Contacts of the helix formed by residues 194 - 211 (chain A) in PDB entry 2XJC
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 TYR 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PHE* 4.2 5.9 - - + -
104A THR* 3.6 13.7 - - - +
105A LEU 3.7 2.5 - - - -
106A TYR 3.4 24.0 - - - -
107A GLY* 3.5 17.7 - - - -
123A HIS* 3.1 26.4 + + - -
169A VAL* 4.0 20.9 - - + -
180A SER* 5.3 1.9 + - - -
181A CYS 4.1 8.2 + - - -
182A GLU 3.6 9.6 - - - -
183A THR 2.8 27.5 + - - +
184A GLY* 3.4 17.7 - - - -
185A PHE* 3.1 44.5 - + - -
193A SER* 1.3 73.0 - - - +
195A ARG* 1.3 56.1 + - - +
197A MET* 3.5 11.7 - - + +
198A PHE* 2.9 30.5 + - - +
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Residues in contact with ARG 195 (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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104A THR* 3.2 38.2 + - + +
148A GLU* 3.2 39.8 + - - +
193A SER* 3.0 10.1 + - - +
194A TYR* 1.3 75.3 - - - +
196A SER* 1.3 60.7 + - - +
198A PHE* 3.4 11.0 + - - +
199A GLN* 3.0 54.5 + - - +
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Residues in contact with SER 196 (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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191A PHE 5.2 0.2 + - - -
192A MET* 3.8 10.4 - - - +
193A SER* 3.1 28.7 + - - -
195A ARG* 1.3 72.4 - - - +
197A MET* 1.3 61.8 + - - +
199A GLN* 3.2 8.1 + - - +
200A ASP* 2.9 37.3 + - - +
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Residues in contact with MET 197 (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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82A TYR* 3.7 21.1 - - + +
102A PHE* 4.5 7.2 - - + -
165A LEU* 4.1 24.7 - - + +
168A LEU* 3.7 36.8 - - + -
169A VAL* 3.9 25.4 - - + -
172A PHE* 4.0 16.6 - - - -
185A PHE* 4.9 1.3 - - - -
192A MET* 3.8 17.2 - - + +
193A SER 3.0 17.5 + - - +
194A TYR* 3.5 13.7 - - + +
196A SER* 1.3 76.9 + - - +
198A PHE* 1.3 62.8 + - - +
200A ASP* 3.3 4.2 + - - +
201A VAL* 3.0 26.0 + - - +
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 3.8 29.4 - + + -
104A THR* 3.7 22.4 - - + -
151A TYR* 3.4 51.4 - + + -
161A GLU* 4.6 3.4 - - - -
165A LEU* 4.0 28.0 - - + -
194A TYR 2.9 18.0 + - - +
195A ARG* 3.7 9.4 - - - +
197A MET* 1.3 76.9 - - - +
199A GLN* 1.3 75.4 + - - +
201A VAL* 3.2 2.4 + - + +
202A ARG* 2.8 49.4 + - + +
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Residues in contact with GLN 199 (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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195A ARG* 3.0 41.1 + - - +
196A SER* 3.2 8.3 + - - +
198A PHE* 1.3 81.9 - - - +
200A ASP* 1.3 61.0 + - - +
202A ARG* 3.6 17.0 - - - +
203A ASP* 2.9 64.2 + - - +
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Residues in contact with ASP 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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77A LEU* 3.7 7.8 - - + +
80A ILE* 4.7 11.3 - - + +
82A TYR* 2.6 46.1 + - + +
192A MET* 5.6 1.2 - - - +
196A SER* 2.9 18.9 + - - +
197A MET 3.5 3.8 - - - +
199A GLN* 1.3 77.9 - - - +
201A VAL* 1.3 62.0 + - - +
203A ASP* 3.4 9.9 + - - +
204A ALA* 2.9 25.1 + - - +
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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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73A THR* 4.7 0.2 - - + -
77A LEU* 4.3 11.0 - - + -
82A TYR* 5.9 0.4 - - - +
161A GLU* 3.7 31.6 - - + +
164A LEU* 4.1 16.8 - - + -
165A LEU* 3.9 20.2 - - + -
168A LEU* 3.4 33.2 - - + -
197A MET 3.0 12.9 + - - +
198A PHE* 3.2 6.9 + - + +
200A ASP* 1.3 73.3 - - - +
202A ARG* 1.3 59.2 + - - +
204A ALA* 3.1 8.5 + - - +
205A VAL* 2.9 31.5 + - + +
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Residues in contact with ARG 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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151A TYR* 3.6 38.0 + - + -
158A ASN* 4.0 3.0 - - - +
161A GLU* 2.8 41.8 + - - -
198A PHE* 2.8 34.0 + - + +
199A GLN* 3.6 21.1 - - - +
201A VAL* 1.3 77.0 - - - +
203A ASP* 1.3 55.1 + - - +
205A VAL* 3.3 18.1 + - - +
206A ASP* 3.0 60.4 + - - +
1489A 5GP 2.9 24.4 + - - -
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Residues in contact with ASP 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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199A GLN* 2.9 52.9 + - - +
200A ASP* 3.7 9.9 - - - +
202A ARG* 1.3 73.0 - - - +
204A ALA* 1.3 53.8 + - - +
206A ASP* 3.4 11.5 + - - +
207A TRP* 2.9 34.9 + - - +
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Residues in contact with ALA 204 (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 THR* 3.8 18.6 - - + +
76A ARG* 3.9 26.5 - - + +
77A LEU* 3.9 17.0 - - + -
80A ILE* 6.2 0.9 - - + -
200A ASP 2.9 17.8 + - - +
201A VAL 3.5 4.0 - - - +
203A ASP* 1.3 74.2 - - - +
205A VAL* 1.3 59.4 + - - +
207A TRP* 3.5 3.3 + - - +
208A VAL* 3.0 33.6 + - - +
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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
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73A THR* 3.7 26.7 - - + +
157A PHE 4.8 7.0 - - - +
160A PRO* 6.2 1.1 - - + -
161A GLU* 3.9 33.7 - - + +
201A VAL 2.9 19.3 + - - +
202A ARG* 3.4 26.7 - - - +
204A ALA* 1.3 70.9 - - - +
206A ASP* 1.3 66.1 + - - +
208A VAL* 3.1 4.6 + - - +
209A HIS* 3.1 46.6 + - + +
1489A 5GP 3.9 5.8 - - - +
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Residues in contact with ASP 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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202A ARG* 3.0 39.2 + - - +
203A ASP* 3.5 15.4 - - - +
204A ALA 3.4 0.2 - - - -
205A VAL* 1.3 78.1 - - - +
207A TRP* 1.3 52.3 + - - +
209A HIS* 3.3 2.8 + - - +
210A TYR* 2.8 38.2 + - + +
1489A 5GP 2.7 40.7 + - - +
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Residues in contact with TRP 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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72A LEU* 5.2 1.1 - - + -
76A ARG* 3.4 71.0 - - + +
203A ASP 2.9 18.1 + - - +
204A ALA 3.6 4.3 - - - +
206A ASP* 1.3 75.2 - - - +
208A VAL* 1.3 64.5 + - + +
210A TYR* 4.8 2.5 - - - -
211A LYS* 2.6 76.4 + - + +
212A GLY* 2.7 31.3 + - - -
213A SER 5.0 0.2 - - - -
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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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69A GLY* 4.9 3.4 - - - +
72A LEU* 3.4 49.8 - - + +
73A THR* 3.8 11.2 - - - +
76A ARG* 4.4 1.1 - - + -
204A ALA 3.0 18.9 + - - +
205A VAL* 3.1 8.7 + - - +
207A TRP* 1.3 90.7 - - + +
209A HIS* 1.3 62.5 + - + +
212A GLY* 3.4 23.2 + - - +
213A SER 5.1 1.1 - - - +
214A LEU* 3.6 36.2 + - + +
215A LYS 5.0 0.5 + - - -
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Residues in contact with HIS 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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65A TYR* 5.1 0.7 - - - -
69A GLY* 6.4 0.2 - - - -
157A PHE* 3.4 35.7 - + + -
205A VAL* 3.1 38.4 + - + +
206A ASP 3.6 8.1 - - - +
208A VAL* 1.3 79.3 - - + +
210A TYR* 1.3 59.6 + - - +
212A GLY 5.7 0.2 - - - -
214A LEU* 3.6 28.7 - - + +
215A LYS* 3.0 31.2 + - - +
1489A 5GP 2.6 58.6 - + + +
1498A GOL 4.0 3.6 + - - +
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Residues in contact with TYR 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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206A ASP* 2.8 22.3 + - + +
207A TRP* 4.8 1.1 - - - -
209A HIS* 1.3 76.3 - - - +
211A LYS* 1.3 87.9 + - + +
212A GLY 3.7 1.3 - - - +
1489A 5GP 4.7 0.7 - - - +
1498A GOL 3.7 32.1 - - - +
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Residues in contact with LYS 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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207A TRP* 2.6 53.5 + - + +
210A TYR* 1.3 103.6 - - + +
212A GLY* 1.3 62.3 + - - +
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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