Contacts of the helix formed by residues 198 - 212 (chain A) in PDB entry 4X2Q
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 PRO 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.8 23.3 - - + -
39A VAL* 3.8 20.2 - - + -
51A VAL* 4.6 4.5 - - + -
109A ASN* 3.5 3.8 - - - +
193A PRO* 4.2 10.5 - - + +
194A ALA 3.9 8.1 - - - +
195A GLU 3.8 4.3 - - - +
196A GLN 3.5 9.4 - - - +
197A THR* 1.3 90.0 - - - +
199A LEU* 1.3 68.6 + - - +
200A SER 3.5 1.3 - - - -
201A ALA* 3.3 5.9 + - - +
202A LEU* 3.1 27.3 + - + +
222A PRO* 3.8 25.1 - - + -
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Residues in contact with LEU 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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17A ILE* 3.7 37.2 - - + +
19A TYR 5.1 3.1 - - - +
20A THR* 5.0 0.2 - - + -
39A VAL* 4.1 15.0 - - + -
48A VAL* 4.3 11.7 - - + -
49A CYS* 3.6 22.7 - - - -
51A VAL* 3.8 20.9 - - + -
105A MET* 3.7 23.5 - - + +
108A LEU* 5.3 2.0 - - + -
109A ASN* 3.3 34.6 + - + +
198A PRO* 1.3 77.1 - - - +
200A SER* 1.3 63.0 - - - +
202A LEU* 3.1 7.8 + - + +
203A TYR 3.1 19.4 + - - -
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Residues in contact with SER 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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102A LEU* 3.9 9.2 - - - +
105A MET* 4.3 17.8 + - - +
106A GLU* 3.0 29.9 + - - -
109A ASN* 4.6 2.8 + - - -
171A PRO* 3.3 19.1 - - - +
172A LEU* 3.8 22.7 + - - +
197A THR* 4.4 4.5 + - - -
199A LEU* 1.3 76.7 - - - +
201A ALA* 1.3 63.3 + - - +
203A TYR 3.6 0.5 + - - -
204A MET* 3.5 24.1 + - - +
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Residues in contact with ALA 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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171A PRO 5.4 2.9 - - - +
172A LEU* 5.2 0.2 - - - -
175A PHE* 3.9 29.2 - - + -
193A PRO* 3.7 32.1 - - + -
197A THR 5.0 0.7 - - - +
198A PRO 3.3 10.0 + - - +
199A LEU 3.2 0.2 - - - -
200A SER* 1.3 83.3 + - - +
202A LEU* 1.3 60.0 + - - +
204A MET* 3.3 19.5 - - - +
220A ILE* 3.4 18.6 - - + +
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Residues in contact with LEU 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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19A TYR* 3.6 29.6 - - + +
20A THR* 4.2 1.8 - - - -
21A LYS 3.4 23.3 - - - +
23A PHE 5.0 0.2 - - - +
28A TRP* 3.4 23.5 - - + -
51A VAL* 3.6 33.4 - - + -
193A PRO* 5.7 0.2 - - + -
198A PRO 3.1 24.4 + - - +
199A LEU* 3.1 4.7 + - - +
201A ALA* 1.3 72.5 - - - +
203A TYR* 1.3 62.2 + - - +
204A MET 3.1 1.3 - - - -
205A GLY* 3.0 15.3 + - - +
206A ALA 3.7 0.9 + - - -
220A ILE* 4.0 25.1 - - + +
222A PRO* 3.9 19.1 - - + -
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Residues in contact with TYR 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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19A TYR* 3.7 36.0 - + - +
97A ARG* 4.9 0.2 + - - -
98A ASP* 2.6 36.3 + - + +
101A VAL* 4.6 17.3 - - + +
102A LEU* 3.5 33.4 - - + -
105A MET* 3.8 30.1 - - + -
199A LEU 3.1 14.1 + - - +
200A SER 3.9 5.2 - - - +
201A ALA 3.4 0.2 - - - -
202A LEU* 1.3 77.1 - - - +
204A MET* 1.3 62.6 + - - +
206A ALA* 3.0 15.9 + - + +
207A LEU* 3.3 25.8 + - + +
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Residues in contact with MET 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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91A LEU* 3.7 24.2 - - + -
95A VAL* 3.8 10.8 - - + -
102A LEU* 4.6 5.2 - - + -
125A VAL* 5.4 0.4 - - + -
129A PHE* 3.7 35.2 - - + -
172A LEU* 3.5 31.0 - - + -
175A PHE* 3.7 24.7 - - + -
200A SER 3.5 3.7 + - - +
201A ALA 3.3 12.7 + - - +
202A LEU 3.1 0.2 - - - -
203A TYR* 1.3 78.6 - - - +
205A GLY* 1.3 54.8 + - - +
207A LEU* 3.2 26.9 + - - +
208A ILE* 2.8 36.3 + - + +
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Residues in contact with GLY 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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23A PHE* 3.5 19.3 - - - -
28A TRP* 4.2 11.9 - - - -
201A ALA 3.5 4.2 + - - -
202A LEU 3.0 12.1 + - - -
204A MET* 1.3 79.0 - - - +
206A ALA* 1.3 60.3 + - - +
208A ILE* 3.3 5.3 + - - +
209A LYS* 3.2 18.9 + - - +
220A ILE* 3.7 19.4 - - - +
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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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19A TYR* 3.5 45.5 - - + +
28A TRP* 4.0 6.9 - - - +
202A LEU 3.7 3.8 + - - -
203A TYR* 3.0 13.8 + - + +
205A GLY* 1.3 75.0 - - - +
207A LEU* 1.3 61.2 + - + +
209A LYS* 3.8 3.8 + - - +
210A GLU* 3.2 28.5 + - - +
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Residues in contact with LEU 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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91A LEU* 3.9 13.6 - - + +
94A LEU* 3.3 25.9 - - + +
95A VAL* 3.9 12.6 - - + -
97A ARG* 3.6 15.3 - - - +
98A ASP* 3.6 21.8 - - - +
102A LEU* 3.8 21.8 - - + -
203A TYR* 3.3 21.0 + - + +
204A MET* 3.2 29.2 + - - +
206A ALA* 1.3 78.0 - - + +
208A ILE* 1.3 60.5 + - - +
210A GLU* 3.8 5.4 - - - +
211A ALA* 2.9 31.0 + - - +
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Residues in contact with ILE 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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23A PHE* 4.2 16.4 - - + -
26A ASN* 4.6 3.8 - - - +
91A LEU* 4.4 11.7 - - + -
175A PHE* 4.5 12.3 - - + -
179A ILE* 5.5 2.2 - - + -
204A MET* 2.8 27.1 + - + +
205A GLY* 3.3 8.7 + - - +
207A LEU* 1.3 74.7 - - - +
209A LYS* 1.3 67.8 + - - +
211A ALA 3.4 6.8 + - - -
213A PHE* 3.2 47.8 + - + -
218A ILE* 3.6 53.6 - - + +
220A ILE* 4.4 6.7 - - + -
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Residues in contact with LYS 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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23A PHE* 4.3 10.5 - - + -
26A ASN* 3.5 50.3 + - - +
27A GLU* 3.9 15.4 + - - -
28A TRP* 5.8 6.6 - - - +
205A GLY 3.2 15.7 + - - +
206A ALA* 4.3 4.5 - - - +
208A ILE* 1.3 76.2 - - - +
210A GLU* 1.3 63.1 + - - +
212A GLY* 3.3 12.8 + - - -
213A PHE 5.0 0.9 - - - +
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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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94A LEU* 3.5 17.4 - - + +
97A ARG* 3.0 40.8 + - - -
206A ALA 3.2 18.8 + - - +
207A LEU* 3.9 10.7 - - - +
208A ILE 3.3 0.2 - - - -
209A LYS* 1.3 78.7 - - - +
211A ALA* 1.3 61.4 + - - +
212A GLY* 3.3 1.2 + - - -
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Residues in contact with ALA 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 LEU* 3.4 20.8 - - + +
90A LYS* 4.1 22.9 - - + +
91A LEU* 4.5 4.5 - - - +
94A LEU* 3.7 15.2 - - + +
207A LEU 2.9 18.4 + - - +
208A ILE 3.6 5.8 - - - +
209A LYS 3.3 0.4 - - - -
210A GLU* 1.3 76.0 - - - +
212A GLY* 1.3 57.1 + - - +
213A PHE* 3.9 20.0 - - + -
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Residues in contact with GLY 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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79A MET* 5.5 1.0 - - - +
87A LEU* 3.5 18.1 - - - +
208A ILE 3.4 0.2 + - - -
209A LYS 3.3 10.2 + - - -
210A GLU 3.2 4.9 - - - -
211A ALA* 1.3 79.1 - - - +
213A PHE* 1.3 66.5 + - - +
214A PRO* 3.7 3.1 - - - +
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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