Contacts of the helix formed by residues 206 - 223 (chain A) in PDB entry 1CEZ
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 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A SER* 3.4 19.6 + - - +
205A HIS* 1.3 70.7 - - - +
207A GLU* 1.3 63.4 + - - +
209A SER* 3.1 10.5 + - - -
210A ILE* 2.8 50.4 + - + +
761A ILE* 4.0 8.5 - - + -
762A ASN 3.2 22.0 - - - +
763A THR* 4.3 5.4 - - - -
764A ASN* 3.3 33.0 + - - +
3T T 3.3 20.4 + - - +
4T A 3.0 32.3 - - + +
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A HIS* 3.6 14.0 + - + +
206A LYS* 1.3 85.1 + - - +
208A ASP* 1.3 60.8 + - - +
211A HIS* 2.9 38.6 + - + -
745A THR* 4.2 10.5 - - + +
747A LEU* 3.6 26.3 - - + +
761A ILE* 3.9 12.5 - - + +
763A THR* 3.7 26.1 + - - +
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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
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101A THR* 3.3 23.4 - - - +
105A PHE* 3.2 36.8 - - + -
204A TRP* 4.7 4.4 - - + -
205A HIS* 3.1 34.0 + - - +
207A GLU* 1.3 79.2 - - - +
209A SER* 1.3 61.1 + - - +
211A HIS* 3.1 6.2 + - - +
212A VAL* 2.9 36.6 + - - +
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Residues in contact with SER 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ALA 3.6 2.0 - - - +
139A SER* 3.7 11.6 + - - -
142A GLY* 3.4 31.0 - - - -
143A ARG* 3.6 4.0 + - - +
146A GLU* 5.8 0.4 - - - -
204A TRP* 4.2 20.1 - - - -
205A HIS 3.0 12.3 + - - -
206A LYS* 3.1 19.8 + - - +
208A ASP* 1.3 75.9 - - - +
210A ILE* 1.3 58.1 + - - +
212A VAL* 3.4 0.7 + - - +
213A GLY 2.8 22.9 + - - -
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Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL 5.4 1.3 - - - +
135A GLN* 4.0 10.1 - - - +
138A ALA* 4.2 6.5 - - + -
139A SER* 3.7 37.5 - - - +
206A LYS* 2.8 39.8 + - + +
209A SER* 1.3 74.1 - - - +
211A HIS* 1.3 59.8 + - - +
213A GLY 4.3 0.4 - - - +
214A VAL* 2.8 47.0 + - + +
747A LEU* 3.7 20.9 - - + -
759A PRO* 4.6 7.4 - - + -
761A ILE* 4.1 23.8 - - + -
4T A 4.9 2.2 - - - +
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Residues in contact with HIS 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A THR* 3.5 32.9 + - + -
102A ALA* 4.0 11.3 + - - +
207A GLU* 2.9 30.4 + - + +
208A ASP* 3.3 11.7 - - - +
210A ILE* 1.3 78.6 - - - +
212A VAL* 1.3 63.4 + - + +
214A VAL* 3.8 0.5 - - - +
215A ARG* 3.1 31.2 + - - -
747A LEU* 4.0 13.0 - - + +
749A LEU* 3.2 34.7 - - + +
106N C 3.6 23.1 + - - -
107N G 2.8 27.9 + - - -
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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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102A ALA* 4.1 17.9 - - - +
105A PHE* 3.9 23.6 - - + -
106A LEU* 3.6 27.5 - - + +
142A GLY* 4.5 2.0 - - - -
145A ILE* 4.0 25.6 - - + -
204A TRP* 3.8 19.3 - - + -
208A ASP 2.9 20.7 + - - +
209A SER 3.6 3.8 - - - +
211A HIS* 1.3 76.1 - - - +
213A GLY* 1.3 64.4 + - - +
215A ARG* 3.3 1.9 + - - +
216A CYS* 3.0 23.8 + - - -
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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
----------------------------------------------------------
138A ALA* 3.3 33.0 - - - -
141A ILE* 4.0 14.3 - - - +
142A GLY* 4.3 0.4 - - - -
209A SER 2.8 14.3 + - - -
210A ILE 3.3 0.4 + - - -
212A VAL* 1.3 73.8 - - - +
214A VAL* 1.3 57.6 + - - +
216A CYS* 3.4 2.6 + - - +
217A ILE* 3.0 33.8 + - - +
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Residues in contact with VAL 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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134A VAL* 4.5 7.2 - - + -
138A ALA* 3.5 9.6 - - + +
210A ILE* 2.8 35.9 + - + +
211A HIS 3.8 1.1 - - - +
213A GLY* 1.3 69.9 - - - +
215A ARG* 1.3 69.9 + - - +
217A ILE* 3.1 7.7 + - - +
218A GLU* 2.8 30.5 + - - +
749A LEU* 3.4 34.1 - - + -
751A PHE* 3.9 27.9 - - + -
757A LEU* 4.1 13.2 - - + -
759A PRO* 5.4 1.3 - - + -
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Residues in contact with ARG 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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88A TRP* 3.8 24.7 - - + -
100A PRO* 4.6 6.0 - - - +
102A ALA* 3.3 34.5 - - + -
106A LEU* 4.5 4.0 - - + -
211A HIS* 3.1 13.7 + - - +
212A VAL 3.8 2.5 - - - +
214A VAL* 1.3 83.8 - - - +
216A CYS* 1.3 61.6 + - - +
218A GLU* 3.3 30.7 + - - +
219A MET* 3.0 30.6 + - + +
749A LEU* 3.9 21.0 - - - +
750A MET* 2.4 40.8 + - - +
751A PHE* 4.5 0.4 - - - +
106N C 3.1 32.9 + - - -
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Residues in contact with CYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MET* 3.7 5.9 - - - +
106A LEU* 4.0 19.3 - - - -
114A VAL* 3.9 21.5 - - - -
118A THR* 3.5 27.6 - - + +
141A ILE* 4.0 12.8 - - + -
145A ILE* 4.6 1.8 - - - -
212A VAL* 3.0 25.7 + - - +
213A GLY 3.7 4.3 - - - +
215A ARG* 1.3 74.6 - - - +
217A ILE* 1.3 67.1 + - - +
219A MET* 3.2 10.3 + - - -
220A LEU* 3.0 22.5 + - - +
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Residues in contact with ILE 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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118A THR* 4.9 2.2 - - - -
122A THR* 4.7 4.3 - - + +
134A VAL* 4.4 10.1 - - + +
137A VAL* 3.6 28.0 - - + -
138A ALA* 3.7 20.6 - - + +
141A ILE* 3.5 14.6 - - + -
213A GLY 3.0 21.1 + - - +
214A VAL* 3.5 7.4 - - - +
216A CYS* 1.3 74.4 - - - +
218A GLU* 1.3 63.8 + - - +
220A LEU* 3.1 10.3 + - + +
221A ILE* 3.0 37.5 + - + +
227A VAL* 4.7 6.3 - - + -
229A LEU* 5.5 0.2 - - + -
244A ILE* 3.8 26.9 - - + -
751A PHE* 4.6 7.2 - - + -
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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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84A ARG* 5.8 1.2 + - - -
88A TRP* 5.4 6.1 + - - -
214A VAL* 2.8 12.8 + - - +
215A ARG* 3.3 47.9 + - - +
217A ILE* 1.3 77.0 - - - +
219A MET* 1.3 65.5 + - + +
221A ILE* 3.4 6.0 + - - +
222A GLU* 3.1 27.2 + - - +
750A MET 3.6 1.6 - - - +
751A PHE* 3.6 23.6 - - + -
752A LEU* 3.5 44.9 + - + +
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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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81A MET* 4.0 9.4 - - + -
84A ARG* 3.9 20.7 - - + +
85A ILE* 3.9 33.0 - - + -
88A TRP* 3.8 53.2 - - + -
106A LEU* 4.5 3.6 - - + -
114A VAL* 5.2 1.6 - - + -
215A ARG* 3.0 25.0 + - + +
216A CYS* 3.2 22.4 + - - +
218A GLU* 1.3 78.2 - - + +
220A LEU* 1.3 60.7 + - - +
222A GLU* 3.4 9.2 - - - +
223A SER* 2.8 34.7 + - - -
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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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81A MET* 3.8 10.7 - - + -
118A THR* 4.1 14.6 - - + +
119A ILE* 3.6 29.4 - - + -
122A THR* 3.9 24.0 - - + +
216A CYS 3.0 12.8 + - - +
217A ILE* 3.1 10.1 + - - +
219A MET* 1.3 73.1 - - - +
221A ILE* 1.3 55.4 + - - +
223A SER* 3.9 0.9 - - - -
224A THR* 2.5 64.3 + - + +
226A MET* 3.8 34.0 + - + -
227A VAL* 4.1 13.9 - - + -
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Residues in contact with ILE 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 ILE* 3.0 25.3 + - + +
218A GLU 3.6 5.6 - - - +
220A LEU* 1.3 71.8 - - - +
222A GLU* 1.3 60.7 + - - +
224A THR 2.5 22.1 - - - +
225A GLY* 4.0 4.5 - - - -
227A VAL* 3.7 36.1 - - + +
228A SER* 4.4 15.0 - - - -
229A LEU* 4.4 7.9 - - + +
751A PHE* 3.7 34.5 - - + -
752A LEU* 4.2 16.6 - - + -
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Residues in contact with GLU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 2.7 46.0 + - - +
218A GLU* 3.1 17.4 + - - +
219A MET* 3.4 12.6 - - - +
221A ILE* 1.3 80.0 - - - +
223A SER* 1.3 66.1 + - - +
224A THR 3.4 1.4 + - - +
752A LEU* 3.3 29.6 - - + +
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Residues in contact with SER 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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80A LYS* 2.9 42.8 - - - +
81A MET* 3.5 18.7 - - - -
84A ARG* 3.5 16.7 - - - +
219A MET 2.8 22.8 + - - -
220A LEU 3.8 1.7 + - - -
222A GLU* 1.3 74.7 - - - +
224A THR* 1.3 66.9 + - - +
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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