Contacts of the strand formed by residues 261 - 271 (chain B) in PDB entry 1TLY
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 GLY 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B ARG* 3.1 20.8 + - - +
235B TYR* 3.3 17.7 - - - -
236B TRP* 2.9 32.9 + - - -
260B THR* 1.3 78.1 - - - +
262B TRP* 1.3 59.8 + - - -
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Residues in contact with TRP 262 (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 HIS* 3.5 7.1 - - - +
26B ARG* 2.7 33.0 + - - +
218B HIS* 4.0 20.4 - + - -
233B ALA* 3.6 34.5 - - + -
234B ARG 3.2 31.9 - - - -
235B TYR* 3.4 35.6 - + + -
236B TRP* 4.4 0.4 - - - -
261B GLY* 1.3 73.5 - - - -
263B GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 263 (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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23B TYR* 3.1 16.2 - - - -
24B HIS* 3.5 11.2 - - - -
233B ALA* 3.9 2.9 - - - -
234B ARG* 2.9 30.7 + - - -
236B TRP* 3.9 10.0 - - - -
262B TRP* 1.3 77.5 - - - +
264B GLY* 1.3 58.4 + - - -
265B TYR* 5.1 0.2 - - - -
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Residues in contact with GLY 264 (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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22B SER* 3.3 0.5 - - - -
23B TYR* 2.9 41.0 + - - +
25B THR* 5.4 0.4 + - - +
232B VAL 3.1 12.1 - - - -
233B ALA* 4.7 0.2 - - - -
263B GLY* 1.3 75.5 - - - -
265B TYR* 1.3 76.3 + - - -
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Residues in contact with TYR 265 (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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20B VAL* 4.0 19.1 - - + -
21B GLY 3.1 7.0 - - - +
22B SER* 3.4 32.3 - - - -
25B THR* 3.4 18.1 + - - -
27B PHE* 3.8 5.4 - - - -
36B TYR* 3.9 12.6 - - - -
230B SER 3.7 0.6 - - - +
231B VAL* 3.6 1.2 - - - +
232B VAL* 2.9 57.5 + - + +
234B ARG* 2.9 48.4 + - + -
236B TRP* 3.6 15.6 - + - -
264B GLY* 1.3 79.5 - - - -
266B LEU* 1.3 70.9 + - - +
267B VAL* 4.2 4.5 - - + -
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Residues in contact with LEU 266 (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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19B VAL 3.7 1.4 - - - +
20B VAL* 3.5 2.8 - - - -
21B GLY* 2.9 36.5 + - - +
230B SER 3.6 1.3 - - - +
231B VAL* 4.0 28.7 - - + -
265B TYR* 1.3 81.1 - - - +
267B VAL* 1.3 64.3 + - - +
268B VAL* 4.3 4.3 - - + -
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Residues in contact with VAL 267 (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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18B ASN* 3.8 31.2 - - + +
19B VAL 3.7 1.8 - - - -
20B VAL* 4.0 23.6 - - + -
38B GLU* 4.7 4.0 - - - +
40B GLU* 5.7 2.0 - - - +
228B HIS* 3.6 5.9 - - + +
229B TYR* 3.2 6.1 - - - -
230B SER* 2.8 57.0 + - - +
232B VAL* 4.9 6.7 - - + -
265B TYR* 4.5 7.2 - - + -
266B LEU* 1.3 82.7 - - - +
268B VAL* 1.3 65.7 + - - +
269B GLY 4.8 0.4 - - - +
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Residues in contact with VAL 268 (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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18B ASN* 3.4 2.2 - - - -
19B VAL* 2.9 42.5 + - + +
227B TRP* 4.3 20.6 - - + -
228B HIS 3.5 3.8 - - - +
229B TYR* 3.9 35.9 - - + -
266B LEU* 5.4 3.8 - - + -
267B VAL* 1.3 78.8 - - - +
269B GLY* 1.3 61.3 + - - +
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Residues in contact with GLY 269 (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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17B VAL 3.1 6.3 - - - -
18B ASN* 3.0 19.9 + - - -
227B TRP* 3.0 24.8 - - - -
228B HIS* 3.2 32.1 + - - -
268B VAL* 1.3 76.0 - - - +
270B TYR* 1.3 60.6 + - - -
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Residues in contact with TYR 270 (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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16B SER* 3.3 5.8 - - - -
17B VAL* 3.0 28.2 + - + +
226B HIS* 3.2 45.8 + + + -
227B TRP* 3.4 45.1 - + + -
228B HIS* 3.7 1.6 - - - -
269B GLY* 1.3 75.6 - - - +
271B ASN* 1.3 60.0 + - - +
272B PHE* 3.3 63.4 + + + -
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Residues in contact with ASN 271 (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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14B HIS* 5.8 4.0 - - + +
15B GLN 3.3 9.9 - - - +
16B SER* 3.0 27.0 + - - -
223B ASN* 3.8 13.3 + - - -
224B TYR 5.2 3.4 + - - -
225B ASP 4.7 3.3 + - - +
226B HIS* 2.7 45.5 + - - +
228B HIS* 2.8 28.7 + - - +
270B TYR* 1.3 71.0 - - - +
272B PHE* 1.3 61.6 - - - +
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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