Contacts of the strand formed by residues 19 - 26 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLN* 4.3 8.5 - - - -
330A SER* 5.1 3.1 - - - -
332A SER* 3.4 21.1 - - - +
334A PHE* 3.1 35.0 - + + -
17B GLY 4.3 0.9 - - - +
18B ALA* 1.3 78.1 - - - +
20B MET* 1.3 59.2 + - - +
21B PHE* 4.7 10.1 - + - -
188B GLN* 3.8 1.7 - - - +
189B TYR* 2.6 65.9 + + + +
190B VAL 4.0 1.6 - - - -
191B GLN* 3.7 22.0 - - - -
196B VAL* 4.3 15.3 - - + -
275B TRP* 4.0 23.3 - + - -
314B ARG* 6.1 0.9 - - - -
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Residues in contact with MET 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A GLN* 2.5 35.0 + - - -
320A SER* 3.6 21.3 + - - +
329A LEU* 3.1 33.0 - - + +
330A SER* 3.6 27.9 + - - +
332A SER* 4.3 3.2 + - - +
19B PHE* 1.3 77.4 - - - +
21B PHE* 1.3 56.7 + - - +
22B THR* 5.6 1.1 - - - -
186B THR* 4.3 11.9 - - - +
187B VAL 3.6 10.8 - - - +
188B GLN* 4.2 16.4 - - + +
189B TYR* 4.9 0.4 - - - -
202B HIS* 3.7 31.0 - - + +
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Residues in contact with PHE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.5 7.6 - - + -
140A PHE* 3.4 29.6 - + - -
318A GLN* 3.8 18.6 - - - -
19B PHE* 4.7 6.3 - + + -
20B MET* 1.3 75.2 - - - +
22B THR* 1.3 93.6 + - - +
23B SER* 3.9 1.8 - - - -
154B THR* 4.1 3.6 + - + -
185B VAL 3.9 0.5 - - - +
186B THR* 3.0 4.3 - - - -
187B VAL 2.9 31.9 + - - -
189B TYR* 4.1 6.9 - - + -
273B GLY 3.5 16.6 - - - -
274B GLY 3.1 26.5 - - - -
275B TRP* 3.5 55.6 - + + -
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLN* 4.9 4.9 + - + -
137A GLY* 4.2 12.7 + - - -
138A LEU* 3.2 32.5 - - + +
279A GLY* 6.1 0.9 - - - -
320A SER* 4.9 5.9 + - - -
20B MET* 5.6 0.5 - - - -
21B PHE* 1.3 87.3 - - - +
23B SER* 1.3 77.2 + - - +
154B THR* 3.6 0.4 - - - -
184B GLN* 4.2 18.8 - - + +
185B VAL 3.3 13.9 - - - +
186B THR* 3.0 26.8 + - + +
273B GLY 4.0 1.9 - - - +
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PHE* 3.9 0.5 - - - -
22B THR* 1.3 75.4 + - - +
24B GLU* 1.3 61.5 + - - +
154B THR* 3.0 34.6 - - - +
155B ILE* 3.8 21.0 + - - -
158B ALA* 4.2 2.4 - - - +
184B GLN* 3.2 4.3 - - - +
185B VAL 2.9 30.5 + - - -
273B GLY* 2.8 28.2 + - - -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLY 4.8 14.4 - - - +
280A GLY* 5.6 4.5 - - - -
23B SER* 1.3 76.1 - - - +
25B SER* 1.3 63.3 + - - +
26B VAL* 5.4 3.9 - - - +
155B ILE* 3.3 21.2 - - - +
158B ALA* 4.1 4.5 - - - -
182B LYS* 3.4 28.4 + - - -
183B THR 2.9 13.2 - - - +
184B GLN* 3.8 13.5 - - + +
266B LYS* 4.6 12.3 + - - -
269B VAL* 3.5 27.9 - - + +
273B GLY* 5.4 1.6 - - - -
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU* 1.3 79.1 - - - +
26B VAL* 1.3 71.9 + - - +
158B ALA* 3.5 17.3 + - - -
159B HIS* 3.0 31.2 - - - -
162B ASN* 3.0 18.3 + - - +
182B LYS* 3.4 3.1 - - - +
183B THR 2.7 32.7 + - - +
269B VAL* 4.3 9.1 - - - +
378B TYR* 4.9 1.9 - - - -
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU* 5.4 5.2 - - - +
25B SER* 1.3 88.1 + - - +
27B GLY* 1.3 62.1 + - - +
30B HIS* 3.6 38.1 - - + +
33B LYS* 3.5 36.7 - - + -
162B ASN* 4.0 6.6 - - - +
181B SER 3.3 10.1 - - - +
182B LYS* 4.3 12.8 - - + -
266B LYS* 4.3 19.3 - - + -
269B VAL* 4.6 4.6 - - + +
377B CYS* 3.9 11.6 - - - -
378B TYR* 4.5 4.5 + - - -
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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