Contacts of the helix formed by residues 205 - 222 (chain A) in PDB entry 4FV3
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 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A HIS* 2.9 71.1 + - + +
140A SER* 5.0 1.4 - - - +
142A ASN* 4.1 20.7 + - - +
144A LEU* 3.5 21.0 - - + +
172A ALA* 4.6 6.9 - - + +
204A THR* 1.4 72.2 - - - +
206A SER* 1.3 61.4 + - - +
208A ASP* 3.2 12.6 + - - +
209A ILE* 3.6 7.2 + - + +
301A GLU* 5.8 5.4 - - + +
403A SO4 2.7 49.8 + - - +
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Residues in contact with SER 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLU* 4.2 1.2 + - - -
204A THR* 2.8 25.3 + - - -
205A LYS* 1.3 77.2 - - - +
207A ILE* 1.4 59.6 + - - +
208A ASP 3.3 0.2 - - - -
209A ILE* 3.6 9.4 + - - -
210A TRP 3.3 12.1 + - - -
296A PRO* 3.5 37.9 + - - +
299A ARG* 2.8 33.2 + - - -
300A ILE 5.7 1.1 - - - -
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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
----------------------------------------------------------
144A LEU* 4.7 1.6 - - + -
146A ARG* 3.5 38.4 - - + +
185A TYR* 4.4 4.3 - - - +
191A TYR 4.7 0.7 - - - +
193A ALA* 4.1 10.6 + - + +
195A GLU* 3.8 17.3 - - - +
196A ILE* 3.8 29.4 - - + -
200A SER* 4.6 3.6 - - - +
202A GLY* 3.7 18.4 - - - +
204A THR* 3.1 27.2 + - - +
206A SER* 1.4 76.7 + - - +
208A ASP* 1.3 77.6 + - - +
210A TRP* 3.6 4.3 + - - +
211A SER* 3.3 24.4 + - - +
299A ARG* 4.4 2.5 - - - +
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Residues in contact with ASP 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 3.8 5.0 - - + +
139A HIS* 2.9 34.6 + - + +
144A LEU* 3.4 4.7 - - - +
145A HIS* 2.8 24.7 + - - +
146A ARG* 2.8 29.7 + - - -
148A LEU* 3.8 19.9 + - + +
205A LYS 3.2 3.4 + - - +
207A ILE* 1.3 82.1 - - - +
209A ILE* 1.4 58.2 + - - +
211A SER* 3.2 7.9 + - - -
212A VAL* 3.0 32.9 + - - +
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 4.3 11.2 - - + -
135A LEU* 3.7 19.3 - - + -
139A HIS* 4.7 2.5 - - + -
205A LYS* 3.6 13.3 + - + +
206A SER* 3.9 11.4 - - - +
207A ILE 3.4 0.6 - - - -
208A ASP* 1.4 71.6 - - - +
210A TRP* 1.4 65.6 + - - +
212A VAL* 3.2 7.2 + - + +
213A GLY* 2.9 20.6 + - - -
291A MET* 4.0 11.4 - - + +
299A ARG* 3.7 17.3 - - + -
300A ILE* 3.2 37.2 - - + +
301A GLU* 4.1 3.4 - - - +
302A VAL* 3.6 35.0 - - + +
305A ALA* 5.1 2.7 - - + -
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Residues in contact with TRP 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TRP 5.2 0.4 + - - -
191A TYR 3.5 16.6 - - - -
192A ARG 3.3 11.3 + - - -
193A ALA* 3.4 24.9 - - + -
194A PRO* 3.6 31.0 - - + -
206A SER 3.3 4.6 + - - -
207A ILE 3.7 8.7 - - - +
208A ASP 3.3 0.2 - - - -
209A ILE* 1.4 78.9 - - - +
211A SER* 1.4 54.9 + - - +
213A GLY* 3.1 4.2 + - - -
214A CYS* 3.0 39.5 + - - -
226A PHE* 3.5 25.5 - + - -
238A ILE* 3.6 25.5 - - + +
242A LEU* 3.9 9.4 - - + -
291A MET 3.9 8.5 - - - -
292A LEU* 3.5 44.7 - - + +
293A THR 3.6 8.1 - - - -
299A ARG* 3.8 25.0 - - - +
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Residues in contact with SER 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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146A ARG 5.6 3.3 - - - -
147A ASP* 5.8 0.3 - - - -
148A LEU* 3.6 33.0 + - - -
191A TYR* 2.9 29.5 + - - +
207A ILE* 3.3 11.7 + - - +
208A ASP* 3.2 12.4 + - - -
210A TRP* 1.4 76.6 - - - +
212A VAL* 1.4 56.9 + - - +
214A CYS* 3.2 5.7 + - - +
215A ILE* 3.0 33.1 + - - +
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Residues in contact with VAL 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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128A LEU* 3.7 26.0 - - + +
131A ILE* 3.9 27.4 - - + -
132A LEU* 4.1 10.5 - - + -
135A LEU* 3.9 16.2 - - + -
148A LEU* 3.8 19.3 - - + -
208A ASP 3.0 15.5 + - - +
209A ILE* 3.2 8.7 + - - +
211A SER* 1.4 70.4 - - - +
213A GLY* 1.3 55.0 + - - +
215A ILE* 3.1 10.3 + - + +
216A LEU* 2.8 32.9 + - - +
291A MET* 4.0 11.2 - - - -
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Residues in contact with GLY 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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209A ILE 2.9 9.9 + - - -
210A TRP 3.1 4.7 + - - -
212A VAL* 1.3 75.9 - - - +
214A CYS* 1.3 54.7 + - - +
216A LEU 3.3 1.0 + - - -
217A ALA* 3.0 24.4 + - - +
288A LEU* 3.1 11.9 - - - +
291A MET* 3.8 26.8 - - - -
292A LEU* 3.7 18.8 - - - -
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Residues in contact with CYS 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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190A TRP 4.0 11.2 - - - +
191A TYR* 3.7 22.7 - - + -
210A TRP* 3.0 47.4 + - - -
211A SER 3.2 7.8 + - - +
213A GLY* 1.3 75.3 - - - +
215A ILE* 1.4 56.3 + - - +
217A ALA* 3.4 3.1 + - - +
218A GLU* 3.0 30.0 + - - +
225A ILE* 4.0 16.0 + - + +
226A PHE* 3.9 21.5 - - - -
292A LEU* 4.0 2.7 - - - -
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Residues in contact with ILE 215 (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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110A LEU* 3.7 28.4 - - + +
128A LEU* 6.3 0.2 - - + -
131A ILE* 4.0 16.2 - - + -
148A LEU* 3.8 12.8 - - + -
149A LYS* 3.7 35.7 - - - +
150A PRO* 4.1 10.3 - - + -
153A LEU* 3.9 19.3 - - + -
191A TYR* 4.3 4.9 - - + -
211A SER 3.0 23.4 + - - +
212A VAL* 3.1 13.0 + - + +
214A CYS* 1.4 73.2 - - - +
216A LEU* 1.4 58.7 + - - +
218A GLU* 3.2 8.0 + - - +
219A MET* 3.0 30.8 + - + +
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Residues in contact with LEU 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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124A ILE* 3.7 26.7 - - + -
128A LEU* 3.9 26.9 - - + +
212A VAL 2.8 15.6 + - - +
213A GLY 3.3 7.2 + - - +
215A ILE* 1.4 71.6 - - - +
217A ALA* 1.4 62.5 - - - +
219A MET* 3.1 21.4 + - + +
220A LEU* 3.2 29.3 + - + +
284A ALA* 3.6 26.2 - - + +
287A LEU* 4.7 1.1 - - + -
288A LEU* 3.8 14.6 - - + +
291A MET* 3.4 28.5 - - + -
310A TYR* 4.7 5.2 - - + -
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Residues in contact with ALA 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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213A GLY 3.0 16.3 + - - +
214A CYS 3.7 4.7 - - - +
216A LEU* 1.4 75.6 - - - +
218A GLU* 1.4 60.7 + - - +
220A LEU* 3.4 12.3 + - - +
221A SER* 3.4 17.5 + - - -
223A ARG 4.7 1.6 - - - -
225A ILE* 3.7 37.7 - - + -
277A PHE* 3.4 19.2 - - + -
288A LEU* 3.9 12.3 - - + +
292A LEU* 4.7 0.2 - - + -
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Residues in contact with GLU 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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111A TYR* 5.6 4.2 - - - -
114A LEU* 3.8 19.2 - - + +
150A PRO* 3.8 15.1 - - + +
190A TRP* 5.7 1.2 - - - -
191A TYR* 2.6 38.2 + - - -
214A CYS 3.0 11.9 + - - +
215A ILE* 3.4 11.0 - - - +
217A ALA* 1.4 73.9 - - - +
219A MET* 1.3 56.5 + - - +
222A ASN* 2.7 36.7 + - - -
223A ARG* 3.5 27.0 - - - +
224A PRO* 3.6 24.8 - - + +
225A ILE 5.1 0.6 - - - +
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Residues in contact with MET 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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110A LEU* 3.9 21.1 - - + -
114A LEU* 3.7 12.1 - - + +
119A LEU* 3.9 23.9 + - + +
124A ILE* 3.5 45.5 - - + +
127A PHE* 3.7 34.8 - - + -
128A LEU* 4.2 18.2 - - + +
131A ILE* 4.4 4.3 - - + -
215A ILE* 3.0 21.2 + - + +
216A LEU* 3.1 26.7 + - + +
218A GLU* 1.3 74.8 - - - +
220A LEU* 1.3 60.8 + - - +
221A SER 3.7 0.2 + - - -
222A ASN* 4.3 8.0 - - - +
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Residues in contact with LEU 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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118A HIS* 5.9 2.4 - - - -
121A ASN* 5.6 2.2 - - - +
124A ILE* 3.8 31.5 - - + +
216A LEU* 3.2 26.7 + - + +
217A ALA* 3.6 15.7 - - - +
218A GLU 3.3 0.6 - - - -
219A MET* 1.3 78.0 - - - +
221A SER* 1.3 57.3 + - - +
222A ASN* 4.9 2.3 - - - +
277A PHE* 3.8 19.8 - - + +
280A ALA* 3.8 21.8 - - + -
281A ASP 5.3 0.2 - - - +
284A ALA* 4.7 10.5 - - + -
285A LEU* 3.9 25.8 - - + -
288A LEU* 4.3 8.3 - - + -
310A TYR* 5.5 0.2 - - - +
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Residues in contact with SER 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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217A ALA 3.4 12.0 + - - -
218A GLU 3.4 1.0 + - - -
220A LEU* 1.3 80.0 - - - +
222A ASN* 1.4 69.7 + - - +
223A ARG* 3.4 35.3 + - - +
225A ILE* 6.0 0.3 - - - -
276A LEU 5.5 1.8 - - - -
277A PHE* 3.6 20.7 - - - -
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Residues in contact with ASN 222 (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* 3.0 46.3 + - - +
117A GLN 2.7 29.0 + - - +
118A HIS* 4.3 13.0 - - - -
119A LEU* 4.6 1.6 + - - +
218A GLU* 2.7 21.6 + - - -
219A MET 4.3 6.9 + - - +
220A LEU 4.9 1.2 - - - +
221A SER* 1.4 76.6 - - - +
223A ARG* 1.3 56.9 + - - +
407A EDO 3.6 25.7 + - - +
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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
------------------------------------------------------------
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