Contacts of the helix formed by residues 198 - 209 (chain A) in PDB entry 5U0A
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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98A LYS* 3.8 2.9 - - - -
155A ALA* 3.8 16.6 - - + +
156A ASN* 3.2 3.7 + - - +
196A ILE* 3.6 0.9 - - - +
197A SER* 1.3 77.3 - - - +
199A VAL* 1.3 61.6 + - - +
200A ASP* 4.6 3.4 - - - +
201A ALA* 3.9 22.7 - - + +
202A VAL* 3.0 26.3 + - - +
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Residues in contact with VAL 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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96A LEU* 3.7 16.4 - - + +
98A LYS* 3.2 35.2 - - + +
198A ASP* 1.3 72.2 - - - +
200A ASP* 1.3 77.5 + - + +
201A ALA 3.0 1.6 - - - -
202A VAL* 3.1 4.6 - - + +
203A ARG* 2.9 58.6 + - + +
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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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198A ASP* 4.6 3.3 - - - +
199A VAL* 1.3 86.9 + - + +
201A ALA* 1.3 83.4 + - - +
203A ARG* 3.5 17.9 - - - +
204A HIS* 2.8 26.6 + - - +
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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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156A ASN* 3.3 26.4 + - - +
198A ASP* 3.9 14.8 + - + -
199A VAL 3.0 0.8 - - - -
200A ASP* 1.3 88.2 + - - +
202A VAL* 1.3 60.6 + - - +
203A ARG 3.3 0.2 - - - -
204A HIS* 3.3 13.0 + - - +
205A ALA* 2.9 19.6 + - - +
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Residues in contact with VAL 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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96A LEU* 6.4 0.4 - - + -
98A LYS* 4.4 2.5 - - - +
156A ASN* 3.5 17.8 - - + +
157A GLY* 3.9 20.6 - - - +
196A ILE* 3.9 14.6 - - + -
198A ASP 3.0 21.8 + - - +
199A VAL* 3.1 13.0 - - + +
201A ALA* 1.3 75.3 - - - +
203A ARG* 1.3 61.3 + - + +
205A ALA* 3.0 6.0 + - + +
206A VAL* 2.7 45.3 + - + +
221A LEU* 4.8 10.5 - - + -
223A LEU* 5.1 12.1 - - + -
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Residues in contact with ARG 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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91A PRO* 2.6 61.7 + - + +
96A LEU* 4.3 9.7 - - - +
199A VAL* 2.9 50.7 + - + +
200A ASP* 3.5 17.9 - - - +
202A VAL* 1.3 76.7 - - + +
204A HIS* 1.3 60.8 + - - +
206A VAL* 3.0 12.8 + - + +
207A LEU* 2.9 34.8 + - + +
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Residues in contact with HIS 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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48A GLN* 5.5 6.3 + - - -
200A ASP 2.8 21.1 + - - +
201A ALA* 3.3 13.6 + - - +
203A ARG* 1.3 77.1 - - - +
205A ALA* 1.3 56.3 + - - +
207A LEU* 3.4 10.3 + - + -
208A ASN* 2.9 50.1 + - + +
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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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152A ARG 6.0 0.7 - - - +
153A ALA* 6.2 0.7 - - - -
156A ASN* 3.6 26.7 - - - +
201A ALA 2.9 6.4 + - - +
202A VAL* 3.0 12.5 + - + +
204A HIS* 1.3 72.9 - - - +
206A VAL* 1.3 59.4 + - - +
208A ASN* 2.6 28.1 - - - +
209A GLY* 2.8 17.5 + - - -
210A ILE* 4.2 20.7 - - + +
219A GLY 5.3 0.2 - - - +
221A LEU* 5.2 2.4 - - + +
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Residues in contact with VAL 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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2A THR* 6.3 2.9 - - + -
52A LEU* 3.5 16.6 - - - +
91A PRO* 6.5 0.7 - - + -
202A VAL* 2.7 28.5 + - + +
203A ARG* 3.0 13.4 + - + +
205A ALA* 1.3 73.8 - - - +
207A LEU* 1.3 62.4 + - + +
209A GLY* 4.0 0.3 + - - -
220A LEU* 5.1 8.4 - - + +
221A LEU* 3.8 48.5 + - + +
223A LEU* 4.0 14.1 - - + -
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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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2A THR* 4.9 15.3 - - - +
47A GLN 5.4 0.3 - - - +
48A GLN* 3.2 41.9 - - + +
52A LEU* 3.4 11.8 - - - +
69A HIS* 3.3 37.2 + - + +
203A ARG* 2.9 19.4 + - + +
204A HIS* 4.0 9.4 - - + +
206A VAL* 1.3 77.3 - - + +
208A ASN* 1.3 66.1 + - + +
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Residues in contact with ASN 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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46A ARG* 3.4 38.6 + - + +
47A GLN 4.1 16.7 - - - +
48A GLN* 5.7 2.7 - - + -
52A LEU* 3.9 5.4 - - - +
204A HIS* 2.9 48.3 + - + +
205A ALA* 2.6 22.2 - - - +
207A LEU* 1.3 84.4 - - + +
209A GLY* 1.3 85.4 + - - +
214A LYS* 3.3 18.5 - - - +
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Residues in contact with GLY 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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46A ARG* 2.6 28.9 + - - -
52A LEU* 3.7 11.6 - - - +
205A ALA 2.8 10.3 + - - -
206A VAL 4.6 0.4 - - - -
207A LEU 3.5 2.0 - - - -
208A ASN* 1.3 94.3 + - - +
210A ILE* 1.3 57.2 + - - +
214A LYS* 3.4 13.2 - - - -
219A GLY 3.6 11.7 - - - -
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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