Contacts of the strand formed by residues 326 - 334 (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 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B LEU* 4.0 20.2 - - + +
270B ALA* 4.0 17.9 - - + -
273B LEU* 5.2 1.8 - - + -
279B ILE* 3.7 27.8 - - + -
321B ALA* 2.8 29.6 + - + +
322B ALA* 3.4 9.5 + - - +
324B ALA* 3.9 17.0 - - + +
325B GLY* 1.3 84.4 - - - +
327B VAL* 1.3 62.6 + - - +
348B LEU* 4.0 22.2 - - + -
349B ALA* 3.3 24.9 - - - +
350B PRO* 3.9 7.2 - - + -
351B ALA* 3.9 8.5 - - - +
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ASP* 5.9 1.1 - - - +
321B ALA* 4.4 3.6 - - - -
326B LEU* 1.3 76.3 - - - +
328B VAL* 1.3 70.8 + - - +
329B GLU* 3.3 9.5 + - + +
348B LEU* 3.2 8.7 - - - -
349B ALA* 2.8 45.6 + - + +
350B PRO 3.7 14.1 - - - +
351B ALA* 4.4 11.2 - - - +
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Residues in contact with VAL 328 (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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317B TRP* 4.4 19.1 - - + +
318B ASP* 3.7 24.1 + - - +
321B ALA* 4.1 15.2 - - + +
327B VAL* 1.3 82.3 - - - +
329B GLU* 1.3 62.0 + - - +
330B GLU* 3.8 21.0 - - - +
331B VAL* 3.9 18.4 - - + -
346B LEU* 4.4 5.6 - - + -
347B VAL 3.7 6.5 - - - +
348B LEU* 3.8 19.3 - - + -
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Residues in contact with GLU 329 (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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278B ARG* 3.0 38.0 + - - -
327B VAL* 3.3 7.6 + - + +
328B VAL* 1.3 74.8 - - - +
330B GLU* 1.3 70.1 + - + +
347B VAL* 3.1 30.3 + - + +
349B ALA* 4.0 19.1 - - + +
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B VAL* 3.3 5.2 - - - +
329B GLU* 1.3 88.6 - - + +
331B VAL* 1.3 70.2 + - - +
332B ARG* 2.9 44.5 + - - +
346B LEU* 3.8 0.2 - - - -
347B VAL* 3.0 44.4 + - + +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ASP* 3.3 25.4 - - - +
328B VAL* 3.9 10.1 - - + -
330B GLU* 1.3 84.2 - - - +
332B ARG* 1.3 65.1 + - - +
333B GLN* 3.6 16.8 + - - +
344B SER* 3.5 25.1 - - - -
345B LEU 3.7 3.6 - - - +
346B LEU* 3.7 31.0 - - + -
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Residues in contact with ARG 332 (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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173B ALA* 3.0 36.5 + - + +
174B TYR* 3.9 26.0 - - - +
175B ASP* 4.3 7.5 - - - +
330B GLU* 2.9 48.6 + - - +
331B VAL* 1.3 73.3 - - - +
333B GLN* 1.3 65.8 + - - +
334B LEU* 3.9 2.1 - - - +
344B SER* 3.4 1.7 - - - -
345B LEU* 3.0 41.6 + - + +
347B VAL* 4.0 18.8 - - - +
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Residues in contact with GLN 333 (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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285B ASP* 5.2 0.2 - - - +
314B ARG* 3.4 29.8 + - - +
331B VAL* 3.6 33.6 + - - +
332B ARG* 1.3 75.0 - - - +
334B LEU* 1.3 69.2 + - - +
335B PRO* 3.4 13.1 - - + +
342B ASP* 3.4 34.2 - - - +
343B LEU 3.7 2.5 - - - -
344B SER* 4.3 6.7 + - - -
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Residues in contact with LEU 334 (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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169B ALA* 3.9 24.9 - - + +
170B PRO* 4.4 14.1 - - + -
173B ALA* 3.7 26.5 - - + -
282B HIS* 4.3 11.9 - - + +
332B ARG 3.9 2.2 - - - +
333B GLN* 1.3 80.9 - - - +
335B PRO* 1.3 68.0 - - - +
336B SER* 3.8 4.3 + - - -
339B ILE* 5.7 1.0 - - - +
341B TYR 5.1 0.3 - - - +
342B ASP* 4.2 1.2 - - - -
343B LEU* 2.8 40.4 + - + +
344B SER* 3.6 33.2 - - - +
345B LEU* 3.8 10.3 - - + +
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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