Contacts of the helix formed by residues 198 - 214 (chain A) in PDB entry 2AYO
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 ASP 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A TYR* 4.4 4.0 - - - -
185A PHE* 5.1 0.9 - - - -
197A GLN* 1.3 79.9 - - - +
199A ALA* 1.3 64.6 + - - +
200A ASN* 2.5 33.9 + - - +
201A GLU* 2.7 20.9 + - - +
202A CYS* 3.3 16.8 + - - +
435A TYR* 3.4 9.5 + - - -
475A TYR* 3.0 19.0 + - - -
42B ARG* 4.2 3.1 - - - -
72B ARG* 3.3 30.9 - - + +
73B LEU 2.8 27.8 + - - +
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Residues in contact with ALA 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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114A TYR* 4.0 9.2 - - + +
118A THR* 3.0 21.6 + - - +
198A ASP* 1.3 70.8 + - - +
200A ASN* 1.3 55.4 + - - +
202A CYS* 2.8 9.0 + - - +
203A TRP* 2.7 32.9 + - + -
423A LEU* 4.1 17.3 - - + -
435A TYR* 2.7 41.2 + - + -
475A TYR* 5.1 2.2 - - + -
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Residues in contact with ASN 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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198A ASP* 2.5 12.5 + - - +
199A ALA* 1.3 75.9 - - - +
201A GLU* 1.3 56.5 + - - +
203A TRP* 2.7 9.3 + - - +
204A ILE* 2.7 52.9 + - - +
273A GLN* 3.1 27.6 + - - -
326A GLN* 3.4 33.6 + - - +
475A TYR* 3.4 26.7 + - + +
476A VAL* 3.4 14.6 - - - +
42B ARG* 4.0 8.7 - - - +
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Residues in contact with GLU 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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184A GLN* 4.3 6.8 - - - +
185A PHE* 3.7 25.6 - - + -
197A GLN* 3.7 6.8 - - - +
198A ASP* 2.7 27.0 + - + +
200A ASN* 1.3 71.6 - - - +
202A CYS* 1.3 60.6 + - - +
204A ILE* 4.0 1.7 - - - +
205A GLN* 2.7 35.1 + - - +
42B ARG* 3.3 28.3 - - - +
49B GLN* 3.2 31.6 + - - +
72B ARG* 3.0 39.2 + - - +
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Residues in contact with CYS 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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114A TYR* 4.5 11.2 - - + -
115A MET* 4.3 16.8 - - - -
118A THR* 3.2 31.2 - - - -
178A LEU* 5.2 2.7 - - + -
182A PHE* 5.5 1.0 - - - -
185A PHE* 4.7 14.1 - - + -
198A ASP 3.3 8.7 + - - +
199A ALA* 2.8 12.0 + - - +
201A GLU* 1.3 77.5 - - - +
203A TRP* 1.3 50.3 + - - -
205A GLN* 2.9 6.5 + - - +
206A MET* 2.5 57.2 + - - +
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Residues in contact with TRP 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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118A THR* 3.5 26.5 - - + -
121A CYS* 3.2 43.3 - - + -
122A ILE* 4.3 14.6 - - + +
199A ALA* 2.7 14.6 + - + +
200A ASN* 2.7 15.7 + - - +
202A CYS* 1.3 68.4 - - - +
204A ILE* 1.3 59.1 + - - +
206A MET* 3.0 2.3 + - - -
207A MET* 2.5 79.4 + - + +
246A PHE* 5.7 0.2 - + - -
273A GLN* 4.7 7.4 - - - +
324A THR* 3.7 21.5 - - + +
423A LEU* 4.0 8.7 - - + -
476A VAL* 3.6 35.4 - - + -
478A LEU* 3.9 19.3 - - + -
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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
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200A ASN* 2.7 39.1 + - - +
201A GLU* 4.0 3.6 - - - +
203A TRP* 1.3 74.3 - - - +
205A GLN* 1.3 64.9 + - - +
207A MET* 3.6 5.8 + - - +
208A ARG* 2.9 26.4 + - + +
273A GLN* 3.8 19.7 - - - +
326A GLN* 4.9 2.7 - - - +
42B ARG* 3.9 13.9 - - - +
44B ILE* 3.8 37.0 - - + -
47B GLY* 3.3 26.0 - - - +
48B LYS* 4.9 0.2 - - - -
49B GLN* 4.5 5.2 - - + +
70B VAL* 6.3 0.4 - - + -
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Residues in contact with GLN 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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182A PHE* 3.3 50.2 - - + +
185A PHE* 5.6 1.9 - - + -
201A GLU* 2.7 25.5 + - - +
202A CYS* 2.9 10.6 + - - +
204A ILE* 1.3 81.0 - - - +
206A MET* 1.3 65.9 + - - +
207A MET 3.1 1.3 - - - -
208A ARG* 3.3 11.1 + - + +
209A VAL* 3.0 25.9 + - - +
49B GLN* 4.1 41.2 + - - +
51B GLU* 6.0 1.6 - - - +
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Residues in contact with MET 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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115A MET* 4.6 11.9 - - + -
118A THR* 3.3 16.6 - - + -
119A VAL* 3.6 27.1 - - + -
122A ILE* 3.8 18.6 - - + -
151A ILE* 4.9 9.0 - - + -
155A LEU* 3.8 28.9 - - + -
174A LEU* 4.7 8.5 - - - -
178A LEU* 4.9 7.2 - - - -
182A PHE* 5.2 2.9 - - - -
202A CYS* 2.5 47.7 + - - +
203A TRP 3.5 4.3 - - - +
205A GLN* 1.3 72.5 - - - +
207A MET* 1.3 60.8 + - - +
209A VAL* 2.6 25.6 - - + +
210A LEU* 3.0 14.6 + - - +
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Residues in contact with MET 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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122A ILE* 4.7 11.7 - - + -
128A LEU* 5.0 2.2 - - - -
203A TRP* 2.5 66.8 + - + +
204A ILE* 3.6 6.7 - - - +
206A MET* 1.3 72.1 - - - +
208A ARG* 1.3 65.6 + - - +
210A LEU* 3.0 14.3 + - - -
211A GLN* 2.8 23.8 + - - +
242A ILE* 3.0 40.5 - - + +
246A PHE* 4.1 32.3 - - + -
272A LEU* 4.9 14.6 - - + -
324A THR* 5.1 2.5 - - + +
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Residues in contact with ARG 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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204A ILE* 2.9 17.2 + - + +
205A GLN* 3.4 18.6 - - + +
207A MET* 1.3 75.2 - - - +
209A VAL* 1.3 68.2 + - - +
211A GLN* 3.2 35.8 - - - +
212A GLN* 3.0 32.2 + - - +
272A LEU* 5.9 1.5 - - - +
47B GLY 4.6 4.9 + - - +
48B LYS* 3.0 58.3 - - + +
49B GLN 5.8 0.2 - - - +
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Residues in contact with VAL 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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147A SER* 5.9 0.7 - - - +
148A ALA* 4.1 26.1 - - + +
151A ILE* 4.6 22.0 - - + -
152A THR* 3.8 16.1 + - - +
155A LEU* 6.2 0.7 - - + -
182A PHE* 4.7 17.3 - - + -
205A GLN 3.0 13.2 - - - +
206A MET* 2.6 32.5 - - + +
208A ARG* 1.3 79.7 - - + +
210A LEU* 1.3 68.8 + - + +
212A GLN* 3.0 22.6 + - - +
213A LYS* 3.2 6.4 + - - +
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Residues in contact with LEU 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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122A ILE* 4.3 24.5 - - + -
128A LEU* 4.6 7.6 - - + -
132A LEU* 4.0 20.2 - - + -
152A THR* 4.2 16.8 - - + +
155A LEU* 4.5 14.8 - - + -
206A MET 3.0 18.4 + - - +
207A MET* 3.4 18.8 - - - +
209A VAL* 1.3 79.1 - - + +
211A GLN* 1.3 58.4 + - - +
212A GLN 3.1 0.2 + - - -
213A LYS 3.1 0.5 + - - -
214A LEU* 2.9 62.4 + - + +
242A ILE* 3.3 18.8 - - + -
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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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207A MET 2.8 15.4 + - - +
208A ARG* 3.2 24.5 - - - +
210A LEU* 1.3 73.0 - - - +
212A GLN* 1.3 61.7 + - - +
214A LEU 4.0 1.7 - - - +
239A LYS 4.8 0.7 - - - +
240A SER* 3.2 24.0 - - - -
242A ILE* 3.2 24.1 - - + +
243A ASP* 3.6 27.3 + - - +
272A LEU* 3.5 20.8 - - - +
46B ALA 4.8 1.7 - - - +
48B LYS* 2.7 35.2 + - - +
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Residues in contact with GLN 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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148A ALA* 3.9 24.4 - - + +
208A ARG* 3.0 47.0 + - - +
209A VAL* 3.0 14.7 + - - +
211A GLN* 1.3 84.9 - - - +
213A LYS* 1.3 70.8 + - + +
214A LEU 4.7 0.9 - - - +
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Residues in contact with LYS 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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135A TYR* 3.8 30.0 + - + +
148A ALA* 4.3 11.4 - - + +
149A GLN* 4.1 31.9 + - - +
152A THR* 3.6 36.6 - - + +
209A VAL 3.2 3.5 + - - +
210A LEU 3.1 2.6 + - - -
212A GLN* 1.3 92.7 - - + +
214A LEU* 1.3 66.8 + - - +
215A GLU* 3.3 6.9 + - - +
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Residues in contact with LEU 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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128A LEU* 3.4 26.7 - - + -
131A ALA* 3.3 38.8 - - + +
132A LEU* 4.3 9.2 - - + +
134A ARG 5.2 0.2 - - - +
135A TYR* 5.0 7.0 - - + -
152A THR* 4.6 7.6 - - + -
210A LEU* 2.9 49.9 + - + +
211A GLN 4.0 4.2 - - - +
212A GLN 4.7 1.4 - - - +
213A LYS* 1.3 74.3 - - - +
215A GLU* 1.3 60.8 + - - +
239A LYS 4.9 0.3 - - - +
240A SER* 3.6 8.3 - - - -
241A LEU* 3.3 33.2 + - + +
242A ILE* 5.0 2.7 - - + +
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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