Contacts of the helix formed by residues 350 - 360 (chain B) in PDB entry 1ULH
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 ASP 350 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330B PHE 3.5 4.4 - - - +
331B SER* 2.4 39.9 + - - +
332B GLY* 4.7 0.2 - - - -
346B ASN 3.4 13.7 + - - +
347B CYS* 3.5 3.2 + - - +
349B VAL* 1.3 76.7 - - - +
351B VAL* 1.3 62.3 + - - +
352B SER* 3.0 11.8 + - - -
353B PHE* 2.5 37.2 + - + +
354B MET* 3.0 22.7 + - - +
373B TYR* 3.7 12.0 + - + -
383B LEU* 3.0 21.7 - - - +
384B LYS* 5.1 2.4 - - - -
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Residues in contact with VAL 351 (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 PRO* 4.7 4.9 - - + -
295B ALA 3.6 13.7 - - - +
296B LEU* 3.4 28.3 - - - +
298B GLY* 3.7 15.7 - - - -
299B ALA 4.3 1.3 - - - +
329B ALA* 4.2 9.0 - - + -
330B PHE* 3.0 27.4 + - + +
349B VAL 3.2 6.0 + - - +
350B ASP* 1.3 71.4 - - - +
352B SER* 1.3 58.7 + - - +
354B MET* 3.7 9.3 + - - +
355B TYR* 2.8 62.1 + - + +
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Residues in contact with SER 352 (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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325B VAL* 3.7 7.1 - - - +
329B ALA* 4.1 8.5 + - - +
330B PHE 4.1 1.2 + - - -
350B ASP* 3.0 18.1 + - - -
351B VAL* 1.3 76.0 - - - +
353B PHE* 1.3 60.2 + - - +
355B TYR* 3.4 4.9 + - - +
356B LEU* 3.1 30.6 + - - +
383B LEU* 3.9 13.0 - - - -
384B LYS* 3.6 28.1 - - - +
387B LEU* 3.5 24.0 - - - +
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Residues in contact with PHE 353 (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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347B CYS* 3.5 45.5 - - + -
350B ASP* 2.5 27.2 + - + +
352B SER* 1.3 70.9 - - - +
354B MET* 1.3 67.9 + - + +
356B LEU* 3.2 25.7 + - + +
357B THR* 3.2 32.8 + - + +
366B LEU* 3.7 35.9 - - + -
369B ILE* 4.4 8.7 - - + -
370B ARG* 3.8 31.4 - - + -
383B LEU* 4.2 8.0 - - + +
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Residues in contact with MET 354 (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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49B LYS 4.1 13.9 - - - +
50B GLY* 5.4 0.4 - - - -
294B PRO* 3.5 39.5 - - + -
299B ALA* 3.7 24.0 - - + -
347B CYS 4.8 9.0 - - - +
348B ASP 4.9 6.3 - - - +
349B VAL* 4.9 6.3 - - - +
350B ASP 3.0 23.0 + - - +
351B VAL* 3.9 12.3 - - - +
353B PHE* 1.3 77.9 - - + +
355B TYR* 1.3 62.8 + - - +
357B THR* 2.6 29.0 + - - -
358B PHE* 3.1 12.5 - - + -
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Residues in contact with TYR 355 (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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293B PHE* 3.4 36.3 - + + -
294B PRO* 3.2 32.2 + - + -
296B LEU* 3.4 29.2 + - + +
303B MET* 3.4 12.8 - - + +
312B ILE* 3.7 23.6 - - + -
325B VAL* 5.7 0.9 - - + -
329B ALA* 5.6 1.8 - - + -
351B VAL* 2.8 38.5 + - + -
352B SER 3.5 9.4 - - - +
354B MET* 1.3 83.6 - - + +
356B LEU* 1.3 61.2 + - - +
358B PHE* 3.0 14.9 + - - +
359B PHE* 3.3 14.9 + - - +
387B LEU* 3.5 29.2 - - + +
391B LEU* 4.1 11.4 - - + -
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Residues in contact with LEU 356 (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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87B ARG* 3.6 1.4 + - - -
352B SER 3.1 19.2 + - - +
353B PHE* 3.5 13.0 - - + +
354B MET 3.2 0.8 - - - -
355B TYR* 1.3 71.1 - - - +
357B THR* 1.3 58.4 + - - +
358B PHE 3.0 9.8 + - - -
359B PHE* 4.6 0.9 - - - +
360B LEU* 3.1 47.0 + - + +
366B LEU* 3.7 13.3 - - + +
369B ILE* 4.1 33.7 - - + -
383B LEU* 4.2 23.3 - - + +
386B ALA* 4.5 4.3 - - + -
387B LEU* 3.7 34.3 - - + +
390B VAL* 4.3 8.5 - - + -
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Residues in contact with THR 357 (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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83B HIS* 4.5 1.2 - - - -
87B ARG* 3.0 33.3 + - - +
89B ILE* 3.1 19.3 - - - +
353B PHE* 3.2 34.9 + - + +
354B MET* 2.6 21.5 + - - -
356B LEU* 1.3 75.5 - - - +
358B PHE* 1.3 63.8 + - - +
366B LEU* 3.9 17.7 - - + -
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Residues in contact with PHE 358 (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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83B HIS* 3.2 22.1 + - - -
84B PHE* 3.3 14.6 - + - -
89B ILE* 3.4 35.7 - - + -
128B ILE* 3.4 31.2 - - + -
291B THR* 3.7 21.8 - - - -
292B PHE 3.9 14.6 - - - -
293B PHE* 3.5 25.4 - + - -
294B PRO* 4.3 11.7 - - + -
354B MET* 3.1 27.4 - - + -
355B TYR 3.4 6.5 - - - +
356B LEU 3.0 0.8 - - - -
357B THR* 1.3 88.4 + - - +
359B PHE* 1.3 81.3 + - + +
360B LEU 4.0 0.7 - - - -
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Residues in contact with PHE 359 (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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83B HIS* 4.7 2.5 - - - -
84B PHE* 5.0 8.3 - + - -
124B VAL* 3.8 11.9 - - + -
127B LEU* 4.6 11.0 - - + -
128B ILE* 3.6 25.4 - - + -
131B ILE* 5.0 9.9 - - + -
293B PHE* 3.4 32.5 - + - -
355B TYR 3.3 12.4 + - - +
356B LEU 4.1 0.2 - - - -
358B PHE* 1.3 93.3 - - + +
360B LEU* 1.3 65.4 + - - +
361B GLU* 3.7 3.7 - - - +
390B VAL* 4.3 25.6 - - + +
391B LEU* 4.2 13.2 - - + -
394B LEU* 3.4 41.1 - - + -
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Residues in contact with LEU 360 (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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87B ARG* 4.3 1.7 - - - +
356B LEU* 3.1 30.3 + - + +
358B PHE 4.0 0.6 - - - -
359B PHE* 1.3 76.6 - - - +
361B GLU* 1.3 72.7 + - - +
362B ASP* 4.2 8.1 - - + +
365B LYS* 4.2 27.1 - - + +
366B LEU* 3.6 45.5 - - + +
369B ILE* 4.0 16.2 - - + -
386B ALA* 6.1 2.2 - - + -
390B VAL* 3.8 25.5 - - + +
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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