Contacts of the helix formed by residues 186 - 203 (chain A) in PDB entry 4F4I
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 PRO 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ARG* 4.5 2.2 - - - +
184A ASP 4.7 0.7 - - - +
185A GLN* 1.3 89.5 - - + +
187A LEU* 1.3 65.4 + - - +
188A GLU* 3.2 7.9 - - + +
189A ASN* 3.0 36.1 + - - +
190A VAL* 3.2 8.8 + - - +
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Residues in contact with LEU 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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13A SER 4.7 0.7 - - - +
14A GLY* 3.5 33.2 - - - +
17A THR* 4.6 25.6 - - + +
18A VAL* 4.9 3.1 - - + -
141A ARG* 3.8 34.1 - - - +
186A PRO* 1.3 73.0 - - - +
188A GLU* 1.3 58.3 + - - +
190A VAL* 3.1 11.7 + - + +
191A VAL* 2.8 36.5 + - - +
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 5.2 4.5 - - - -
25A ARG* 5.3 0.5 + - - -
186A PRO* 4.9 5.6 - - + -
187A LEU* 1.3 78.1 - - - +
189A ASN* 1.3 66.7 + - - +
191A VAL* 3.6 8.1 + - - +
192A GLU* 3.1 26.0 + - + +
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Residues in contact with ASN 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLN* 3.7 24.9 - - + +
186A PRO* 3.0 36.4 + - - +
188A GLU* 1.3 85.8 - - - +
190A VAL* 1.3 60.1 + - - +
192A GLU* 4.4 7.2 - - - +
193A ASP* 2.9 39.7 + - - +
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER 4.4 6.5 - - - +
18A VAL* 3.3 24.2 - - + -
131A LEU* 3.5 21.1 - - + -
181A VAL* 3.5 10.7 - - + +
182A ASN 3.3 24.5 - - - +
183A ALA* 3.5 15.0 - - - +
185A GLN* 3.9 9.2 - - + +
186A PRO 3.2 12.1 + - - +
187A LEU* 3.1 14.4 + - + +
189A ASN* 1.3 74.0 - - - +
191A VAL* 1.3 68.0 + - - +
193A ASP* 4.7 0.4 - - - -
194A THR* 2.9 29.3 + - - -
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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
----------------------------------------------------------
17A THR* 4.4 5.4 - - + -
18A VAL* 4.0 23.1 - - + -
21A GLU* 3.2 56.3 - - + +
22A VAL* 4.0 8.4 - - + +
25A ARG* 4.2 18.6 - - - +
187A LEU 2.8 23.5 + - - +
188A GLU* 3.6 5.6 - - - +
190A VAL* 1.3 78.1 - - - +
192A GLU* 1.3 58.4 + - - +
194A THR* 3.2 2.9 + - - -
195A TYR* 3.0 26.0 + - - +
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Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 2.7 44.6 + - - +
188A GLU* 3.1 15.7 + - + +
189A ASN* 3.5 9.2 + - - +
190A VAL 3.4 0.2 - - - -
191A VAL* 1.3 77.9 - - - +
193A ASP* 1.3 67.7 + - - +
195A TYR* 3.1 3.2 + - - +
196A GLN* 2.7 61.8 + - + +
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Residues in contact with ASP 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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181A VAL* 3.6 16.3 - - + +
182A ASN 5.3 0.2 + - - -
185A GLN* 2.9 35.0 + - - +
189A ASN* 2.9 19.7 + - - +
192A GLU* 1.3 76.7 - - - +
194A THR* 1.3 62.7 + - - +
196A GLN* 4.0 8.5 - - - +
197A THR* 2.6 35.8 + - - +
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Residues in contact with THR 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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7A PHE* 3.9 11.9 - - + -
18A VAL* 3.2 29.1 - - + +
22A VAL* 4.2 2.7 - - + -
129A ILE* 3.9 13.9 - - + -
131A LEU* 3.6 5.9 - - - +
181A VAL* 3.1 21.1 - - - +
190A VAL 2.9 23.5 + - - -
191A VAL 3.6 2.0 - - - -
193A ASP* 1.3 77.0 - - - +
195A TYR* 1.3 56.9 + - - +
197A THR* 3.2 5.4 + - - -
198A ILE* 2.9 47.1 + - + +
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Residues in contact with TYR 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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22A VAL* 4.1 17.7 - - + +
25A ARG* 3.2 74.1 + - + +
26A LEU* 4.1 20.5 - - + +
28A LYS* 5.7 1.0 - - - +
191A VAL 3.0 12.9 + - - +
192A GLU 3.1 7.8 + - - +
194A THR* 1.3 74.4 - - - +
196A GLN* 1.3 66.7 + - - +
198A ILE* 2.7 26.3 + - - +
199A ILE* 2.8 48.0 + - + +
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Residues in contact with GLN 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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25A ARG* 4.9 0.2 - - - +
192A GLU* 2.7 43.3 + - + +
193A ASP* 4.0 8.1 - - - +
195A TYR* 1.3 86.3 - - - +
197A THR* 1.3 61.4 + - - +
199A ILE* 3.6 21.7 - - - +
200A LYS* 3.1 28.6 + - - +
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Residues in contact with THR 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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127A LEU* 4.3 4.2 - - + +
129A ILE* 3.6 25.1 - - + -
179A LYS* 3.6 37.0 - - + +
181A VAL* 4.8 5.6 - - + +
193A ASP* 2.6 24.1 + - - +
194A THR* 3.3 6.6 - - - -
195A TYR 3.1 1.0 - - - -
196A GLN* 1.3 78.9 - - - +
198A ILE* 1.3 61.5 + - - +
200A LYS* 3.9 7.5 - - - +
201A TYR* 3.4 18.5 + - - +
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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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5A ILE* 3.7 26.9 - - + -
7A PHE* 3.7 17.0 - - + -
22A VAL* 3.7 24.0 - - + -
26A LEU* 3.8 22.7 - - + -
89A LEU* 5.1 0.4 - - + -
127A LEU* 4.3 9.4 - - + -
129A ILE* 4.1 15.7 - - + -
194A THR* 2.9 34.5 + - + +
195A TYR* 2.7 14.7 + - - +
197A THR* 1.3 70.8 - - - +
199A ILE* 1.3 60.9 + - + +
201A TYR* 3.1 4.5 + - - +
202A LEU* 3.0 31.3 + - + +
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Residues in contact with ILE 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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26A LEU* 4.1 13.5 - - + -
30A TYR* 5.3 4.5 - - + -
195A TYR* 2.8 64.0 + - + +
196A GLN* 3.6 27.6 - - - +
198A ILE* 1.3 69.5 - - - +
200A LYS* 1.3 77.1 + - + +
202A LEU* 4.3 6.5 - - - +
203A GLU* 2.8 63.0 + - + +
204A LYS* 5.5 2.0 - - - +
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Residues in contact with LYS 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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179A LYS* 5.7 12.8 - - - +
196A GLN 3.1 20.9 + - - +
197A THR* 3.9 7.2 - - - +
199A ILE* 1.3 83.4 - - + +
201A TYR* 1.3 59.8 + - - +
204A LYS* 3.4 50.7 + - + +
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Residues in contact with TYR 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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3A ALA* 4.2 15.9 - - + -
5A ILE* 5.0 1.3 - - + -
126A ASP* 3.1 49.7 + - + +
127A LEU* 3.8 37.2 - - + -
179A LYS* 6.4 2.0 - - - -
197A THR 3.4 5.5 + - - +
198A ILE 3.1 9.6 + - - +
200A LYS* 1.3 80.1 - - - +
202A LEU* 1.3 77.4 + - + +
204A LYS 3.5 19.0 + - - +
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Residues in contact with LEU 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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1A MET* 5.6 6.1 - - - +
3A ALA* 3.4 33.4 - - + -
5A ILE* 4.2 3.4 - - + -
26A LEU* 4.0 13.9 - - + -
30A TYR* 3.4 42.3 + - + +
87A VAL* 3.8 22.0 - - + -
198A ILE* 3.0 34.6 + - + +
199A ILE* 3.1 2.9 + - - +
201A TYR* 1.3 88.0 - - + +
203A GLU* 1.3 60.3 + - - +
204A LYS 3.2 5.1 + - - +
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Residues in contact with GLU 203 (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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30A TYR* 3.5 17.4 + - + +
199A ILE* 2.8 43.2 + - + +
202A LEU* 1.3 75.4 - - - +
204A LYS* 1.3 82.9 + - - +
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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