Contacts of the helix formed by residues 225 - 237 (chain 2) in PDB entry 5U8T
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 SER 225 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2162 LEU 4.0 10.1 + - - -
2172 GLU* 4.1 1.2 + - - -
2182 TYR* 2.2 34.2 + - - -
2192 THR* 3.3 17.1 - - - +
2202 ASP 4.8 1.6 - - - +
2232 GLY 3.5 1.3 - - - -
2242 ARG* 1.3 75.5 - - - +
2262 VAL* 1.3 64.4 + - - +
2272 TYR* 3.2 8.5 + - - -
2282 GLY* 3.5 10.4 + - - -
2292 ALA* 3.3 20.8 + - - +
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Residues in contact with VAL 226 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2182 TYR* 6.1 2.2 - - + -
2202 ASP* 5.3 3.5 - - + +
2212 GLU* 5.1 8.7 - - - +
2242 ARG 3.3 4.5 + - - +
2252 SER* 1.3 70.9 - - - +
2272 TYR* 1.3 72.1 + - + +
2292 ALA* 3.2 7.0 + - - +
2302 ARG* 2.9 64.5 + - + +
2432 GLU* 5.3 4.9 - - - +
2452 ASN* 4.7 13.5 - - - +
2482 HIS* 3.9 27.8 - - + -
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Residues in contact with TYR 227 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2142 PHE* 2.8 51.2 + + - -
2152 LEU* 2.9 30.3 - - + +
2162 LEU* 3.1 23.3 - - - +
2182 TYR* 3.2 43.4 - + + -
2252 SER* 4.2 0.9 - - - -
2262 VAL* 1.3 83.1 - - + +
2282 GLY* 1.3 65.3 + - - +
2302 ARG* 2.9 6.6 + - - +
2312 ILE* 2.8 38.0 + - + +
2422 LEU* 5.9 7.2 - - + -
2432 GLU 5.9 2.5 - - - -
2442 VAL* 5.5 11.9 - - + -
2452 ASN* 5.8 3.8 - - + -
2482 HIS* 4.2 7.8 + - - -
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Residues in contact with GLY 228 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2162 LEU 5.0 0.8 + - - -
2252 SER* 3.5 11.1 + - - -
2272 TYR* 1.3 78.0 - - - +
2292 ALA* 1.3 55.0 + - - +
2312 ILE* 4.3 7.4 - - - -
2322 ARG* 3.0 32.7 + - - +
2822 HIS* 3.5 19.4 - - - -
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Residues in contact with ALA 229 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2242 ARG 5.6 0.7 - - - +
2252 SER 3.3 12.8 + - - +
2262 VAL* 3.2 11.6 + - - +
2272 TYR 3.0 0.6 - - - -
2282 GLY* 1.3 78.3 - - - +
2302 ARG* 1.3 56.3 - - - +
2322 ARG* 3.7 18.3 + - - +
2332 THR* 2.1 37.1 + - - -
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Residues in contact with ARG 230 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2262 VAL* 2.9 41.3 + - + +
2272 TYR* 2.9 5.6 + - - +
2292 ALA* 1.3 78.5 - - - +
2312 ILE* 1.3 60.1 + - - +
2322 ARG 3.2 1.1 - - - -
2332 THR* 3.2 15.4 - - - -
2342 LEU* 2.8 41.4 + - + +
2422 LEU* 5.1 14.6 - - + -
2432 GLU* 3.1 40.8 + - - +
2452 ASN* 5.3 3.6 - - - +
4772 THR* 5.2 16.4 + - - +
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Residues in contact with ILE 231 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2152 LEU 5.7 0.9 - - - +
2162 LEU* 5.7 2.0 - - + -
2272 TYR* 2.8 29.3 + - + +
2282 GLY* 4.0 4.3 - - - +
2302 ARG* 1.3 75.2 - - - +
2322 ARG* 1.3 59.0 + - - +
2342 LEU 4.2 4.7 - - - -
2352 GLY 2.9 28.2 + - - -
2422 LEU* 4.0 17.7 - - + +
2752 ALA* 4.3 1.6 - - + +
2782 ALA* 3.6 28.0 - - + +
2792 THR* 3.3 36.4 - - + +
2822 HIS* 3.3 34.1 - - + +
2832 TYR* 3.1 6.7 - - + -
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Residues in contact with ARG 232 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2282 GLY 3.0 24.1 + - - +
2292 ALA* 3.7 17.0 + - - +
2312 ILE* 1.3 76.4 - - - +
2332 THR* 1.3 58.8 + - - +
2362 GLU* 2.9 42.6 + - - +
2822 HIS* 3.3 20.1 - - - +
2832 TYR* 2.9 31.5 + - - +
4782 GLU* 5.2 9.5 + - - +
361E LYS* 4.0 28.4 - - - +
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Residues in contact with THR 233 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2292 ALA* 2.1 30.4 + - - +
2302 ARG* 3.0 22.0 + - - -
2322 ARG* 1.3 74.7 - - - +
2342 LEU* 1.3 67.5 + - + +
2362 GLU* 2.8 12.6 + - - +
2372 MET* 2.3 36.3 + - + +
4772 THR* 6.4 1.8 - - + -
357E LYS* 4.4 18.2 + - - +
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Residues in contact with LEU 234 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2302 ARG* 2.8 16.7 + - + +
2312 ILE* 3.1 11.4 - - - +
2332 THR* 1.3 84.4 - - + +
2352 GLY* 1.3 54.7 + - - +
2372 MET* 3.5 17.7 - - + -
2382 ASN* 3.2 18.2 - - - +
2392 SER* 3.1 27.1 - - - +
2402 GLU* 4.3 3.8 + - - +
2412 SER 3.0 36.8 - - - +
2422 LEU* 4.4 9.1 - - + +
2792 THR* 4.9 4.3 - - - +
2862 TYR* 3.4 7.0 + - - -
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Residues in contact with GLY 235 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2312 ILE 2.9 15.2 + - - -
2322 ARG 3.4 0.4 - - - -
2342 LEU* 1.3 63.6 + - - -
2362 GLU* 1.3 59.9 + - - -
2372 MET 3.1 3.1 - - - -
2382 ASN* 2.7 25.5 + - - +
2792 THR* 4.9 1.0 - - - +
2832 TYR* 3.2 19.4 - - - -
2862 TYR* 2.6 27.3 + - - -
360E HIS 4.8 0.5 - - - +
364E ALA* 4.2 9.8 - - - +
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Residues in contact with GLU 236 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2322 ARG* 2.9 30.6 + - - +
2332 THR* 2.8 10.2 + - - +
2352 GLY* 1.3 70.7 - - - +
2372 MET* 1.3 60.3 + - - +
2382 ASN* 4.0 6.1 + - - -
2832 TYR* 3.9 4.2 + - - +
357E LYS* 2.9 57.4 - - + +
358E ARG* 3.3 9.5 + - - -
360E HIS* 3.1 37.8 - - + +
361E LYS* 3.1 39.0 - - + +
364E ALA* 4.4 0.2 - - - +
370E LEU* 5.6 0.3 - - - +
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Residues in contact with MET 237 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2332 THR* 2.3 35.7 + - + +
2342 LEU* 3.5 24.9 - - + -
2362 GLU* 1.3 68.4 - - - +
2382 ASN* 1.3 76.6 + - - +
2392 SER* 2.9 17.4 + - - -
357E LYS* 4.6 13.6 - - - +
370E LEU* 5.3 8.6 - - + +
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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