Contacts of the helix formed by residues 315 - 324 (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 GLU 315 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B HIS* 4.5 10.4 + - - +
313B THR* 2.6 31.1 + - - -
314B ARG* 1.3 77.5 + - + +
316B LYS* 1.3 87.0 + - - +
317B TRP 3.2 1.1 + - - -
318B ASP* 3.7 20.2 + - - +
319B GLY 4.3 2.1 + - - -
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Residues in contact with LYS 316 (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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62A GLU* 3.6 31.5 + - - -
65A LEU* 6.2 0.6 - - - +
69A ARG* 5.5 3.4 - - - +
259B ASP* 6.1 0.9 - - - +
311B LEU 5.7 2.0 - - - -
312B ARG* 4.2 23.0 - - + +
313B THR* 3.0 32.8 + - - +
315B GLU* 1.3 99.1 + - - +
317B TRP* 1.3 62.2 + - - +
318B ASP 3.5 0.2 - - - -
319B GLY* 3.6 3.6 + - - -
320B LEU* 3.3 20.1 + - - +
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Residues in contact with TRP 317 (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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254B LEU* 3.7 10.3 - - + -
266B LEU* 5.8 0.2 - - + -
281B ILE* 3.6 43.3 - - + -
283B GLU* 3.5 29.4 - - + -
284B ARG 3.6 15.5 + - - -
285B ASP* 3.7 18.5 + - - +
312B ARG* 3.1 40.9 + - + -
313B THR 3.5 19.7 - - - -
314B ARG 4.2 5.6 - - - +
315B GLU 3.2 0.8 - - - -
316B LYS* 1.3 76.5 - - - +
318B ASP* 1.3 66.6 + - - +
320B LEU* 3.1 30.9 + - + +
321B ALA* 2.9 27.1 + - + +
328B VAL* 4.5 9.4 - - + -
346B LEU* 3.9 23.9 - - + +
348B LEU* 6.0 0.9 - - + -
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Residues in contact with ASP 318 (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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314B ARG 4.8 4.9 + - - +
315B GLU* 3.7 14.3 + - - +
316B LYS 3.5 0.2 - - - -
317B TRP* 1.3 77.6 - - - +
319B GLY* 1.3 56.2 + - - +
321B ALA* 4.0 1.8 - - - +
322B ALA* 3.2 28.1 + - - +
327B VAL* 5.9 1.2 - - - +
328B VAL* 3.7 29.0 + - - +
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Residues in contact with GLY 319 (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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315B GLU 4.3 2.8 + - - -
316B LYS 3.6 7.5 + - - -
317B TRP 3.1 0.6 - - - -
318B ASP* 1.3 76.1 - - - +
320B LEU* 1.3 65.6 + - - +
322B ALA* 4.1 4.6 - - - +
323B SER* 3.3 22.7 + - - -
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 4.5 0.9 - - + -
259B ASP* 3.9 44.2 - - + +
262B ALA* 4.3 8.5 - - + -
263B VAL* 3.8 11.3 - - + +
266B LEU* 4.0 20.7 - - + +
312B ARG* 3.8 25.1 - - - +
316B LYS 3.3 13.3 + - - +
317B TRP* 3.1 38.7 + - + +
319B GLY* 1.3 76.7 - - - +
321B ALA* 1.3 62.7 + - - +
323B SER* 3.3 14.3 + - - -
324B ALA* 3.3 11.3 + - - +
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Residues in contact with ALA 321 (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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266B LEU* 4.9 3.6 - - - +
317B TRP* 2.9 16.9 + - + +
318B ASP 4.0 3.8 - - - +
320B LEU* 1.3 77.7 - - - +
322B ALA* 1.3 61.8 + - - +
324B ALA* 3.0 11.2 + - - -
325B GLY 3.3 0.2 + - - -
326B LEU* 2.8 39.7 + - - +
327B VAL* 4.3 2.2 - - - +
328B VAL* 4.1 13.9 - - + +
348B LEU* 3.9 27.6 - - + -
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Residues in contact with ALA 322 (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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318B ASP 3.2 17.3 + - - +
319B GLY* 4.1 6.1 - - - +
320B LEU 3.4 0.2 - - - -
321B ALA* 1.3 78.8 - - - +
323B SER* 1.3 57.8 - - - +
325B GLY* 2.9 20.1 + - - -
326B LEU 3.4 11.8 + - - +
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Residues in contact with SER 323 (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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263B VAL* 3.7 28.2 - - - +
267B THR* 4.9 0.7 + - - -
319B GLY 3.3 16.8 + - - -
320B LEU* 3.5 6.7 - - - -
321B ALA 3.2 0.2 - - - -
322B ALA* 1.3 77.9 - - - +
324B ALA* 1.3 57.1 + - - +
325B GLY 3.3 1.0 + - - -
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Residues in contact with ALA 324 (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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263B VAL* 4.0 5.8 - - + +
266B LEU* 3.6 31.9 - - + -
267B THR* 3.9 24.2 + - - +
270B ALA* 4.4 10.4 - - - +
320B LEU 3.3 7.0 + - - +
321B ALA 3.0 10.4 + - - +
323B SER* 1.3 76.2 - - - +
325B GLY* 1.3 61.2 + - - +
326B LEU* 3.6 12.4 + - + +
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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