Contacts of the strand formed by residues 19 - 26 (chain A) in PDB entry 1O9T
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 19 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLY 4.3 0.2 - - - +
18A ALA* 1.3 77.4 - - - +
20A MET* 1.3 69.6 + - - +
21A PHE* 4.7 4.9 - + + -
188A GLN* 3.8 1.6 - - - +
189A TYR* 2.8 61.3 + + + +
191A GLN* 3.5 26.5 - - + -
196A VAL* 4.4 14.8 - - + -
275A TRP* 3.9 22.0 - + - -
314A ARG* 6.0 1.1 - - - -
318B GLN* 5.1 2.2 - - - +
330B SER* 5.2 2.5 - - - -
332B SER* 3.6 21.1 - - - +
334B PHE* 3.3 32.1 - + + -
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Residues in contact with MET 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 1.3 78.7 - - - +
21A PHE* 1.3 56.1 + - - +
22A THR* 5.6 1.3 - - - -
186A THR* 4.3 13.2 - - - +
187A VAL 3.6 11.2 - - - +
188A GLN* 4.2 16.8 - - + +
202A HIS* 3.7 30.5 - - + +
318B GLN* 2.6 34.3 + - - -
320B SER* 3.8 19.3 + - - +
329B LEU* 3.3 31.2 - - + +
330B SER* 3.7 27.0 + - - +
332B SER* 4.5 3.4 + - - +
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Residues in contact with PHE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 4.7 5.8 - + + -
20A MET* 1.3 74.3 - - - +
22A THR* 1.3 93.3 + - - +
23A SER* 3.9 2.2 - - - -
154A THR* 4.1 3.2 + - + -
185A VAL 3.9 0.5 - - - +
186A THR* 3.0 4.2 - - - -
187A VAL 2.9 32.7 + - - -
189A TYR* 4.1 7.4 - - + -
273A GLY 3.5 16.8 - - - -
274A GLY 3.0 27.6 - - - -
275A TRP* 3.5 54.7 - + + -
138B LEU* 3.7 6.7 - - + -
140B PHE* 3.5 25.6 - + - -
318B GLN* 3.8 21.5 - - - -
320B SER* 5.4 0.2 - - - -
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Residues in contact with THR 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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20A MET* 5.6 1.6 - - - -
21A PHE* 1.3 86.2 - - - +
23A SER* 1.3 75.2 + - - +
154A THR* 3.6 0.9 - - - -
184A GLN* 4.6 15.3 - - + +
185A VAL 3.3 14.4 - - - +
186A THR* 3.0 27.1 + - + +
273A GLY 4.0 1.9 - - - +
136B GLN* 5.1 6.0 + - + -
137B GLY* 4.5 12.9 + - - +
138B LEU* 3.3 32.4 - - + +
320B SER* 5.0 5.5 + - - -
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Residues in contact with SER 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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21A PHE* 3.9 0.7 - - - -
22A THR* 1.3 74.1 + - - +
24A GLU* 1.3 62.7 + - - +
154A THR* 3.0 35.3 - - - +
155A ILE* 3.8 19.7 + - - -
158A ALA* 4.2 2.4 - - - +
184A GLN* 3.2 4.3 - - - +
185A VAL 2.9 31.0 + - - -
273A GLY* 2.8 27.1 + - - -
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Residues in contact with GLU 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 SER* 1.3 77.0 - - - +
25A SER* 1.3 62.6 + - - +
26A VAL* 5.6 2.0 - - - -
155A ILE* 3.3 20.3 - - - +
158A ALA* 4.1 4.0 - - - -
182A LYS* 3.3 21.7 + - - -
183A THR 2.9 13.7 - - - +
184A GLN* 3.5 16.6 + - + +
266A LYS* 4.6 2.3 - - - -
269A VAL* 3.5 27.9 - - + +
273A GLY* 5.4 2.1 - - - -
1401A MG 2.4 29.9 - - - -
279B GLY 4.7 13.7 - - - +
280B GLY* 5.7 3.8 - - - -
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Residues in contact with SER 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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24A GLU* 1.3 76.9 - - - +
26A VAL* 1.3 71.3 + - - +
158A ALA* 3.5 17.3 + - - -
159A HIS* 3.0 31.8 - - - -
162A ASN* 3.0 18.9 + - - +
182A LYS* 3.4 2.9 - - - +
183A THR 2.6 36.5 + - - +
269A VAL* 4.3 9.8 - - - +
378A TYR* 4.9 2.1 - - - -
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Residues in contact with VAL 26 (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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24A GLU* 5.4 4.7 - - - +
25A SER* 1.3 88.3 + - - +
27A GLY* 1.3 62.1 + - - +
30A HIS* 3.6 37.0 - - + +
33A LYS* 3.5 37.0 - - + +
162A ASN* 4.0 6.8 - - - +
181A SER 3.3 10.3 - - - +
182A LYS* 4.3 12.3 - - + -
266A LYS* 4.3 19.3 - - + -
269A VAL* 4.6 3.5 - - + +
377A CYS* 3.9 11.8 - - - -
378A TYR* 4.5 3.6 + - - -
1397B ATP 4.8 1.1 - - - +
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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