* 3.0 39.8 + - - -
227A MET* 3.6 24.5 - - + +
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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
----------------------------------------------------------
188A LEU 2.9 16.9 + - - +
189A LYS* 3.5 11.2 - - - +
190A ASP 3.2 0.2 - - - -
191A GLN* 1.3 75.1 - - - +
193A MET* 1.3 62.3 + - - +
195A LEU* 3.2 6.4 + - - +
196A ARG* 3.0 61.3 + - - +
227A MET* 3.8 22.9 - - + -
230A THR* 4.6 1.6 - - + -
232A GLN* 4.3 12.6 - - + +
233A THR* 3.8 15.5 - - + -
236A LEU* 4.6 0.2 - - - +
324A VAL* 4.2 17.0 - - + -
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Residues in contact with MET 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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39A TYR* 5.9 1.8 - - - +
63A TYR* 3.3 32.1 - - + +
64A ALA* 3.7 17.3 - - - -
76A PRO* 3.4 32.1 - - + +
77A GLN* 3.9 13.9 - - - +
78A ARG* 4.1 9.0 - - + +
189A LYS 3.0 13.2 + - - +
190A ASP 3.6 7.4 - - - +
192A VAL* 1.3 78.9 - - - +
194A ALA* 1.3 56.8 + - - +
196A ARG* 3.4 15.4 + - + +
197A TRP* 3.0 27.8 + - + +
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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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63A TYR* 3.6 36.0 - - + -
114A LEU* 4.2 2.1 - - + +
163A ILE* 4.1 28.0 - - + -
190A ASP 2.9 13.6 + - - +
191A GLN 3.5 7.6 - - - +
193A MET* 1.3 77.0 - - - +
195A LEU* 1.3 61.4 + - - +
197A TRP* 3.2 4.4 + - - +
198A ILE* 3.0 28.8 + - - +
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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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131A VAL* 4.0 29.6 - - + -
133A ILE* 5.5 3.4 - - + -
163A ILE* 5.6 2.7 - - + -
191A GLN* 2.8 18.4 + - + +
192A VAL 3.2 4.9 + - - +
194A ALA* 1.3 77.5 - - - +
196A ARG* 1.3 57.2 + - - +
198A ILE* 3.0 10.9 + - + +
199A LYS 2.9 24.6 + - - -
212A ILE* 5.7 1.3 - - + -
214A VAL* 4.0 17.3 - - + -
227A MET* 3.8 35.2 - - + -
233A THR* 4.2 7.6 - - + -
236A LEU* 3.2 24.4 - - + +
237A PHE* 3.8 24.0 - - + -
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Residues in contact with ARG 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 36.8 + - - +
193A MET* 3.6 17.0 - - + +
195A LEU* 1.3 74.3 - - - +
197A TRP* 1.3 63.9 + - - +
199A LYS* 3.4 2.1 + - - +
200A ASN* 3.0 37.4 + - - +
232A GLN* 2.8 58.2 + - - +
236A LEU* 3.6 17.5 - - + +
322A ASP* 5.4 3.4 + - - -
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Residues in contact with TRP 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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37A THR* 3.7 14.3 + - + -
38A GLU* 3.9 5.4 - - - -
39A TYR* 3.3 41.4 - + - +
61A ILE* 3.5 33.6 - - + +
62A PRO 4.2 4.4 + - - -
63A TYR* 4.1 20.9 - - + +
114A LEU* 3.7 30.5 - - + -
116A VAL* 4.5 7.6 - - + -
161A ILE* 5.0 2.9 - - + -
193A MET* 3.0 14.7 + - + +
194A ALA 3.5 8.3 - - - +
195A LEU 3.2 0.2 - - - -
196A ARG* 1.3 75.8 - - - +
198A ILE* 1.3 67.2 + - + +
200A ASN* 4.7 0.4 - - - +
201A ASN* 2.7 72.3 + - + +
202A CYS 5.3 0.4 - - - -
205A PHE* 3.9 18.4 - + - -
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Residues in contact with ILE 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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114A LEU* 4.3 2.2 - - + -
129A VAL* 4.1 18.6 - - + -
131A VAL* 3.6 36.3 - - + -
161A ILE* 3.8 40.4 - - + -
163A ILE* 4.2 9.2 - - + -
194A ALA 3.0 20.2 + - - +
195A LEU* 3.0 13.5 + - + +
197A TRP* 1.3 87.5 - - + +
199A LYS* 1.3 65.3 + - - +
201A ASN 4.5 0.2 - - - +
202A CYS* 2.9 29.6 + - + +
212A ILE* 4.4 10.3 - - + -
236A LEU* 5.8 0.2 - - + -
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Residues in contact with LYS 199 (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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195A LEU 2.9 8.1 + - - +
196A ARG* 4.0 4.0 - - - +
198A ILE* 1.3 77.9 - - - +
200A ASN* 1.3 66.6 + - - +
202A CYS* 4.3 1.9 - - - -
203A ALA* 5.4 0.3 + - - +
209A PRO* 3.3 46.2 + - + +
210A ASP* 3.7 13.1 + - - -
212A ILE* 4.0 7.8 - - + +
235A GLY 3.6 15.0 - - - -
236A LEU* 3.3 48.9 - - + +
238A HIS* 4.3 4.9 + - - -
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Residues in contact with ASN 200 (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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38A GLU* 3.5 21.5 + - + +
196A ARG* 3.0 25.2 + - - +
197A TRP* 4.7 0.2 - - - +
198A ILE 3.1 0.2 - - - -
199A LYS* 1.3 82.9 - - - +
201A ASN* 1.3 72.6 + - - +
203A ALA* 5.3 4.4 + - - +
204A ASN* 4.5 5.0 + - - +
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Residues in contact with ASN 201 (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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37A THR* 3.3 9.0 - - - -
38A GLU* 2.8 55.5 + - - +
197A TRP* 2.7 63.1 + - + +
200A ASN* 1.3 82.8 - - - +
202A CYS* 1.3 60.5 + - - +
203A ALA 3.2 3.1 - - - -
204A ASN* 2.9 37.2 + - - +
205A PHE* 3.4 8.3 - - + -
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Residues in contact with CYS 202 (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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129A VAL* 3.9 27.8 - - + -
159A VAL* 5.7 2.0 - - + +
161A ILE* 4.9 8.1 - - + -
197A TRP* 5.3 0.8 - - - -
198A ILE* 2.9 32.9 + - + +
199A LYS 4.3 0.7 - - - -
200A ASN 3.9 0.2 - - - -
201A ASN* 1.3 76.6 - - - +
203A ALA* 1.3 63.7 + - - +
205A PHE* 3.0 19.1 + - - +
207A GLY* 2.8 21.3 + - - -
209A PRO* 3.6 38.1 - - - -
212A ILE* 4.5 4.3 - - - -
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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
------------------------------------------------------------
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