Contacts of the strand formed by residues 17 - 25 (chain A) in PDB entry 5A19
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 THR 17 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY* 1.3 86.2 - - - +
18A PHE* 1.3 64.7 + - - +
187A GLN* 3.4 32.1 + - - +
188A TYR 3.2 15.0 - - - +
189A MET* 4.6 8.3 - - + -
190A GLN* 5.7 0.2 - - - -
198A ILE* 4.0 12.8 - - + -
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Residues in contact with PHE 18 (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 THR* 1.3 78.0 - - - +
19A LEU* 1.3 75.3 + - - +
20A PHE* 4.2 10.3 - + + -
187A GLN* 3.5 2.6 - - - -
188A TYR* 2.8 68.1 + + + -
189A MET 4.4 2.9 - - - -
190A GLN* 4.3 32.3 - - + +
195A VAL* 4.0 9.2 - - + -
274A TRP* 3.9 17.3 - + - -
408A PEG 3.7 33.4 - - - -
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Residues in contact with LEU 19 (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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18A PHE* 1.3 83.8 - - - +
20A PHE* 1.3 64.5 + - - +
21A THR* 5.5 0.4 - - - +
185A THR* 4.2 11.4 - - + -
186A VAL 3.5 1.8 - - - +
187A GLN* 3.8 27.4 - - + +
201A HIS* 3.6 51.1 - - + +
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Residues in contact with PHE 20 (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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18A PHE* 4.1 8.9 + + + -
19A LEU* 1.3 77.8 - - - +
21A THR* 1.3 90.9 + - - +
153A THR* 3.3 8.4 - - - +
185A THR* 4.3 0.2 - - - -
186A VAL 2.9 30.1 + - - -
188A TYR* 4.0 9.9 - - + -
272A GLY 3.9 3.4 - - - -
273A GLY* 3.7 23.6 - - - -
274A TRP* 3.2 72.7 - + + -
408A PEG 4.7 15.9 - - - -
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Residues in contact with THR 21 (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 LEU* 5.5 0.5 - - - +
20A PHE* 1.3 82.0 - - - +
22A SER* 1.3 68.8 + - - +
153A THR* 4.6 0.2 - - - -
183A GLN* 3.6 34.5 - - + +
184A VAL 3.4 5.2 - - - +
185A THR* 2.7 34.9 + - - +
272A GLY 3.5 7.6 - - - +
273A GLY* 5.3 0.3 - - - -
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Residues in contact with SER 22 (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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21A THR* 1.3 72.8 + - - +
23A GLU* 1.3 60.6 + - - +
153A THR* 2.6 32.0 + - - -
154A ILE* 3.7 17.8 + - - +
157A ALA* 4.2 3.8 - - - +
183A GLN* 3.5 5.7 - - - +
184A VAL* 2.8 32.1 + - - +
272A GLY* 2.7 31.6 + - - -
274A TRP* 4.0 4.3 - - - -
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Residues in contact with GLU 23 (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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22A SER* 1.3 74.1 - - - +
24A SER* 1.3 62.7 + - - +
25A VAL* 5.2 3.8 - - - -
154A ILE* 3.0 20.6 - - - +
157A ALA* 3.9 4.7 - - - -
181A LYS* 4.3 20.0 + - - +
182A THR 3.3 14.6 - - - +
183A GLN* 4.1 20.0 - - + +
265A LYS* 5.0 3.7 - - - +
267A ILE* 6.5 0.7 - - + -
268A VAL* 3.5 25.0 - - + +
272A GLY* 5.2 1.9 - - - -
403A PPK 3.4 24.8 + - - -
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Residues in contact with SER 24 (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 GLU* 1.3 76.0 - - - +
25A VAL* 1.3 81.8 + - - +
157A ALA* 3.6 16.7 - - - +
158A HIS* 2.8 36.9 + - - -
161A ASN* 3.2 18.2 + - - +
181A LYS* 3.6 0.5 - - - +
182A THR 3.0 29.5 + - - +
268A VAL* 3.9 9.6 - - - +
377A TYR* 4.9 1.9 - - - -
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Residues in contact with VAL 25 (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 GLU* 5.2 3.4 - - - +
24A SER* 1.3 88.8 + - - +
26A GLY* 1.3 65.4 + - - +
29A HIS* 3.8 14.6 - - + -
32A LYS* 3.6 33.8 - - + +
161A ASN* 3.6 9.3 + - - +
180A SER 3.5 9.2 - - - +
181A LYS* 3.9 30.1 - - + -
265A LYS* 4.0 28.0 - - + -
268A VAL* 4.1 7.3 - - + +
376A ALA* 5.4 0.3 - - - +
377A TYR* 5.0 10.4 + - - -
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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