Contacts of the helix formed by residues 205 - 221 (chain A) in PDB entry 4L7F
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 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A HIS* 5.3 0.4 - - - -
195A GLU* 4.5 0.2 - - - +
203A LYS* 3.5 29.9 + - - +
204A GLU* 1.3 74.6 - - - +
206A VAL* 1.3 66.6 + - - +
207A ASP 3.1 1.1 - - - +
208A LEU* 3.0 24.1 + - + +
306A ALA* 2.9 35.3 + - - +
309A ARG* 3.0 28.5 + - - +
310A ILE 3.1 29.3 + - - +
311A SER* 4.4 8.9 - - - +
312A VAL* 5.1 2.2 - - - +
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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
----------------------------------------------------------
148A ILE* 3.3 26.7 - - + -
150A ARG* 3.7 20.1 - - + +
193A ALA* 3.6 17.3 - - + +
195A GLU* 3.5 28.2 + - + +
196A VAL* 3.9 20.6 - - + -
202A TYR* 4.2 8.1 - - + -
203A LYS 3.2 19.2 + - - +
204A GLU 3.0 0.8 + - - +
205A ASN* 1.3 80.9 + - - +
207A ASP* 1.3 68.5 + - - +
209A TRP* 3.4 18.0 + - - +
210A SER* 3.8 6.1 + - - -
309A ARG* 3.6 1.1 - - - +
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Residues in contact with ASP 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 3.9 23.0 - - + +
143A HIS* 2.7 29.2 + - + +
148A ILE* 3.8 1.9 - - - +
149A HIS* 2.9 29.6 + - - +
150A ARG* 2.6 30.9 + - - -
151A ASP 4.5 0.3 + - - -
152A LEU* 5.0 3.6 + - + +
204A GLU 3.1 7.1 + - - +
205A ASN 3.1 0.8 - - - -
206A VAL* 1.3 81.8 - - - +
208A LEU* 1.3 60.5 + - - +
209A TRP 3.3 0.2 - - - -
210A SER* 3.3 10.8 + - - -
211A VAL* 3.1 30.1 + - - +
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Residues in contact with LEU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.4 33.0 - - + -
139A ILE* 5.8 0.6 - - + +
205A ASN* 3.0 20.4 + - + +
207A ASP* 1.3 76.7 - - - +
209A TRP* 1.3 62.0 + - - +
211A VAL* 3.4 4.5 + - + +
212A GLY 2.9 23.2 + - - -
301A MET* 3.0 44.8 - - + +
309A ARG* 4.2 2.9 - - + -
310A ILE* 2.3 50.7 - - + +
311A SER 4.4 6.7 - - - -
312A VAL* 4.4 9.2 - - + +
315A ALA* 3.9 8.3 - - + -
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Residues in contact with TRP 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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190A TYR 5.0 0.4 + - - -
191A TYR 3.5 15.9 - - - -
192A ARG 3.4 12.6 + - - -
193A ALA* 3.4 24.2 - - + -
194A PRO* 3.4 29.4 - - + -
205A ASN 3.5 2.8 + - - -
206A VAL 3.4 12.4 + - - +
207A ASP 3.3 0.2 - - - -
208A LEU* 1.3 79.1 - - - +
210A SER* 1.3 57.1 + - - +
212A GLY* 3.0 3.6 + - - -
213A CYS* 2.9 41.6 + - - -
225A PHE* 3.6 23.4 - + - -
233A GLN* 5.7 0.2 - - - +
237A VAL* 4.0 14.1 - - + -
241A LEU* 3.5 22.7 - - + -
301A MET 3.9 14.4 - - - -
302A LEU* 3.7 9.0 - - + +
303A VAL 3.6 45.1 - - - -
304A ILE* 3.9 3.1 - - + -
309A ARG* 3.9 10.2 - - - +
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Residues in contact with SER 210 (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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150A ARG 4.4 9.0 + - - -
152A LEU* 3.7 35.4 + - - -
191A TYR* 2.7 28.5 + - - -
192A ARG* 4.6 0.7 - - - -
193A ALA 4.8 0.5 + - - -
206A VAL 4.0 8.1 + - - -
207A ASP* 3.3 11.7 + - - -
208A LEU 3.3 0.4 - - - -
209A TRP* 1.3 79.6 - - - +
211A VAL* 1.3 63.4 + - - +
213A CYS* 3.2 4.7 + - - +
214A ILE* 3.0 29.1 + - - +
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 4.1 21.3 - - + +
135A MET* 4.7 14.4 - - + -
136A LEU* 4.2 28.3 - - + -
139A ILE* 4.7 8.5 - - + -
152A LEU* 3.9 19.5 - - + -
207A ASP 3.1 16.8 + - - +
208A LEU* 3.7 10.3 - - + +
209A TRP 3.3 0.2 - - - -
210A SER* 1.3 76.2 - - - +
212A GLY* 1.3 58.4 + - - +
214A ILE* 3.2 9.7 + - - +
215A MET* 2.8 27.2 + - - +
301A MET* 4.0 17.3 - - + -
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Residues in contact with GLY 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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208A LEU 2.9 13.9 + - - -
209A TRP 3.0 4.4 + - - -
211A VAL* 1.3 76.3 - - - +
213A CYS* 1.3 56.7 + - - +
215A MET* 3.4 1.1 + - - -
216A GLY* 2.9 25.6 + - - -
298A LEU* 3.5 10.0 - - - +
301A MET* 3.6 26.9 - - - +
302A LEU* 3.8 16.0 - - - +
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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
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190A TYR 4.0 10.1 - - - +
191A TYR* 3.6 22.5 - - + -
209A TRP* 2.9 43.7 + - - -
210A SER 3.2 8.5 + - - +
212A GLY* 1.3 76.5 - - - +
214A ILE* 1.3 62.4 + - - +
217A GLU* 3.1 25.5 + - - +
224A LEU* 3.9 15.7 + - + +
225A PHE* 3.8 26.0 - - - -
302A LEU* 4.0 2.0 - - - -
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Residues in contact with ILE 214 (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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115A LEU* 3.8 23.3 - - + -
119A ILE* 4.3 9.8 - - + +
135A MET* 4.0 18.4 - - + -
152A LEU* 4.0 27.6 - - + +
153A LYS* 4.1 15.5 - - - +
154A PRO* 3.9 10.5 - - + -
157A ILE* 4.1 15.0 - - + -
191A TYR* 3.9 15.7 - - + -
210A SER 3.0 18.1 + - - +
211A VAL* 3.6 7.2 - - - +
213A CYS* 1.3 74.1 - - - +
215A MET* 1.3 59.3 + - - +
217A GLU* 3.3 7.0 + - - +
218A MET* 2.9 33.0 + - + +
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Residues in contact with MET 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET* 6.6 0.2 - - - -
132A LEU* 3.6 32.5 - - + +
211A VAL 2.8 21.2 + - - +
212A GLY* 3.7 4.9 - - - +
214A ILE* 1.3 72.6 - - - +
216A GLY* 1.3 63.8 + - - +
218A MET* 3.2 8.7 + - + +
219A VAL* 3.1 31.5 + - + +
294A ALA* 3.5 45.3 - - + +
297A LEU* 4.0 10.5 - - + -
298A LEU* 3.8 16.4 - - + -
301A MET* 3.6 23.8 - - - -
320A TYR* 3.8 19.7 - - + -
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Residues in contact with GLY 216 (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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212A GLY 2.9 17.0 + - - -
215A MET* 1.3 75.8 - - - +
217A GLU* 1.3 56.1 + - - +
219A VAL* 3.3 6.5 + - - +
220A CYS* 3.0 30.1 + - - -
224A LEU* 3.7 14.8 - - - -
275A PHE* 3.7 21.4 - - - -
298A LEU* 3.6 8.2 - - - +
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Residues in contact with GLU 217 (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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116A CYS* 5.9 1.7 - - - -
119A ILE* 4.0 32.5 - - + +
154A PRO* 4.6 1.4 - - - +
191A TYR* 2.5 40.7 + - - -
213A CYS 3.1 16.1 + - - +
214A ILE* 3.6 4.9 - - - +
216A GLY* 1.3 73.9 - - - +
218A MET* 1.3 59.2 + - - +
220A CYS* 4.3 0.2 - - - -
221A HIS* 2.8 30.5 + - - -
222A LYS 3.5 28.5 - - - +
223A ILE* 3.8 21.4 + - - +
224A LEU* 4.0 2.0 + - - +
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Residues in contact with MET 218 (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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115A LEU* 4.4 4.7 - - + -
119A ILE* 4.2 31.0 - - + +
123A LEU* 3.8 15.4 - - + +
128A MET* 3.5 52.9 - - + +
131A LEU* 4.2 17.5 - - + -
132A LEU* 4.8 11.0 - - + -
135A MET* 4.1 26.9 - - + -
214A ILE* 2.9 17.8 + - + +
215A MET* 3.3 10.1 - - - +
217A GLU* 1.3 76.1 - - - +
219A VAL* 1.3 63.2 + - - +
221A HIS* 3.8 17.8 + - - -
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Residues in contact with VAL 219 (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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128A MET* 4.5 15.0 - - - -
215A MET* 3.1 21.2 + - + +
216A GLY 3.5 7.6 - - - +
217A GLU 3.2 0.2 - - - -
218A MET* 1.3 80.5 - - - +
220A CYS* 1.3 60.1 + - - +
221A HIS* 3.7 9.2 + - - -
275A PHE* 4.1 14.1 - - + -
279A LEU* 3.3 44.4 - - + +
280A PHE* 3.7 43.5 - - + -
294A ALA* 5.6 1.1 - - + -
298A LEU* 4.5 9.9 - - + -
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Residues in contact with CYS 220 (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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216A GLY 3.0 18.9 + - - +
219A VAL* 1.3 76.0 - - - +
221A HIS* 1.3 71.0 + - - +
222A LYS* 3.2 41.5 + - + +
224A LEU* 3.7 15.0 - - - -
274A LEU 5.6 0.4 - - - +
275A PHE* 4.8 6.1 - - + -
279A LEU* 3.8 31.6 - - + +
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Residues in contact with HIS 221 (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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119A ILE* 3.1 31.5 + - - +
120A GLN* 3.8 11.8 + - - -
121A MET 3.1 19.1 + - - -
122A GLU* 3.5 26.7 + - - -
123A LEU 5.4 1.0 + - - -
217A GLU* 2.8 16.7 + - - -
218A MET 3.8 10.3 + - - -
219A VAL 3.8 13.0 + - - -
220A CYS* 1.3 79.8 - - - +
222A LYS* 1.3 57.9 + - - +
279A LEU 5.7 0.7 - - - -
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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
------------------------------------------------------------
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