Contacts of the strand formed by residues 273 - 284 (chain B) in PDB entry 1TW2
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 LEU 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B LYS* 5.2 5.5 + - - +
245B ALA 3.6 14.8 - - - +
246B ASP 4.2 1.8 - - - +
248B ILE* 3.9 15.9 - - + -
269B CYS 3.3 6.0 + - - +
270B ALA* 3.5 17.2 - - - +
271B GLU 3.3 4.5 - - - +
272B ALA* 1.3 77.9 - - - +
274B GLU* 1.3 70.8 + - - +
275B PRO* 3.9 1.9 - - - +
277B GLY* 3.6 20.4 - - - +
278B ARG* 3.8 27.1 - - - +
279B ILE* 4.1 23.1 - - + +
326B LEU* 5.2 2.0 - - + -
348B LEU 4.9 1.3 - - - +
350B PRO* 4.5 20.4 - - + -
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Residues in contact with GLU 274 (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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180B ARG* 3.6 22.7 + - - +
243B ARG* 5.2 5.7 + - - -
244B LYS* 3.9 30.0 - - - +
245B ALA* 3.1 31.0 + - - +
246B ASP* 3.6 21.6 - - - +
272B ALA 3.7 0.4 + - - -
273B LEU* 1.3 80.8 - - - +
275B PRO* 1.3 84.2 - - + +
276B GLY 3.4 0.5 + - - -
277B GLY* 3.0 15.3 + - - +
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Residues in contact with PRO 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ASP* 5.0 2.8 - - - +
273B LEU 3.9 1.8 - - - +
274B GLU* 1.3 100.6 - - + +
276B GLY* 1.3 60.1 + - - +
277B GLY 3.3 0.5 + - - -
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Residues in contact with GLY 276 (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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174B TYR* 5.5 0.3 + - - -
274B GLU 3.4 0.6 + - - -
275B PRO* 1.3 70.7 - - - +
277B GLY* 1.3 62.7 + - - +
278B ARG* 4.2 23.5 + - - +
350B PRO* 6.4 0.6 - - - +
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Residues in contact with GLY 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 5.7 0.2 - - - -
246B ASP* 3.0 24.0 - - - -
273B LEU* 3.6 18.6 - - - +
274B GLU 3.0 15.6 + - - -
275B PRO 3.2 1.4 + - - -
276B GLY* 1.3 80.4 - - - +
278B ARG* 1.3 76.0 + - - -
350B PRO* 4.5 6.4 - - - +
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Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 3.3 27.7 + - + +
246B ASP 3.1 6.5 + - - -
247B ALA* 3.4 6.6 - - - +
248B ILE 3.1 22.3 + - - -
273B LEU* 3.8 4.2 - - - +
276B GLY* 4.2 24.0 + - - +
277B GLY* 1.3 85.3 + - - -
279B ILE* 1.3 63.9 + - - +
280B LEU* 3.9 13.8 + - + +
329B GLU* 3.0 37.6 + - - -
347B VAL* 4.2 7.4 - - + -
348B LEU 3.4 15.5 - - - +
349B ALA* 3.2 21.4 - - - +
350B PRO* 5.1 3.0 - - - +
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 3.3 17.0 - - + +
250B LEU* 4.2 23.8 - - + -
266B LEU* 4.2 9.9 - - + -
269B CYS* 3.7 29.8 - - + +
270B ALA* 3.7 18.8 - - - +
273B LEU* 4.1 11.9 - - + -
278B ARG* 1.3 75.6 - - - +
280B LEU* 1.3 64.7 + - - +
281B ILE* 4.6 3.4 - - + -
326B LEU* 3.7 28.7 - - + -
346B LEU 3.4 3.3 - - - +
347B VAL* 3.5 1.9 - - - -
348B LEU* 2.8 48.0 + - + +
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Residues in contact with LEU 280 (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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174B TYR* 3.7 57.0 - - + -
176B TRP* 3.9 8.5 - - + -
192B PHE* 6.1 0.4 - - + -
247B ALA* 4.5 4.9 - - + -
248B ILE 2.8 9.8 + - - +
249B ILE* 3.4 30.4 - - + +
250B LEU 2.8 26.2 + - - -
278B ARG* 4.2 11.0 - - + +
279B ILE* 1.3 79.9 - - - +
281B ILE* 1.3 62.9 + - - +
282B HIS 3.7 1.1 + - - -
345B LEU* 3.9 21.7 - - + +
346B LEU 3.3 2.9 - - - -
347B VAL* 3.8 16.2 - - + -
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Residues in contact with ILE 281 (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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250B LEU* 3.4 14.4 - - + +
254B LEU* 3.8 20.9 - - + -
266B LEU* 4.5 2.2 - - + -
279B ILE* 4.6 9.4 - - + -
280B LEU* 1.3 72.1 - - - +
282B HIS* 1.3 60.5 + - - +
283B GLU* 4.2 13.0 - - + +
317B TRP* 3.6 41.5 - - + -
344B SER 3.6 1.2 - - - +
345B LEU* 3.2 6.0 - - - -
346B LEU* 2.8 56.3 + - + +
348B LEU* 3.8 34.5 - - + -
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Residues in contact with HIS 282 (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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166B ALA 5.2 1.4 + - - -
167B PHE* 4.7 8.6 - + - -
170B PRO* 3.2 35.9 - - + +
192B PHE* 4.0 11.4 - + + -
250B LEU 3.0 7.6 + - - +
251B SER* 3.2 32.5 - - - +
252B PHE* 3.0 53.5 + + - -
280B LEU 3.7 2.8 + - - +
281B ILE* 1.3 68.8 - - - +
283B GLU* 1.3 62.4 + - - +
334B LEU* 4.3 5.9 - - + +
343B LEU* 4.3 30.4 - - + +
344B SER 3.4 11.4 + - - -
345B LEU* 3.9 11.0 - - + +
1600B ERT 4.5 6.6 - - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B LEU 5.2 0.2 - - - +
252B PHE* 4.0 30.0 + - + -
253B VAL 4.0 2.9 + - - -
254B LEU* 3.5 14.9 + - - +
255B LEU* 3.2 44.9 + - + +
281B ILE* 3.8 14.3 + - + +
282B HIS* 1.3 77.3 - - - +
284B ARG* 1.3 75.3 + - + +
310B ALA 4.8 1.7 - - - +
311B LEU* 4.6 5.5 - - - +
312B ARG* 5.0 2.8 + - - -
317B TRP* 3.5 23.8 - - + -
343B LEU* 3.4 14.0 - - - +
344B SER* 2.9 29.2 + - - -
346B LEU* 4.9 2.8 - - + +
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Residues in contact with ARG 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PHE* 4.6 4.9 - - + -
283B GLU* 1.3 85.9 - - + +
285B ASP* 1.3 62.0 + - - +
286B ASP* 3.0 34.6 + - - +
293B ASN* 5.3 0.6 + - - -
295B GLN 3.1 26.8 + - - -
296B PHE* 3.7 15.2 - - - +
299B LEU* 4.3 16.4 - - - +
311B LEU* 3.8 41.6 - - + +
312B ARG 3.7 6.9 + - - +
317B TRP* 3.6 23.0 + - - -
341B TYR* 3.1 49.1 + - - +
342B ASP 4.3 7.0 - - - +
343B LEU* 4.7 5.2 - - - -
344B SER* 3.8 3.8 - - - -
346B LEU* 5.0 1.3 - - - +
1600B ERT 5.7 0.8 - - - +
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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