Contacts of the helix formed by residues 209 - 225 (chain A) in PDB entry 4C8B
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 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A SER* 3.3 8.5 + - - +
208A ILE* 1.3 92.4 - - + +
210A HIS* 1.3 61.3 + - - +
211A ASP 3.7 0.9 - - - -
212A ILE* 3.4 22.3 - - + +
213A TYR 3.9 0.3 + - - -
277A PRO* 3.5 34.1 + - + +
278A ASP* 4.6 8.1 + - - +
280A ARG* 2.6 61.7 + - + +
281A PRO 4.1 10.8 - - - +
282A SER* 4.4 4.3 - - - +
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Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A HIS* 3.6 61.6 + + + +
146A ASP* 5.3 0.8 - - - -
192A TYR 4.2 2.8 + - - -
193A MET* 4.4 16.0 - - + +
194A PRO* 3.5 30.4 - - + +
197A ASN* 3.1 28.4 + - - +
207A SER* 4.2 6.6 + - - +
208A ILE 3.6 1.6 - - - -
209A LYS* 1.3 75.0 - - - +
211A ASP* 1.3 69.7 + - - +
212A ILE 3.1 1.6 - - - -
213A TYR* 2.9 15.2 + - - +
214A SER* 3.2 22.7 + - - -
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Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 3.9 4.5 - - + +
136A HIS* 2.7 28.9 + - + +
143A LEU* 3.8 1.6 - - - +
144A HIS* 2.9 29.1 + - - +
145A HIS* 2.8 34.7 + - - -
146A ASP 4.6 0.2 + - - -
147A LEU* 3.8 10.9 - - + +
208A ILE 5.3 1.0 + - - -
210A HIS* 1.3 77.7 - - - +
212A ILE* 1.3 57.5 + - - +
214A SER* 3.3 9.7 + - - -
215A TYR* 2.9 28.6 + - - +
283A PHE* 3.6 19.5 - - + -
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE 5.5 0.7 - - - +
209A LYS* 3.4 26.6 - - + +
211A ASP* 1.3 75.9 - - - +
213A TYR* 1.3 67.8 + - - +
215A TYR* 3.4 14.0 + - + -
216A ALA* 3.1 18.7 + - - +
272A GLY* 3.6 12.0 - - - +
280A ARG* 3.8 21.5 - - + -
281A PRO* 3.3 34.8 - - + +
283A PHE* 3.4 23.1 - - + -
286A CYS* 3.6 31.6 - - - -
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Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE 4.1 7.3 + - - -
192A TYR 3.5 13.5 - - - -
193A MET 3.4 19.2 + - - -
194A PRO* 3.6 25.8 - - + -
195A PRO* 3.8 12.6 - - + -
209A LYS 4.1 6.3 - - - +
210A HIS 2.9 9.7 + - - +
212A ILE* 1.3 78.7 - - - +
214A SER* 1.3 66.3 + - - +
216A ALA* 3.1 13.2 + - - +
217A VAL* 3.3 28.0 + - + +
242A VAL* 3.4 21.8 - - - +
247A ARG* 3.4 35.5 + - - -
248A PRO* 5.7 0.9 - - - +
272A GLY 3.4 10.8 - - - +
273A TRP* 3.6 23.3 - - + -
280A ARG* 4.0 11.2 - - - +
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Residues in contact with SER 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.7 35.6 + - - +
192A TYR* 2.8 29.5 + - - +
210A HIS* 3.2 23.7 + - - -
211A ASP* 3.4 8.3 - - - -
213A TYR* 1.3 77.5 - - - +
215A TYR* 1.3 58.2 + - - +
217A VAL* 3.2 5.4 + - - +
218A ILE* 3.0 32.0 + - - +
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Residues in contact with TYR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 2.8 44.7 + - + +
128A ILE* 3.6 30.5 - - + -
129A ALA* 3.8 11.6 - - + +
147A LEU* 4.7 2.7 - - + +
211A ASP 2.9 17.3 + - - +
212A ILE* 3.7 21.1 - - + +
213A TYR 3.2 0.2 - - - -
214A SER* 1.3 75.6 - - - +
216A ALA* 1.3 54.5 + - - +
218A ILE* 3.6 12.1 - - + +
219A THR* 2.7 53.3 + - - -
268A LEU* 5.0 9.2 - - + -
283A PHE* 3.8 19.1 - + + -
286A CYS* 4.4 16.6 - - + -
290A LEU* 3.4 18.2 - - + +
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE 3.1 12.4 + - - +
213A TYR 3.1 10.8 + - - +
215A TYR* 1.3 77.2 - - - +
217A VAL* 1.3 60.7 + - - +
219A THR* 3.2 7.8 + - - -
220A TRP* 2.9 27.9 + - - +
268A LEU 4.9 0.4 - - - +
269A ILE* 3.4 34.9 - - - +
272A GLY* 3.7 14.6 - - - -
273A TRP* 3.7 9.6 - - + +
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Residues in contact with VAL 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE 3.6 23.8 - - - +
192A TYR* 3.8 22.7 - - + -
213A TYR* 3.3 29.1 + - + +
214A SER 3.2 5.6 + - - +
216A ALA* 1.3 76.2 - - - +
218A ILE* 1.3 53.2 + - - +
220A TRP* 3.1 4.5 + - - +
221A GLU* 2.8 32.2 + - - +
228A PRO* 3.8 28.5 - - + -
229A PHE* 6.5 0.2 - - + -
248A PRO* 4.8 9.0 - - + -
273A TRP* 4.2 20.6 - - + -
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Residues in contact with ILE 218 (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 7.6 - - + -
125A LEU* 4.6 2.9 - - + -
128A ILE* 4.2 25.8 - - + -
147A LEU* 4.1 28.0 - - + -
148A LYS* 4.1 15.7 - - - +
149A THR* 4.3 8.5 - - + -
152A ILE* 5.0 9.0 - - + -
192A TYR* 3.7 17.5 - - + -
214A SER 3.0 22.6 + - - +
215A TYR* 3.6 11.4 - - + +
217A VAL* 1.3 76.9 - - - +
219A THR* 1.3 51.6 + - - +
221A GLU* 3.1 10.0 + - - +
222A VAL* 2.7 44.4 + - + +
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Residues in contact with THR 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 3.6 33.7 - - + +
215A TYR* 2.7 38.4 + - + -
216A ALA* 3.4 7.0 - - - -
217A VAL 3.2 0.2 - - - -
218A ILE* 1.3 77.6 - - - +
220A TRP* 1.3 63.2 + - - +
222A VAL* 3.1 2.4 + - - +
223A LEU* 3.1 31.6 + - + +
265A MET* 5.1 8.5 - - - +
268A LEU* 5.9 6.1 - - + -
269A ILE* 3.6 23.3 - - + -
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Residues in contact with TRP 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ALA 2.9 16.5 + - - +
217A VAL 3.3 7.2 - - - +
219A THR* 1.3 73.4 - - - +
221A GLU* 1.3 61.2 + - - +
223A LEU* 3.4 3.1 + - - +
224A SER* 2.7 42.1 + - - -
226A LYS* 3.6 39.9 - - + -
227A GLN 4.0 7.0 - - - -
228A PRO* 3.6 26.7 - - + -
229A PHE 5.2 0.9 - - - -
248A PRO* 3.4 23.3 - - + +
249A VAL* 3.0 36.9 + - + -
250A ILE* 4.0 13.7 - - + +
254A SER* 4.0 17.6 + - - -
255A LEU* 4.1 13.3 - - + +
269A ILE* 4.0 12.0 - - + +
273A TRP* 3.8 28.5 - + + -
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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
----------------------------------------------------------
104A ASN* 4.3 1.4 - - - +
107A LEU* 3.9 8.9 - - + +
108A HIS* 3.0 27.2 + - - +
149A THR* 3.4 17.2 + - + +
192A TYR* 2.5 42.3 + - - -
217A VAL 2.8 13.1 + - - +
218A ILE* 3.1 10.1 + - - +
220A TRP* 1.3 80.0 - - + +
222A VAL* 1.3 57.1 + - - +
224A SER* 3.7 5.4 - - - -
225A ARG* 2.8 31.5 + - - -
226A LYS 3.6 15.7 - - - +
227A GLN* 4.4 3.5 - - - +
228A PRO* 3.9 17.7 - - + +
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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
----------------------------------------------------------
103A LEU* 3.9 24.2 - - + -
107A LEU* 3.9 31.2 - - + +
121A ARG* 2.9 60.3 + - + +
124A ILE* 5.3 2.9 - - + -
125A LEU* 4.0 23.3 - - + -
218A ILE* 2.7 24.2 + - + +
219A THR 3.1 4.0 + - - +
221A GLU* 1.3 75.9 - - - +
223A LEU* 1.3 59.1 + - + +
224A SER 3.5 0.3 + - - -
225A ARG 4.1 1.0 + - - -
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Residues in contact with LEU 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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118A TRP* 3.8 25.6 - - + -
121A ARG* 3.6 7.1 + - + +
122A PHE* 4.3 20.9 - - + -
125A LEU* 4.5 13.7 - - + -
219A THR* 3.1 29.1 + - + +
222A VAL* 1.3 81.5 - - + +
224A SER* 1.3 51.8 + - - +
254A SER 4.4 0.7 - - - +
255A LEU* 3.7 18.1 - - + +
259A ILE* 4.0 21.7 - - + +
265A MET* 4.0 28.9 - - + -
266A ILE* 6.6 0.2 - - + -
269A ILE* 4.4 9.0 - - + -
1317A EDO 2.6 21.4 + - - -
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Residues in contact with SER 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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110A LYS* 5.5 0.2 - - - -
220A TRP* 2.7 40.2 + - - -
221A GLU 3.4 2.3 + - - -
223A LEU* 1.3 77.8 - - - +
225A ARG* 1.3 71.1 + - - +
226A LYS* 3.1 27.8 + - - +
254A SER 3.2 26.1 - - - +
255A LEU* 3.9 5.6 - - - -
1317A EDO 3.1 17.2 + - - -
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Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU 2.9 23.3 + - - -
107A LEU* 2.7 38.4 + - + +
108A HIS* 3.7 12.7 + - - -
109A ARG 4.1 0.6 + - - -
110A LYS* 3.0 53.0 + - - +
113A TYR* 2.7 32.9 + - - +
114A PRO* 3.7 17.4 + - - +
115A ASP* 4.5 0.2 - - - +
116A VAL* 3.8 16.9 - - - +
121A ARG* 4.0 21.5 - - - +
221A GLU 2.8 14.8 + - - -
222A VAL 4.2 4.3 - - - +
224A SER* 1.3 79.1 - - - +
226A LYS* 1.3 60.9 + - - +
1317A EDO 3.8 21.2 + - - +
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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