Contacts of the helix formed by residues 252 - 259 (chain B) in PDB entry 1TUB
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 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ARG* 5.4 5.8 - - + +
4B ILE* 5.4 0.9 - - + -
133B GLN* 3.4 37.8 + - + +
134B GLY* 3.8 8.5 - - - +
165B ILE* 6.0 0.3 - - - +
167B ASN* 3.6 21.6 - - - +
199B ASP* 5.1 0.5 - - - +
238B VAL* 3.7 10.5 - - + +
243B ARG* 2.5 52.1 - - + +
250B ALA 3.8 0.6 + - - +
251B ASP* 1.3 73.8 - - - +
253B ARG* 1.3 57.8 + - - +
254B LYS 3.1 0.2 - - - -
255B LEU* 2.7 51.9 + - + +
256B ALA* 3.3 4.2 + - - +
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Residues in contact with ARG 253 (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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98A ASP* 2.5 16.8 + - - +
99A ALA 4.5 4.0 - - - +
100A ALA* 5.8 1.3 - - - +
101A ASN* 5.9 2.2 - - - +
102A ASN* 5.4 2.7 - - - +
105A ARG* 2.3 58.4 - - - +
407A TRP* 3.6 26.9 - - + -
411A GLU* 4.8 5.1 + - - -
133B GLN* 2.4 50.2 - - + +
163B ASP* 5.0 12.1 + - - +
164B ARG* 6.3 0.6 - - - +
165B ILE* 4.1 15.5 - - + +
251B ASP* 2.3 10.6 + - + +
252B LEU* 1.3 71.1 - - - +
254B LYS* 1.3 62.8 + - + -
255B LEU 2.9 1.6 - - - -
256B ALA* 3.0 12.9 + - - +
257B VAL* 3.3 16.6 + - - +
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Residues in contact with LYS 254 (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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71A GLU* 4.1 4.6 + - - -
99A ALA 6.2 0.7 - - - -
101A ASN* 2.7 31.0 - - + +
500A GTP 2.6 57.5 + - - +
248B LEU* 4.5 0.6 - - - +
249B ASN* 2.2 30.2 + - - -
250B ALA* 3.1 22.0 - - + +
251B ASP* 2.3 33.6 + - + +
253B ARG* 1.3 68.9 - - - +
255B LEU* 1.3 55.3 + - - +
257B VAL* 4.7 2.5 - - - +
258B ASN* 1.9 55.9 + - - +
352B LYS* 3.3 11.7 - - - +
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Residues in contact with LEU 255 (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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167B ASN* 4.7 5.8 - - - +
200B GLU* 1.3 65.5 - - - +
202B TYR* 4.1 4.5 - - - +
238B VAL* 3.0 43.3 - - + +
242B LEU* 5.0 13.9 - - + -
250B ALA* 5.2 4.5 - - + +
251B ASP 4.3 2.2 - - - +
252B LEU* 2.7 40.3 + - + +
254B LYS* 1.3 82.8 - - - +
256B ALA* 1.2 51.0 + - - -
258B ASN* 4.1 3.8 - - - +
259B MET* 3.5 17.7 + - + +
316B ALA* 5.5 7.9 - - + -
318B VAL* 5.8 5.6 - - + -
352B LYS* 5.5 0.4 - - - +
378B ILE* 5.3 11.2 - - + -
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Residues in contact with ALA 256 (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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407A TRP* 2.5 56.1 + - + -
165B ILE* 2.8 2.2 - - + -
199B ASP* 2.3 35.4 - - - +
200B GLU* 2.1 16.6 + - - -
252B LEU 3.3 2.8 + - - +
253B ARG 3.0 5.1 + - - +
255B LEU* 1.2 72.3 - - - +
257B VAL* 1.2 53.6 + - - +
260B VAL* 3.5 14.6 - - - +
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ASN* 4.6 4.5 - - + +
102A ASN* 3.9 22.0 - - - +
180A ALA* 5.6 0.2 - - - +
181A VAL* 3.4 23.1 - - + +
404A PHE* 2.6 53.8 - - + -
407A TRP* 2.7 50.3 - - + -
408A TYR* 5.1 0.9 - - + -
253B ARG 3.3 9.2 + - - +
254B LYS* 4.4 3.6 - - - +
256B ALA* 1.2 73.2 - - - +
258B ASN* 1.3 64.4 + - - +
259B MET 3.4 0.2 - - - -
260B VAL 3.9 4.9 - - - -
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Residues in contact with ASN 258 (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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101A ASN* 4.6 3.0 + - - -
179A THR* 4.0 26.7 + - - +
180A ALA* 4.7 7.2 - - - +
181A VAL* 4.2 3.8 - - - +
404A PHE* 5.0 0.3 - - - -
254B LYS* 1.9 42.0 + - - +
255B LEU* 4.1 4.7 - - + +
257B VAL* 1.3 86.1 - - - +
259B MET* 1.3 57.4 + - + +
314B THR* 2.7 34.4 - - - +
315B VAL 5.7 0.7 - - - -
316B ALA* 4.6 7.6 - - + +
352B LYS* 3.0 42.2 + - + +
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Residues in contact with MET 259 (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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200B GLU* 4.4 1.6 - - - +
255B LEU* 3.5 16.3 + - + +
258B ASN* 1.3 78.2 - - + +
260B VAL* 1.2 65.8 + - - +
261B PRO* 2.8 13.5 - - - +
268B PHE* 2.4 50.2 - - + -
314B THR* 3.0 20.7 + - - +
316B ALA* 3.3 26.7 - - + -
378B ILE* 3.0 23.1 - - + -
379B GLY* 2.3 57.2 - - - +
380B ASN* 2.9 20.4 + - - -
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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