Contacts of the helix formed by residues 197 - 213 (chain A) in PDB entry 5CXV
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 PHE 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A VAL* 5.1 0.9 - - + -
193A ALA 2.9 13.8 + - - +
195A ALA 3.6 0.4 - - - -
196A ALA* 1.3 78.3 - - - +
198A TYR* 1.3 82.8 + + - +
199A LEU 3.4 1.6 - - - -
200A PRO* 3.2 5.2 - - - +
201A VAL* 2.9 44.4 + - + +
374A PHE* 3.6 23.1 - + - -
375A ILE* 4.8 2.2 - - - -
378A TRP* 3.5 48.9 - + + -
379A THR* 4.1 16.8 - - + -
382A ASN* 3.3 37.9 - - + +
501A 0HK 3.4 18.2 - - - +
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Residues in contact with TYR 198 (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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190A PHE* 5.0 8.7 - + - -
193A ALA* 3.1 26.9 + - + -
194A MET* 3.4 29.5 + - + +
197A PHE* 1.3 89.0 - + - +
199A LEU* 1.3 59.4 + - - +
201A VAL* 3.2 5.5 + - + +
202A THR* 2.9 38.3 + - + +
382A ASN* 3.0 50.1 + - + +
383A ILE* 3.4 20.9 + - + +
386A LEU* 4.0 13.5 - - + +
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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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194A MET* 3.1 19.8 + - + +
195A ALA* 4.4 4.5 - - - +
198A TYR* 1.3 76.5 - - - +
200A PRO* 1.3 68.7 - - + +
202A THR* 2.8 26.5 + - + +
203A VAL* 2.9 28.1 + - + +
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Residues in contact with PRO 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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110A GLN* 5.3 1.1 - - - +
113A VAL* 3.6 25.1 - - + -
114A MET* 5.9 1.3 - - - -
117A LEU* 3.7 26.1 - - + +
195A ALA 3.4 16.4 - - - +
196A ALA* 3.3 18.8 - - - +
197A PHE 3.2 12.1 - - - +
199A LEU* 1.3 96.1 - - + +
201A VAL* 1.3 56.5 + - + +
203A VAL* 3.8 1.9 - - + +
204A MET* 2.9 39.2 + - + +
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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
----------------------------------------------------------
197A PHE* 2.9 46.0 + - + +
198A TYR* 3.6 5.8 - - - +
200A PRO* 1.3 75.5 - - - +
202A THR* 1.3 62.0 + - + +
204A MET* 3.2 9.6 + - + +
205A CYS* 2.9 42.0 + - - -
374A PHE* 3.7 28.9 - - + -
375A ILE* 4.5 18.6 - - + -
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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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198A TYR* 2.9 23.7 + - + +
199A LEU* 2.8 33.4 + - + +
201A VAL* 1.3 78.6 - - + +
203A VAL* 1.3 62.7 + - - +
205A CYS* 3.3 5.6 + - - +
206A THR* 2.9 31.6 + - - -
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Residues in contact with VAL 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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117A LEU* 3.8 19.5 - - + -
121A PHE* 3.9 26.0 - - + -
199A LEU* 2.9 43.4 + - + +
200A PRO* 3.8 3.6 - - + +
202A THR* 1.3 79.1 + - - +
204A MET* 1.3 63.8 + - - +
206A THR* 3.9 5.0 - - - -
207A LEU* 2.9 34.9 + - + +
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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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113A VAL* 4.7 4.5 - - + +
116A LEU* 3.5 33.0 - - + -
117A LEU* 4.0 14.1 - - + -
120A SER* 3.7 22.0 + - - +
200A PRO* 2.9 44.9 + - + +
201A VAL* 3.2 14.1 + - + +
203A VAL* 1.3 77.9 - - - +
205A CYS* 1.3 58.7 + - - +
207A LEU* 3.5 4.1 - - - +
208A TYR* 2.9 30.2 + - - +
371A LEU* 3.9 22.2 - - + +
374A PHE* 3.8 25.8 - - + -
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Residues in contact with CYS 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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201A VAL* 2.9 27.2 + - - +
202A THR* 3.8 5.8 - - - +
204A MET* 1.3 76.1 - - - +
206A THR* 1.3 65.1 + - - +
208A TYR* 3.3 9.1 + - - +
209A TRP* 3.0 24.6 + - - +
375A ILE* 4.2 24.9 - - - -
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Residues in contact with THR 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 THR* 2.9 20.2 + - - -
203A VAL* 3.9 5.4 - - - -
205A CYS* 1.3 76.5 - - - +
207A LEU* 1.3 69.5 + - + +
209A TRP* 3.5 5.2 + - - +
210A ARG* 2.9 29.7 + - + +
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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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117A LEU* 5.6 0.2 - - + -
120A SER* 3.8 16.6 - - - +
121A PHE* 3.8 60.6 - - + +
124A TYR* 4.1 27.1 - - + -
203A VAL* 2.9 26.8 + - + +
204A MET* 3.5 4.3 - - - +
206A THR* 1.3 76.6 - - + +
208A TYR* 1.3 56.7 + - - +
210A ARG* 2.5 33.2 + - + +
211A ILE* 2.9 22.5 + - + +
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Residues in contact with TYR 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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120A SER* 5.8 0.6 - - - -
123A ARG* 4.0 26.3 + - - +
204A MET 2.9 19.8 + - - +
205A CYS* 3.3 10.3 + - - +
207A LEU* 1.3 70.7 - - - +
209A TRP* 1.3 65.7 + - - +
211A ILE* 3.3 13.0 + - - +
212A TYR* 3.0 26.1 + + + +
364A ALA* 5.1 2.0 + - + -
367A LEU* 5.1 2.7 - - + -
368A SER* 3.3 39.5 - - - -
371A LEU* 4.4 18.6 - - + -
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Residues in contact with TRP 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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205A CYS 3.0 17.7 + - - +
206A THR* 3.8 5.2 - - - +
207A LEU 2.9 1.2 + - - -
208A TYR* 1.3 79.3 - - + +
210A ARG* 1.3 64.9 + - - +
212A TYR* 2.9 21.1 + - + +
213A ARG* 3.0 14.1 + - - +
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Residues in contact with ARG 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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124A TYR* 4.1 26.7 - - + -
206A THR* 2.9 25.8 + - + +
207A LEU* 2.5 20.7 + - + +
209A TRP* 1.3 71.4 - - - +
211A ILE* 1.3 60.7 + - - +
213A ARG* 3.1 31.6 + - - +
214A GLU* 3.2 41.2 + - - +
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Residues in contact with ILE 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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120A SER* 4.5 3.4 - - - +
123A ARG* 4.1 36.1 - - + +
124A TYR* 3.8 41.5 - - + +
127A VAL* 3.7 27.6 - - + -
128A THR* 6.2 0.4 - - + -
207A LEU* 2.9 42.4 + - + +
208A TYR* 3.6 11.4 - - - +
210A ARG* 1.3 72.1 - - - +
212A TYR* 1.3 67.6 + - - +
214A GLU* 3.1 15.0 + - - +
215A THR* 3.1 19.9 + - - +
504A PGE 4.1 5.4 - - - +
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Residues in contact with TYR 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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123A ARG* 5.4 1.5 - - - +
208A TYR* 3.0 21.0 + + + +
209A TRP* 2.9 16.6 + - + +
211A ILE* 1.3 76.6 - - - +
213A ARG* 1.3 60.2 + - + +
214A GLU 3.7 0.5 + - - -
215A THR* 4.5 7.6 + - - -
216A GLU 5.6 0.5 + - - -
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Residues in contact with ARG 213 (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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209A TRP 3.0 13.1 + - - +
210A ARG* 3.1 28.4 + - - +
211A ILE 3.1 0.6 - - - -
212A TYR* 1.3 78.8 - - + +
214A GLU* 1.3 64.4 + - - +
215A THR 3.9 0.2 - - - -
216A GLU* 5.2 4.4 + - - +
217A ASN* 4.2 8.7 + - - -
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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