Contacts of the helix formed by residues 202 - 222 (chain A) in PDB entry 4NEF
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 TRP 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ALA* 3.7 26.7 - - + +
128A GLY* 5.0 2.0 - - - -
131A VAL* 3.8 26.7 - - + -
200A ASP* 4.3 14.6 + - - +
201A HIS* 1.4 74.1 - - - +
203A VAL* 1.4 81.1 + - + +
205A TRP* 3.1 7.2 + - - +
206A ILE* 2.7 61.1 + - + +
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.5 1.6 - - + -
127A ALA* 3.7 21.1 - - + +
130A ALA* 3.8 15.5 - - + +
131A VAL* 3.6 28.5 - - - +
134A GLU* 4.3 3.8 - - + +
179A THR* 4.4 1.6 - - + -
200A ASP* 3.4 19.5 - - + +
201A HIS 3.3 0.4 - - - -
202A TRP* 1.4 108.7 - - + +
204A PHE* 1.3 71.8 + - + +
207A GLY* 3.0 29.3 + - - -
208A PRO* 3.5 1.7 - - - +
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Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASN* 3.2 52.0 - - + -
120A ALA* 3.9 3.6 - - - -
121A LEU* 4.0 14.4 - - + -
134A GLU* 4.7 2.5 - - - -
179A THR* 3.6 30.5 - - + -
182A SER* 3.7 12.8 + - - +
185A PRO* 3.6 18.7 - - - +
188A SER* 3.2 22.4 - - - +
199A ASP 3.7 9.9 - - - -
200A ASP 3.2 24.5 - - - -
201A HIS* 3.3 24.1 + - - +
203A VAL* 1.3 79.8 - - + +
205A TRP* 1.3 59.5 + - + +
208A PRO* 3.4 21.6 - - - +
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Residues in contact with TRP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 5.4 6.1 - - + -
90A VAL* 6.0 2.7 - - + -
94A LEU* 3.7 27.1 - - + -
185A PRO* 3.7 38.0 + - + -
188A SER* 4.9 0.2 - - - -
189A LEU* 4.1 23.6 - - + -
201A HIS* 3.0 51.2 + + - +
202A TRP* 3.1 9.1 + - - +
204A PHE* 1.3 83.8 - - + +
206A ILE* 1.4 68.4 + - + +
207A GLY 3.5 0.2 - - - -
208A PRO* 3.7 1.4 - - - +
209A LEU* 3.2 50.4 + - + +
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Residues in contact with ILE 206 (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* 3.9 12.6 - - + -
202A TRP* 2.7 46.5 + - + +
205A TRP* 1.4 72.7 - - + +
207A GLY* 1.3 59.0 + - - +
209A LEU* 4.1 6.2 - - + +
210A VAL* 2.9 52.9 + - + +
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL* 3.4 27.3 - - - +
134A GLU* 3.8 11.4 - - - -
135A LEU* 3.4 11.0 - - - +
203A VAL 3.0 15.2 + - - -
206A ILE* 1.3 76.1 - - - +
208A PRO* 1.4 65.7 - - - +
210A VAL* 4.0 1.0 - - - +
211A GLY 3.1 18.5 + - - -
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Residues in contact with PRO 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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70A ALA* 3.9 9.6 - - + -
134A GLU* 3.5 23.1 - - - +
138A THR* 3.3 26.2 - - + +
182A SER* 3.9 7.6 - - - +
183A MET 3.8 16.4 - - - +
184A ASN 4.1 0.2 - - - +
185A PRO* 4.1 6.7 - - + -
203A VAL 3.5 7.4 - - - +
204A PHE* 3.4 29.4 - - - +
205A TRP 3.7 2.9 - - - +
207A GLY* 1.4 85.4 - - - +
209A LEU* 1.4 54.9 + - - +
211A GLY 3.3 0.5 + - - -
212A ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 4.2 3.8 - - + +
70A ALA* 4.0 15.9 - - - +
73A VAL* 3.8 38.1 - - + -
185A PRO* 4.5 8.1 - - + -
205A TRP* 3.2 47.7 + - + +
206A ILE* 4.1 7.4 - - + +
208A PRO* 1.4 74.7 - - - +
210A VAL* 1.3 59.3 + - + +
212A ALA* 3.7 1.4 - - - +
213A ILE* 3.1 42.3 + - + +
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Residues in contact with VAL 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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135A LEU* 3.7 24.0 - - + -
206A ILE* 2.9 41.9 + - + +
207A GLY* 4.2 1.8 - - - +
209A LEU* 1.3 71.1 - - + +
211A GLY* 1.3 58.7 + - - +
213A ILE* 3.4 10.2 + - + +
214A LEU* 2.9 39.3 + - + +
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Residues in contact with GLY 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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135A LEU* 3.3 33.1 - - - +
138A THR* 4.5 0.7 - - - -
139A LEU* 3.4 20.4 - - - -
207A GLY 3.1 12.5 + - - -
208A PRO 3.7 2.9 - - - -
210A VAL* 1.3 76.6 - - - +
212A ALA* 1.4 54.7 + - - +
214A LEU* 3.6 3.9 + - - +
215A GLY 3.0 22.3 + - - -
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Residues in contact with ALA 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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70A ALA* 3.3 37.5 - - + +
73A VAL* 5.7 0.2 - - + -
74A ALA* 3.6 7.0 - - + +
138A THR* 4.0 2.6 - - + +
142A VAL* 3.6 22.8 - - + +
208A PRO 2.9 16.9 + - - +
209A LEU 3.7 4.5 - - - +
211A GLY* 1.4 73.3 - - - +
213A ILE* 1.4 60.2 + - + +
215A GLY 3.3 0.7 + - - -
216A SER* 2.9 30.5 + - - -
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Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 3.8 26.2 - - + -
74A ALA* 5.1 0.4 - - - +
77A VAL* 4.2 21.3 - - + -
209A LEU* 3.1 34.5 + - + +
210A VAL* 4.0 10.3 - - + +
212A ALA* 1.4 73.1 - - - +
214A LEU* 1.3 57.2 + - - +
216A SER* 3.3 6.7 + - - -
217A LEU* 2.9 48.7 + - + +
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Residues in contact with LEU 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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135A LEU* 4.3 19.1 - - + -
139A LEU* 3.7 20.2 - - + -
210A VAL* 2.9 36.1 + - + +
211A GLY* 3.6 6.1 - - - +
213A ILE* 1.3 77.2 - - - +
215A GLY* 1.3 55.8 + - - +
217A LEU* 3.4 7.3 + - + +
218A LEU* 2.9 46.4 + - + +
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Residues in contact with GLY 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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139A LEU* 3.6 10.5 - - - +
142A VAL* 3.8 12.0 - - - +
143A LEU* 3.3 28.7 - - - +
211A GLY 3.0 15.4 + - - -
212A ALA 3.3 2.9 + - - -
214A LEU* 1.3 71.9 - - - +
216A SER* 1.4 58.8 + - - +
218A LEU* 4.3 0.7 - - - -
219A TYR* 3.0 26.9 + - - +
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Residues in contact with SER 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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74A ALA* 2.6 37.8 + - - -
77A VAL* 3.8 5.5 - - - +
78A GLY* 3.4 13.0 + - - -
142A VAL* 3.7 5.1 - - - +
146A PHE* 3.7 5.1 - - - -
212A ALA 2.9 17.3 + - - -
213A ILE* 3.6 6.3 - - - -
215A GLY* 1.4 74.6 - - - +
217A LEU* 1.4 60.0 + - - +
219A TYR* 4.9 0.2 - - - -
220A ASN* 2.9 44.5 + - - +
221A TYR* 5.2 0.4 - - - -
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Residues in contact with LEU 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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77A VAL* 3.6 23.6 - - + -
213A ILE* 2.9 36.7 + - + +
214A LEU* 3.9 6.5 - - + +
216A SER* 1.4 72.2 - - - +
218A LEU* 1.3 61.8 + - + +
221A TYR* 2.9 60.2 + - + +
222A VAL* 3.6 3.1 + - - +
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Residues in contact with LEU 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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139A LEU* 4.3 20.2 - - + -
143A LEU* 4.7 3.1 - - + -
214A LEU* 2.9 28.5 + - + +
215A GLY* 3.8 5.4 - - - +
217A LEU* 1.3 76.5 - - - +
219A TYR* 1.3 53.6 + - - +
222A VAL* 3.2 19.8 + - + +
223A LEU* 2.7 42.1 + - + +
14D PHE* 4.2 27.1 - - + -
18D LEU* 3.8 35.9 - - + -
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Residues in contact with TYR 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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143A LEU* 4.2 15.7 - - + -
146A PHE* 3.6 34.1 - + + -
147A ALA* 3.5 27.2 - - + +
150A ASP* 2.6 29.4 + - - +
152A ARG* 4.9 0.7 - - - -
153A ARG* 4.2 2.1 - - - -
215A GLY 3.0 19.0 + - - +
216A SER 4.1 2.2 - - - +
217A LEU 3.4 0.2 - - - -
218A LEU* 1.3 75.9 - - - +
220A ASN* 1.4 73.3 + - - +
221A TYR 3.6 0.2 + - - -
223A LEU* 4.2 10.5 - - + +
224A PHE* 2.8 60.4 + + + +
58D ALA 3.9 20.9 - - - -
62D ILE* 4.3 14.4 - - + -
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Residues in contact with ASN 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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78A GLY* 3.5 24.6 - - - +
80A HIS* 4.1 6.4 + - - -
146A PHE* 3.2 38.8 - - - -
216A SER* 2.9 25.3 + - - +
219A TYR* 1.4 81.8 - - - +
221A TYR* 1.3 75.5 + - + +
224A PHE 4.4 5.1 - - - +
225A PRO* 3.3 21.5 - - - +
226A PRO* 3.8 12.9 - - + +
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Residues in contact with TYR 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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77A VAL* 3.8 19.7 + - + +
78A GLY* 5.4 1.4 - - - -
79A CYS* 6.1 0.3 - - - +
216A SER 4.9 0.2 - - - -
217A LEU* 2.9 49.8 + - + +
220A ASN* 1.3 94.7 - - + +
222A VAL* 1.3 67.9 + - + +
225A PRO* 3.6 16.0 - - - +
11D ARG* 4.0 4.9 + - - -
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Residues in contact with VAL 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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217A LEU 3.6 4.0 + - - +
218A LEU* 3.2 29.7 + - + +
221A TYR* 1.3 81.7 - - + +
223A LEU* 1.3 60.7 + - - +
225A PRO* 4.5 0.2 - - - -
11D ARG* 2.9 36.9 + - + +
14D PHE* 4.1 32.1 - - + -
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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
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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