Contacts of the helix formed by residues 200 - 213 (chain A) in PDB entry 5A91
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 ALA 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A LYS* 4.4 0.6 - - - +
85A GLU* 2.8 29.0 + - + +
199A LEU* 1.3 73.0 - - - +
201A GLU* 1.3 61.5 + - - +
202A THR 4.6 0.4 - - - +
203A GLN* 3.2 21.3 + - - +
204A ARG* 2.8 25.1 + - - +
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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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199A LEU 3.8 0.9 + - - -
200A ALA* 1.3 74.6 - - - +
202A THR* 1.3 64.9 + - - +
204A ARG* 2.7 45.9 + - - -
205A ALA* 2.9 27.8 + - + +
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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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200A ALA* 3.4 1.0 - - - +
201A GLU* 1.3 80.5 - - - +
203A GLN* 1.3 72.9 + - - +
205A ALA* 3.4 6.3 + - - +
206A GLN* 2.9 27.7 + - + +
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Residues in contact with GLN 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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81A LEU* 3.3 45.7 - - + +
84A SER* 3.0 24.2 + - - +
85A GLU* 3.6 25.7 - - + +
91A LEU* 5.1 4.6 - - + +
199A LEU* 4.1 12.3 - - + -
200A ALA* 3.2 23.7 + - - +
202A THR* 1.3 88.1 - - - +
204A ARG* 1.3 64.2 + - - +
206A GLN* 3.2 7.4 + - - +
207A LEU* 2.9 19.8 + - - +
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Residues in contact with ARG 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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193A LEU 3.5 17.0 - - - +
194A THR 2.8 44.9 + - - +
195A LEU* 4.3 16.4 - - - +
196A GLY 4.4 12.1 - - - +
199A LEU* 3.8 20.7 - - + +
200A ALA 2.8 20.3 + - - +
201A GLU* 2.7 43.6 + - - +
203A GLN* 1.3 71.1 - - - +
205A ALA* 1.3 73.2 + - - +
207A LEU* 3.2 4.2 + - - +
208A VAL* 3.0 40.0 + - - +
251A TRP* 5.6 1.6 - - - -
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Residues in contact with ALA 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 GLU* 2.9 28.4 + - + +
202A THR* 3.6 6.7 - - - +
204A ARG* 1.3 86.7 - - - +
206A GLN* 1.3 58.1 + - - +
208A VAL* 3.3 6.5 + - - +
209A THR* 2.9 34.4 + - - +
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Residues in contact with GLN 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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81A LEU* 4.0 10.1 - - + -
91A LEU* 5.3 8.4 - - + +
120A ALA* 5.7 2.4 - - - +
202A THR* 2.9 16.6 + - + +
203A GLN* 3.2 11.9 + - - +
205A ALA* 1.3 74.3 - - - +
207A LEU* 1.3 65.6 + - - +
209A THR* 3.3 14.4 + - - +
210A TRP* 3.0 71.4 + - + +
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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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74A VAL* 4.5 15.3 - - + +
77A ALA* 5.2 1.1 - - + -
78A ALA* 4.6 3.8 - - + -
81A LEU* 3.8 17.4 - - + +
127A LEU* 3.7 27.4 - - + -
193A LEU* 3.7 44.6 - - + +
194A THR* 4.0 9.9 - - + -
199A LEU* 4.1 10.1 - - + -
203A GLN 2.9 13.3 + - - +
204A ARG 3.6 7.9 - - - +
206A GLN* 1.3 76.8 - - - +
208A VAL* 1.3 62.1 + - + +
210A TRP* 3.2 6.2 + - + +
211A LEU* 2.9 37.2 + - + +
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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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194A THR* 3.5 39.9 - - + +
204A ARG* 3.0 29.7 + - - +
205A ALA* 3.7 7.2 - - - +
207A LEU* 1.3 75.7 - - - +
209A THR* 1.3 64.5 + - - +
211A LEU* 3.2 7.3 + - + +
212A LYS* 2.9 54.3 + - + +
251A TRP* 3.7 18.8 - - + -
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Residues in contact with THR 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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128A GLN* 3.7 4.9 + - - +
205A ALA* 2.9 22.2 + - - +
206A GLN* 3.6 18.8 - - - +
208A VAL* 1.3 76.3 - - - +
210A TRP* 1.3 67.1 + - + +
212A LYS* 3.4 8.6 + - - +
213A GLY* 3.1 17.5 + - - -
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Residues in contact with TRP 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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77A ALA* 4.4 8.1 - - + -
81A LEU* 3.8 33.4 - - + -
91A LEU* 5.0 3.1 - - + -
119A LEU 5.1 0.2 - - - -
120A ALA* 3.3 36.8 - - + -
123A GLY* 4.0 15.5 - - - -
124A ALA* 3.5 32.1 - - + +
127A LEU* 3.8 32.2 - - + +
128A GLN* 3.0 31.7 + - + +
206A GLN* 3.0 52.1 + - + +
207A LEU* 3.5 11.7 - - - +
209A THR* 1.3 79.3 - - + +
211A LEU* 1.3 62.7 + - - +
213A GLY 3.1 3.5 + - - -
214A ASN* 3.3 6.1 + - - +
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Residues in contact with LEU 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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74A VAL* 4.0 24.7 - - + -
127A LEU* 4.6 12.3 - - + -
190A LEU* 4.3 11.4 - - + -
194A THR* 3.5 32.3 - - + -
207A LEU* 2.9 30.9 + - + +
208A VAL* 3.2 5.6 + - - +
210A TRP* 1.3 75.2 - - - +
212A LYS* 1.3 63.3 + - - +
214A ASN* 3.1 14.4 + - - +
222A ARG* 3.4 1.0 + - - -
232A GLY* 3.2 16.0 - - - -
233A ASP* 3.1 39.4 + - - +
234A LYS* 4.2 2.0 - - + +
247A ILE 5.5 0.7 - - - +
249A VAL* 5.0 6.1 - - + -
251A TRP* 6.4 2.0 - - + -
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Residues in contact with LYS 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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208A VAL* 2.9 41.9 + - + +
209A THR* 3.8 6.7 - - - +
211A LEU* 1.3 76.0 - - - +
213A GLY* 1.3 58.1 + - - +
214A ASN 3.2 4.3 + - - +
222A ARG* 3.5 14.2 + - - -
230A VAL* 3.7 26.8 - - + +
231A VAL 3.5 20.1 - - - +
232A GLY* 4.2 1.1 - - - -
251A TRP* 3.7 25.6 - - + -
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Residues in contact with GLY 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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128A GLN* 3.4 29.4 + - - -
209A THR 3.1 10.5 + - - -
210A TRP 3.1 0.8 + - - -
212A LYS* 1.3 75.3 - - - +
214A ASN* 1.3 66.7 + - - +
215A THR* 3.3 12.1 + - - +
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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