Contacts of the helix formed by residues 197 - 214 (chain A) in PDB entry 4FG7
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 LYS 197 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A HIS* 3.0 78.2 + - + +
134A ASP* 5.1 2.0 + - - +
136A GLY* 4.7 5.9 - - - -
138A VAL* 4.1 12.3 - - + -
169A GLU* 4.1 21.5 + - - +
196A SER* 1.3 72.1 + - - +
198A ALA* 1.3 65.4 + - - +
199A VAL 3.1 0.7 + - - -
200A ASP 3.3 10.3 + - - -
201A CYS* 3.7 5.9 + - - -
266A THR* 6.5 0.9 - - + -
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Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLU* 4.3 2.2 - - - +
196A SER* 3.2 10.5 + - - +
197A LYS* 1.3 77.9 - - - +
199A VAL* 1.3 62.4 + - - +
201A CYS* 3.1 16.2 + - - -
202A TRP 3.2 6.1 + - - -
261A PRO* 4.1 27.1 - - + +
264A ARG* 2.9 41.3 + - + +
265A PHE 5.5 0.9 - - - -
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 4.5 0.9 - - + -
140A ARG* 3.9 42.2 - - + +
185A VAL* 6.4 0.4 - - - -
186A ALA* 4.4 6.9 + - + +
188A GLU* 4.2 13.0 - - + +
189A VAL* 3.8 30.7 - - + -
196A SER* 3.2 26.5 - - - +
198A ALA* 1.3 79.3 - - - +
200A ASP* 1.3 64.3 + - - +
202A TRP* 3.4 12.0 + - - +
203A SER* 3.5 14.5 + - - +
264A ARG* 3.8 4.9 - - - +
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Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 4.1 6.6 - - + +
132A LEU* 5.7 0.3 - - - +
133A HIS* 3.2 32.2 + - + +
138A VAL* 3.3 7.7 - - - +
139A HIS* 2.7 28.1 + - - +
140A ARG* 2.7 30.4 + - - -
141A ASP 4.4 0.2 + - - -
142A LEU* 3.7 24.1 + - + +
197A LYS 3.3 2.0 + - - -
199A VAL* 1.3 73.8 - - - +
201A CYS* 1.3 66.9 + - - +
203A SER* 3.2 7.5 + - - -
204A ILE* 3.0 28.0 + - - +
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Residues in contact with CYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 6.0 0.7 - - - -
133A HIS* 4.0 4.0 - - - -
197A LYS* 3.8 13.2 - - - -
198A ALA* 3.1 11.2 + - - +
200A ASP* 1.3 76.9 - - - +
202A TRP* 1.3 63.1 - - - +
204A ILE* 3.5 10.5 + - - +
205A GLY 3.3 13.2 + - - -
256A LEU* 3.4 23.8 - - + +
264A ARG* 4.3 3.1 - - - -
265A PHE 3.3 27.8 - - - +
266A THR* 3.9 3.8 - - - -
267A CYS* 3.7 37.7 - - - -
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Residues in contact with TRP 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLY 4.6 2.2 + - - -
184A TYR 3.6 14.6 + - - -
185A VAL 3.5 12.3 + - - -
186A ALA* 3.6 16.4 - - + -
187A PRO* 3.5 35.7 - - + -
198A ALA 3.2 5.1 + - - -
199A VAL 3.6 8.5 - - - +
200A ASP 3.2 0.4 - - - -
201A CYS* 1.3 73.9 - - - +
203A SER* 1.3 58.6 + - - +
205A GLY* 2.8 23.7 + - - -
206A VAL* 3.1 26.9 + - + +
218A PHE* 3.8 29.4 - + - -
230A ILE* 4.6 3.4 - - + -
233A ALA* 3.8 14.6 - - + -
235A TYR* 4.8 1.6 - + - -
256A LEU 3.8 9.2 - - - -
257A MET* 3.5 46.1 - - + +
258A GLU 3.7 20.4 - - - -
259A LYS 4.2 1.6 - - - -
264A ARG* 3.8 17.8 - - - +
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG 5.5 3.1 + - - -
142A LEU* 3.7 35.1 + - - +
184A TYR* 2.8 27.2 + - - -
185A VAL* 4.9 0.5 - - - -
199A VAL* 3.5 11.5 + - - +
200A ASP* 3.2 11.8 + - - -
202A TRP* 1.3 79.6 - - - +
204A ILE* 1.3 58.4 + - - +
206A VAL* 3.2 5.8 + - - +
207A ILE* 2.9 32.8 + - - +
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 4.0 31.7 - - + +
125A VAL* 4.1 17.0 - - + -
126A LEU* 3.8 27.8 - - + -
129A VAL* 4.0 33.0 - - + -
142A LEU* 4.2 10.5 - - + -
200A ASP 3.0 19.8 + - - +
201A CYS* 3.8 9.2 - - - +
202A TRP 3.1 0.4 + - - -
203A SER* 1.3 75.7 - - - +
205A GLY* 1.3 63.2 + - - +
207A ILE* 3.3 9.1 + - + +
208A ALA* 3.0 22.0 + - - +
256A LEU* 4.3 8.3 - - + -
267A CYS* 4.6 1.8 - - - -
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Residues in contact with GLY 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A CYS 3.3 4.4 + - - -
202A TRP 2.8 8.8 + - - -
204A ILE* 1.3 77.7 - - - +
206A VAL* 1.3 57.7 + - - +
208A ALA* 3.1 6.6 + - - +
209A TYR* 2.9 28.9 + - - +
253A ILE* 4.1 7.0 - - - +
256A LEU* 3.9 25.3 - - - +
257A MET* 3.8 13.8 - - - +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLY 3.5 17.7 - - - +
184A TYR* 3.4 31.4 - - + -
202A TRP* 3.1 36.5 + - + +
203A SER* 3.6 8.3 - - - +
205A GLY* 1.3 77.4 - - - +
207A ILE* 1.3 61.8 + - - +
209A TYR* 3.3 3.5 + - - +
210A ILE* 3.1 23.9 + - + +
216A PRO* 5.8 0.4 - - + -
217A PRO* 3.9 18.6 - - + -
218A PHE* 4.7 0.9 - - + -
257A MET* 3.8 24.9 - - + -
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Residues in contact with ILE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.3 8.5 - - + -
107A ILE* 5.8 0.4 - - + +
121A LEU* 5.0 0.4 - - + -
122A ILE* 4.2 8.7 - - + -
125A VAL* 5.6 3.4 - - + -
142A LEU* 4.1 11.9 - - + -
143A LYS* 3.9 26.7 - - - +
144A PRO* 4.0 20.6 - - + -
147A LEU* 4.0 27.8 - - + -
184A TYR* 4.5 4.0 - - + -
203A SER 2.9 23.8 + - - +
204A ILE* 3.7 11.7 - - + +
205A GLY 3.2 0.2 - - - -
206A VAL* 1.3 76.5 - - - +
208A ALA* 1.3 61.6 + - - +
210A ILE* 3.4 8.0 + - - +
211A LEU* 3.0 38.7 + - + +
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Residues in contact with ALA 208 (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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118A ALA* 6.1 0.2 - - - -
122A ILE* 4.0 22.0 - - + +
204A ILE 3.0 13.1 + - - +
205A GLY* 3.1 11.2 + - - +
207A ILE* 1.3 74.9 - - - +
209A TYR* 1.3 66.1 + - - +
211A LEU* 3.2 6.7 + - - +
212A LEU* 3.0 29.0 + - - +
252A PHE* 4.5 12.6 - - + -
253A ILE* 4.2 17.7 - - + -
275A TRP* 5.1 6.7 - - + -
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Residues in contact with TYR 209 (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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205A GLY 2.9 12.1 + - - +
206A VAL* 3.5 13.0 - - - +
208A ALA* 1.3 78.2 - - - +
210A ILE* 1.3 60.7 + - - +
212A LEU 3.4 0.3 + - - -
213A CYS* 3.3 37.9 + - - -
215A TYR* 3.5 16.3 - + - -
216A PRO 3.8 2.0 - - - -
217A PRO* 3.4 46.7 + - + +
235A TYR* 4.3 6.3 - + - -
236A GLU 2.6 24.7 + - - -
237A PHE* 3.6 27.4 - + - -
238A ASP* 3.9 5.4 + - - -
242A TRP* 3.4 36.5 + + - -
253A ILE* 4.1 9.7 - - + +
257A MET* 4.4 5.8 - - - -
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Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 4.2 27.4 - - + +
112A PHE* 4.9 0.2 - - - +
144A PRO* 4.7 5.2 - - + -
184A TYR* 3.3 44.0 - - + +
206A VAL* 3.1 17.6 + - + +
207A ILE* 3.9 4.5 - - - +
209A TYR* 1.3 75.2 - - - +
211A LEU* 1.3 58.1 + - - +
214A GLY* 2.7 33.7 + - - +
215A TYR* 3.7 28.3 - - - +
216A PRO* 3.7 21.5 - - + -
217A PRO* 4.2 1.8 - - + -
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Residues in contact with LEU 211 (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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103A LEU* 4.1 19.7 - - + -
107A ILE* 4.1 11.0 - - + -
112A PHE* 3.5 2.8 - - - +
113A TYR* 2.7 69.6 + - + +
118A ALA* 3.9 24.9 - - + +
121A LEU* 3.7 24.9 - - + -
122A ILE* 4.0 16.4 - - + -
207A ILE* 3.0 27.0 + - + +
208A ALA* 3.2 5.1 + - - +
210A ILE* 1.3 76.7 - - - +
212A LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 212 (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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112A PHE* 3.8 18.9 - - - +
113A TYR 4.1 7.4 - - - +
115A GLU* 4.0 19.5 - - + -
118A ALA* 3.8 23.6 - - + -
208A ALA 3.0 13.2 + - - +
209A TYR 4.0 3.4 - - - +
210A ILE 3.2 0.4 - - - -
211A LEU* 1.3 80.1 - - - +
213A CYS* 1.3 57.4 + - - +
242A TRP* 4.1 10.3 - - + -
245A ILE* 4.0 28.7 - - + +
249A ALA* 4.0 22.2 - - + -
253A ILE* 3.8 28.0 - - + -
275A TRP* 4.0 19.3 - - + -
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Residues in contact with CYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 4.0 12.9 - - - +
209A TYR* 3.3 33.1 + - - -
212A LEU* 1.3 77.7 - - - +
214A GLY* 1.3 58.5 + - - +
215A TYR* 3.3 59.3 - - + +
241A TYR* 5.0 9.2 - - + +
242A TRP* 3.6 23.6 - - + +
245A ILE* 5.9 0.7 - - + -
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Residues in contact with GLY 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 4.8 5.1 - - - +
111A GLY 3.2 25.7 - - - +
112A PHE* 3.9 1.2 - - - +
210A ILE* 2.7 29.9 + - - +
212A LEU 3.9 0.4 - - - -
213A CYS* 1.3 72.5 - - - +
215A TYR* 1.3 61.1 + - - +
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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
------------------------------------------------------------
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