Contacts of the helix formed by residues 194 - 212 (chain A) in PDB entry 2JG7
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 THR 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLU* 3.3 21.5 - - + -
107A MET* 4.6 4.5 - - + -
164A ALA 4.9 0.5 + - - -
165A PHE* 3.7 24.6 - - + +
168A PRO* 3.6 25.2 - - + +
191A ALA* 3.0 21.9 + - - +
193A THR* 1.3 86.4 - - - +
195A PRO* 1.4 63.4 - - - +
197A THR* 3.4 3.8 + - - -
198A SER* 3.2 20.5 + - - -
344A HIS* 4.0 17.0 - - + +
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Residues in contact with PRO 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.8 20.4 - - + -
39A SER* 4.2 9.6 - - - +
51A VAL* 3.8 29.6 - - + +
53A GLN* 5.9 0.2 - - + -
106A GLU* 3.3 9.2 - - - +
190A GLY 6.3 0.2 - - - -
191A ALA 3.9 3.5 - - - +
192A PRO* 3.1 19.5 - - + +
193A THR* 3.3 3.4 - - - +
194A THR* 1.4 88.3 - - - +
196A LEU* 1.3 58.4 + - - +
198A SER* 3.2 10.6 + - - +
199A VAL* 2.9 33.4 + - - +
223A CYS* 4.3 13.2 - - + -
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.0 20.0 - - + +
22A ASN* 3.5 29.2 - - - +
39A SER* 3.7 27.6 - - - +
48A ILE* 3.8 31.2 - - + -
49A ALA* 4.0 15.7 - - + +
50A ARG 4.4 0.4 - - - +
51A VAL* 3.8 14.1 - - + -
102A LEU* 3.7 16.1 - - + +
106A GLU* 3.1 15.6 + - - +
195A PRO* 1.3 77.5 - - - +
197A THR* 1.3 56.6 + - - +
199A VAL* 3.4 4.1 + - - +
200A ALA* 2.9 29.8 + - - +
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Residues in contact with THR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 4.8 3.6 - - + -
102A LEU* 3.8 20.7 - - + +
103A VAL* 4.2 12.4 - - + -
106A GLU* 2.7 31.3 + - - +
168A PRO* 3.7 28.4 - - + +
169A VAL* 3.5 32.1 - - + -
194A THR* 3.7 6.4 - - - -
195A PRO 3.3 0.2 - - - -
196A LEU* 1.3 70.9 - - - +
198A SER* 1.3 64.7 + - - +
200A ALA* 3.7 0.7 - - - +
201A VAL* 3.0 26.1 + - + +
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PRO* 5.2 0.9 + - - +
188A TRP* 3.4 25.5 - - - -
190A GLY* 3.8 24.4 - - - -
194A THR* 3.2 13.0 + - - -
195A PRO* 3.2 14.8 + - - +
197A THR* 1.3 79.0 - - - +
199A VAL* 1.3 53.5 + - - +
202A THR* 2.8 38.3 + - - -
221A MET* 3.8 12.8 - - - -
223A CYS* 4.3 7.8 - - - -
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.8 20.2 - - + -
22A ASN* 4.5 6.7 - - + -
23A PRO 3.6 26.5 - - - +
24A GLY* 4.5 0.7 - - - -
30A TRP* 4.1 4.6 - - + -
51A VAL* 4.2 20.0 - - + -
195A PRO 2.9 23.3 + - - +
196A LEU* 3.7 4.3 - - - +
198A SER* 1.3 70.3 - - - +
200A ALA* 1.3 54.4 + - - +
202A THR* 3.2 2.4 + - - -
203A LYS* 2.7 55.6 + - - +
221A MET* 3.9 17.7 - - + -
223A CYS* 4.5 0.9 - - - -
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Residues in contact with ALA 200 (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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16A LEU* 4.2 27.4 - - + +
18A LEU* 4.5 4.2 - - + +
99A LEU* 4.0 12.1 - - + -
102A LEU* 3.6 21.8 - - + -
196A LEU 2.9 21.2 + - - +
197A THR 3.7 2.9 - - - +
199A VAL* 1.3 74.5 - - - +
201A VAL* 1.3 63.2 + - - +
203A LYS* 3.4 3.5 + - - +
204A ILE* 3.2 28.8 + - - +
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Residues in contact with VAL 201 (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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92A LEU* 5.2 2.9 - - + -
99A LEU* 4.2 12.8 - - + -
121A TYR* 4.0 15.5 - - + -
169A VAL* 3.9 33.9 - - + -
172A TYR* 3.9 21.3 - - + -
188A TRP* 3.7 22.0 - - + -
197A THR 3.0 21.3 + - - +
198A SER 3.7 3.1 - - - +
200A ALA* 1.3 72.8 - - - +
202A THR* 1.3 66.1 + - - +
204A ILE* 3.0 12.5 + - - +
205A VAL* 3.0 24.0 + - + +
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Residues in contact with THR 202 (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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26A TYR* 3.9 27.8 - - + -
30A TRP* 3.7 16.6 - - + -
172A TYR* 6.0 1.6 - - - -
188A TRP* 3.6 10.7 - - - -
198A SER 2.8 21.3 + - - -
199A VAL 3.6 4.0 - - - -
201A VAL* 1.3 76.0 - - - +
203A LYS* 1.3 53.4 + - - +
205A VAL* 3.4 5.9 + - + +
206A ALA* 2.7 37.4 + - - +
219A CYS 4.3 7.4 - - - +
221A MET* 3.2 31.3 - - + +
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Residues in contact with LYS 203 (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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16A LEU 3.7 16.4 - - - +
17A GLY* 3.4 30.1 + - - +
18A LEU* 5.2 0.4 - - + -
22A ASN* 5.4 1.8 - - - -
23A PRO* 5.6 8.7 - - - +
30A TRP* 3.6 40.1 - - + +
199A VAL* 2.7 40.7 + - + +
200A ALA 3.4 6.7 - - - +
201A VAL 3.2 0.2 - - - -
202A THR* 1.3 72.5 - - - +
204A ILE* 1.3 62.4 + - + +
206A ALA* 3.4 1.4 + - - +
207A GLU* 3.1 25.5 + - - +
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.4 10.5 - - + +
88A ILE* 4.9 1.1 - - + +
91A ALA* 3.7 34.2 - - + +
92A LEU* 4.1 18.4 - - + +
95A LYS* 4.1 33.0 - - + -
99A LEU* 3.9 27.6 - - + -
200A ALA 3.2 16.7 + - - +
201A VAL* 3.0 7.9 + - - +
203A LYS* 1.3 78.0 - - + +
205A VAL* 1.3 65.4 + - + +
207A GLU* 3.5 6.3 + - - +
208A VAL* 3.5 21.0 + - - +
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 4.0 27.4 - - + -
92A LEU* 5.9 1.3 - - + -
121A TYR* 3.8 22.7 - - + +
172A TYR* 4.8 5.2 - - + +
176A ASN* 4.9 0.9 - - - +
201A VAL* 3.0 24.9 + - + +
202A THR* 3.8 5.8 - - + +
204A ILE* 1.3 74.8 - - + +
206A ALA* 1.3 67.1 + - - +
208A VAL* 3.2 10.2 + - - +
209A LEU* 3.1 23.2 + - + +
219A CYS* 3.6 39.3 - - + -
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Residues in contact with ALA 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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26A TYR* 3.5 38.1 - - + +
30A TRP* 4.1 13.2 - - + +
202A THR 2.7 22.2 + - - +
203A LYS 3.7 4.0 - - - +
205A VAL* 1.3 73.6 - - - +
207A GLU* 1.3 57.4 + - - +
209A LEU* 3.3 8.7 + - - +
210A GLU* 2.9 37.9 + - - +
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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
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95A LYS* 6.0 1.7 - - - -
203A LYS 3.1 17.1 + - - +
204A ILE* 3.8 7.0 - - - +
205A VAL 3.2 0.2 - - - -
206A ALA* 1.3 74.1 - - - +
208A VAL* 1.3 54.2 + - + +
210A GLU* 3.3 10.9 + - - +
211A GLN* 2.8 62.6 + - + +
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Residues in contact with VAL 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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84A ILE* 4.2 11.2 - - + +
87A GLN* 3.8 32.3 - - + +
88A ILE* 4.0 22.4 - - + -
91A ALA* 3.6 32.1 - - + -
204A ILE 3.5 9.1 + - - +
205A VAL 3.2 8.2 + - - +
207A GLU* 1.3 74.7 - - + +
209A LEU* 1.3 63.7 + - - +
211A GLN* 3.4 8.4 + - + +
212A ASN* 2.7 38.5 + - - +
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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
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73A TRP* 5.3 0.9 - - + -
84A ILE* 4.1 16.4 - - + -
88A ILE* 5.6 1.6 - - + -
180A LEU* 5.8 1.1 - - + -
205A VAL* 3.1 21.8 + - + +
206A ALA* 3.6 9.9 - - - +
208A VAL* 1.3 75.4 - - + +
210A GLU* 1.3 61.2 + - - +
212A ASN* 3.2 8.3 + - - -
214A LEU* 3.0 63.4 + - + +
215A PRO 4.3 1.6 - - - +
216A GLY* 3.7 31.6 - - - +
218A ILE* 4.3 15.3 - - + -
219A CYS* 3.9 30.5 - - + +
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Residues in contact with GLU 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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26A TYR* 2.7 30.4 + - - +
28A GLY 4.2 7.1 - - - +
30A TRP* 5.0 3.7 + - - -
206A ALA* 2.9 23.1 + - - +
207A GLU* 3.7 10.3 - - - +
209A LEU* 1.3 72.9 - - + +
211A GLN* 1.3 67.1 + - - +
212A ASN 3.1 1.3 - - - -
213A ASN* 3.0 18.0 + - - +
214A LEU 4.5 8.7 - - - +
216A GLY* 5.4 1.6 - - - +
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Residues in contact with GLN 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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87A GLN* 5.4 1.3 - - - +
207A GLU* 2.8 57.8 + - + +
208A VAL* 3.6 9.0 - - - +
210A GLU* 1.3 73.5 - - - +
212A ASN* 1.3 64.1 + - - +
213A ASN* 3.5 9.5 + - - +
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Residues in contact with ASN 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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83A GLU* 5.8 0.2 - - - +
84A ILE* 3.6 29.4 - - + +
87A GLN* 2.9 34.9 + - - +
208A VAL* 2.7 31.0 + - - +
209A LEU 3.2 3.8 + - - +
210A GLU 3.1 1.0 - - - -
211A GLN* 1.3 82.1 - - - +
213A ASN* 1.3 71.5 + - - +
214A LEU* 3.3 13.4 + - + +
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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