Contacts of the helix formed by residues 217 - 235 (chain A) in PDB entry 4ZTF
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 SER 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A PHE* 4.4 9.8 - - - -
127A ILE 4.7 1.7 + - - -
128A ASP* 5.7 0.7 - - - -
183A HIS* 3.6 11.8 + - - -
184A SER* 4.1 2.1 - - - -
185A ASP* 3.9 18.6 + - - +
209A SER* 3.3 14.9 + - - -
214A PRO* 3.0 14.5 + - - -
216A SER* 1.3 75.2 - - - +
218A GLY* 1.3 62.8 + - - +
219A LYS 3.2 2.9 - - - -
220A VAL* 2.9 32.7 + - - +
221A GLU* 3.0 18.0 + - - -
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Residues in contact with GLY 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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214A PRO 3.3 3.0 + - - -
215A GLN 2.9 20.4 + - - -
216A SER 3.2 3.0 + - - -
217A SER* 1.3 74.0 - - - +
219A LYS* 1.4 55.1 + - - +
221A GLU* 4.2 1.3 - - - -
222A ARG* 2.9 34.5 + - - +
4C G 3.3 24.0 + - - -
5C T 3.6 11.6 - - - -
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Residues in contact with LYS 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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117A ARG* 4.0 23.8 - - - +
118A PRO* 4.8 4.8 - - - +
126A PHE* 3.9 30.0 - - + -
146A VAL* 4.4 15.1 - - + +
147A ASP 5.0 1.1 - - - -
148A GLY* 3.1 42.2 + - - +
151A GLY* 5.4 5.4 - - - -
217A SER 2.9 1.4 + - - -
218A GLY* 1.4 76.3 - - - +
220A VAL* 1.3 60.8 + - - +
222A ARG* 4.0 2.9 - - - +
223A LYS* 3.5 17.5 + - - +
5C T 3.6 33.0 + - - +
6C C 3.1 30.3 + - - +
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Residues in contact with VAL 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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126A PHE* 3.8 23.1 - - + +
127A ILE 4.0 7.2 - - - +
128A ASP* 3.7 29.2 - - + +
144A VAL* 3.6 41.7 - - + +
146A VAL* 3.8 12.1 - - + -
217A SER* 2.9 31.3 + - - +
219A LYS* 1.3 73.3 - - - +
221A GLU* 1.4 65.9 + - + +
223A LYS* 3.0 3.3 + - - +
224A ASN* 2.9 27.4 + - - +
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Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP* 2.9 12.6 - - - +
185A ASP* 4.3 2.1 - - - +
214A PRO* 3.3 30.2 - - - +
217A SER* 3.0 17.1 + - - +
218A GLY 3.8 6.1 - - - +
220A VAL* 1.4 74.6 - - - +
222A ARG* 1.3 58.3 + - - +
224A ASN* 2.9 43.5 + - - +
225A SER 3.4 0.2 + - - -
404A X2P 2.9 39.0 + - + +
406A MG 2.0 31.8 - - - -
4C G 3.9 0.2 - - - +
16D C 3.3 23.0 + - + +
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Residues in contact with ARG 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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218A GLY 2.9 19.1 + - - +
219A LYS 4.0 4.3 - - - +
221A GLU* 1.3 77.2 - - - +
223A LYS* 1.3 59.5 + - - +
225A SER* 3.3 20.6 + - - -
226A ASP* 2.7 34.6 + - - +
229A ARG* 5.2 0.4 - - - +
4C G 4.0 0.2 - - - +
5C T 3.1 27.3 + - - +
6C C 2.9 57.1 + - - +
7C A 2.8 35.6 + - - -
14D G 3.9 8.1 - - - +
15D A 3.9 11.6 - - - -
16D C 3.5 4.9 + - - -
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Residues in contact with LYS 223 (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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144A VAL* 4.6 0.4 - - + -
146A VAL* 3.7 21.3 - - + -
151A GLY* 3.0 24.5 + - - -
153A THR* 3.3 35.7 + - + +
219A LYS 3.5 6.8 + - - +
220A VAL 3.0 9.6 + - - +
222A ARG* 1.3 78.6 - - - +
224A ASN* 1.4 61.1 + - - +
226A ASP* 3.2 18.0 + - - +
227A ILE* 3.0 35.9 + - + +
253A LEU* 4.6 22.8 + - + +
254A ASN* 5.3 0.4 + - - -
265A PRO* 4.1 14.8 - - - +
6C C 6.4 2.0 - - - -
7C A 5.7 2.8 + - - -
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Residues in contact with ASN 224 (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 ASP* 3.1 19.2 + - - +
130A ILE* 3.5 25.6 - - + +
144A VAL* 3.3 28.9 - - - +
220A VAL* 2.9 17.6 + - - +
221A GLU* 2.9 34.7 + - - +
223A LYS* 1.4 75.6 - - - +
225A SER* 1.3 54.2 + - - +
227A ILE* 3.5 2.9 + - - +
228A LYS* 3.0 35.0 + - - +
406A MG 3.7 1.0 - - - -
16D C 3.6 17.4 + - - +
17D A 4.1 1.6 + - - +
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Residues in contact with SER 225 (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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221A GLU 3.4 2.2 + - - -
222A ARG* 3.3 27.4 + - - -
223A LYS 3.2 0.4 - - - -
224A ASN* 1.3 78.5 - - - +
226A ASP* 1.3 58.8 + - - +
228A LYS* 3.9 1.7 - - - +
229A ARG* 2.8 36.9 + - - +
15D A 4.5 16.9 + - - -
16D C 3.4 34.0 + - - -
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Residues in contact with ASP 226 (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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222A ARG* 2.7 34.4 + - - +
223A LYS* 3.2 21.7 + - + +
225A SER* 1.3 78.3 - - - +
227A ILE* 1.4 55.9 + - - +
229A ARG* 3.3 29.6 + - - +
230A LEU* 3.0 31.4 + - - +
253A LEU* 3.9 25.0 - - + +
6C C 5.5 1.6 - - - +
7C A 3.8 19.0 + - - +
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Residues in contact with ILE 227 (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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130A ILE* 4.2 13.0 - - + -
142A VAL* 5.2 2.9 - - + -
144A VAL* 3.7 25.6 - - + -
153A THR* 4.3 1.1 - - + -
155A LEU* 3.5 38.8 - - + -
223A LYS* 3.0 31.0 + - + +
224A ASN* 3.8 5.4 - - - +
225A SER 3.3 0.2 - - - -
226A ASP* 1.4 74.8 - - - +
228A LYS* 1.3 58.3 + - + +
230A LEU* 3.9 1.7 - - - +
231A LEU* 3.0 51.0 + - + +
246A LEU* 4.9 3.8 - - + -
249A VAL* 4.1 11.1 - - + +
253A LEU* 3.7 20.4 - - + -
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Residues in contact with LYS 228 (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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130A ILE* 3.8 30.7 - - + +
131A GLY 5.8 0.6 - - - +
133A LEU* 4.2 15.6 - - + +
224A ASN 3.0 20.0 + - - +
225A SER* 3.9 3.6 - - - +
227A ILE* 1.3 76.0 - - + +
229A ARG* 1.4 55.8 + - - +
231A LEU* 3.8 10.0 - - + +
232A THR* 2.7 40.2 + - - +
16D C 4.3 14.3 + - - +
17D A 2.7 45.3 + - - +
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Residues in contact with ARG 229 (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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222A ARG* 5.1 0.8 - - - +
225A SER* 2.8 25.7 + - - +
226A ASP* 3.3 30.4 + - - +
228A LYS* 1.4 72.0 - - - +
230A LEU* 1.4 57.0 + - - +
232A THR* 3.4 8.1 - - - -
233A LYS* 3.2 63.1 + - - +
7C A 2.9 28.0 + - - -
8C T 2.8 34.0 + - - -
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A ASP 3.0 17.5 + - - +
227A ILE 4.0 2.5 - - - +
229A ARG* 1.4 73.0 - - - +
231A LEU* 1.4 64.1 + - - +
233A LYS* 3.3 16.4 + - + +
234A LEU* 3.1 48.9 + - + +
249A VAL* 4.0 24.7 - - + -
252A ALA* 3.7 29.8 - - + -
253A LEU* 4.0 18.6 - - + -
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Residues in contact with LEU 231 (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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133A LEU* 5.1 12.1 - - + -
142A VAL* 5.7 0.9 - - + -
227A ILE* 3.0 38.9 + - + +
228A LYS* 3.8 9.9 - - + +
230A LEU* 1.4 75.1 - - - +
232A THR* 1.4 63.4 + - - +
234A LEU* 3.4 3.2 + - - -
235A LEU* 3.0 37.2 + - + +
242A TRP* 4.0 25.4 - - + +
245A LEU* 3.7 26.2 - - + -
246A LEU* 4.4 13.2 - - + -
249A VAL* 3.6 23.1 - - + +
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Residues in contact with THR 232 (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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228A LYS* 2.7 26.7 + - - +
229A ARG* 3.4 8.2 - - - +
230A LEU 3.2 0.2 - - - -
231A LEU* 1.4 77.2 - - - +
233A LYS* 1.4 63.1 + - + +
235A LEU* 3.2 5.7 + - - +
236A VAL* 3.2 25.7 + - + +
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Residues in contact with LYS 233 (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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229A ARG* 3.2 54.8 + - - +
230A LEU* 3.3 20.2 + - + +
232A THR* 1.4 74.8 - - + +
234A LEU* 1.3 66.3 + - + +
236A VAL* 3.4 25.2 + - + +
238A ARG* 5.6 0.7 + - - -
8C T 4.5 3.4 + - - -
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Residues in contact with LEU 234 (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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230A LEU* 3.1 37.9 + - + +
231A LEU 3.9 4.0 - - - +
233A LYS* 1.3 76.7 - - + +
235A LEU* 1.3 62.1 + - - +
236A VAL 3.4 0.2 - - - -
238A ARG* 3.7 24.9 + - - -
245A LEU* 3.9 33.8 - - + +
248A VAL* 4.6 13.0 - - + -
249A VAL* 4.1 21.3 - - + -
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Residues in contact with LEU 235 (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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231A LEU* 3.0 27.1 + - + +
232A THR* 3.2 6.9 + - - +
233A LYS 3.2 0.2 - - - -
234A LEU* 1.3 78.2 - - - +
236A VAL* 1.4 65.4 + - - +
237A GLY 3.3 0.7 + - - -
238A ARG* 3.1 27.3 + - + +
239A PRO 3.4 22.9 - - - +
240A THR* 4.0 26.5 - - + +
241A LYS* 3.7 14.4 - - + +
242A TRP* 4.2 22.2 - - + -
245A LEU* 3.6 24.0 - - + -
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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