Contacts of the helix formed by residues 294 - 301 (chain B) in PDB entry 1T5A
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 ARG 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B VAL* 2.9 23.8 + - + +
293B ALA* 1.3 69.0 - - - +
295B GLY* 1.3 57.4 + - - +
297B LEU* 4.0 8.5 - - - -
298B GLY 2.6 29.5 + - - -
306B VAL* 4.1 18.3 - - + +
310B GLN* 3.0 26.5 + - - +
326B CYS* 3.7 15.1 - - - -
327B ALA 2.9 20.7 + - - +
328B THR* 3.0 19.4 + - - -
330B MET* 3.5 12.3 - - - +
347B ASP* 2.4 46.9 + - - -
533B OXL 3.6 0.2 + - - -
342D ARG* 2.7 41.3 + - + +
343D ALA 4.3 0.6 - - - +
346D SER* 3.7 10.1 + - - -
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Residues in contact with GLY 295 (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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178B ASP* 4.6 8.7 - - - -
294B ARG* 1.3 76.8 - - - +
296B ASP* 1.3 58.6 + - - -
298B GLY 3.2 1.9 + - - -
299B ILE* 3.5 7.0 - - - +
328B THR* 3.2 21.5 - - - +
533B OXL 2.7 20.6 + - - -
342D ARG* 2.9 26.3 + - - -
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Residues in contact with ASP 296 (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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210B ASN* 3.4 23.9 + - - +
244B PHE* 3.4 21.5 - - + -
272B GLU* 2.4 44.6 - - + +
293B ALA 3.7 0.2 + - - -
295B GLY* 1.3 70.6 - - - +
297B LEU* 1.3 60.0 + - - +
299B ILE* 3.1 6.0 + - - +
300B GLU* 2.8 31.9 + - - +
533B OXL 2.7 11.1 + - - +
602B MG 2.4 16.1 - - - -
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Residues in contact with LEU 297 (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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271B ILE 4.2 9.9 - - - +
272B GLU 3.4 15.2 + - - +
273B ASN* 3.7 25.8 - - - +
277B VAL* 3.9 13.5 - - + -
292B VAL* 4.3 12.3 - - + -
293B ALA 3.3 16.5 + - - +
294B ARG* 3.2 5.3 + - - +
296B ASP* 1.3 79.1 - - - +
298B GLY* 1.3 58.2 + - - +
300B GLU* 4.3 0.7 - - - -
301B ILE* 2.9 51.9 + - + +
306B VAL* 4.4 13.5 - - + -
309B ALA* 4.0 22.9 - - + -
313B MET* 4.1 13.7 - - + -
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Residues in contact with GLY 298 (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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294B ARG 2.6 15.1 + - - -
296B ASP 3.2 0.2 - - - -
297B LEU* 1.3 73.1 - - - +
299B ILE* 1.3 61.6 + - - +
301B ILE 3.1 11.9 - - - +
303B ALA* 4.0 14.5 + - - +
306B VAL* 3.8 17.4 - - - +
342D ARG* 3.3 26.6 + - - -
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Residues in contact with ILE 299 (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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175B TYR* 3.9 26.3 - - + -
178B ASP* 3.7 10.1 - - - +
179B GLY* 3.4 31.2 - - - +
210B ASN* 3.3 38.6 - - + +
212B PRO* 3.5 14.3 - - - +
295B GLY 3.5 15.3 - - - +
296B ASP* 3.6 6.7 - - - +
297B LEU 3.1 0.4 - - - -
298B GLY* 1.3 80.9 - - - +
300B GLU* 1.3 64.3 + - - +
301B ILE* 3.3 3.5 + - - +
339D ARG* 6.0 3.4 - - + -
342D ARG* 3.5 16.6 - - - +
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Residues in contact with GLU 300 (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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210B ASN* 2.7 34.8 + - - -
211B LEU 3.9 23.0 + - - +
212B PRO* 4.1 20.4 - - + +
213B GLY 4.8 4.1 + - - +
214B ALA 5.5 1.0 - - - +
216B VAL* 6.0 1.4 - - - +
244B PHE* 5.0 7.2 - - - -
272B GLU 3.6 10.4 - - - +
273B ASN* 3.5 33.9 - - + +
274B HIS* 4.0 9.5 + - + +
296B ASP* 2.8 14.1 + - - +
297B LEU 4.0 2.7 - - - +
299B ILE* 1.3 79.0 - - - +
301B ILE* 1.3 64.0 + - + +
302B PRO* 4.8 0.5 - - - +
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Residues in contact with ILE 301 (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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274B HIS* 4.1 36.1 - - + +
297B LEU* 2.9 42.8 + - + +
298B GLY* 3.1 18.7 - - - +
299B ILE 4.1 2.4 - - - -
300B GLU* 1.3 85.0 - - + +
302B PRO* 1.3 79.9 - - + +
305B LYS* 4.1 28.3 - - + +
306B VAL* 4.3 5.4 - - + +
309B ALA* 4.6 2.7 - - + -
35D ILE* 3.9 29.2 - - + -
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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