Contacts of the helix formed by residues 318 - 328 (chain T) in PDB entry 4UJ3
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 CYS 318 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308T TRP* 4.0 22.0 - - + -
313T THR* 4.0 17.5 - - + -
315T ASP* 3.2 27.4 + - - +
316T ARG 3.5 0.2 - - - -
317T THR* 1.3 84.6 + - - +
319T PRO* 1.3 77.5 - - + +
320T PHE 4.1 0.4 - - - -
321T LEU* 3.6 26.9 - - - -
322T ASP* 3.1 19.6 + - - +
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Residues in contact with PRO 319 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304T GLU* 3.3 30.3 - - + +
307T LEU* 5.9 7.2 - - + -
308T TRP* 6.1 0.9 - - + -
317T THR 3.9 0.6 - - - +
318T CYS* 1.3 92.6 - - + +
320T PHE* 1.3 65.2 + - + +
322T ASP* 3.6 8.0 + - + +
323T LYS* 3.6 9.4 + - - +
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Residues in contact with PHE 320 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301T LEU 5.6 0.7 - - - -
304T GLU* 4.0 18.4 + - - +
305T PHE* 3.8 43.7 - + + -
308T TRP* 3.6 45.8 - + + -
318T CYS 3.3 0.4 - - - -
319T PRO* 1.3 84.4 - - + +
321T LEU* 1.3 85.4 + - + +
323T LYS* 3.7 4.2 + - - +
324T ILE* 3.6 40.2 + - + +
421T ILE* 3.6 26.9 - - + -
441T VAL* 3.8 21.5 - - + -
445T ARG* 6.1 0.2 - - - -
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Residues in contact with LEU 321 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308T TRP* 4.8 0.9 - - - +
313T THR 3.8 10.3 - - - +
314T MET* 3.7 26.2 - - + +
315T ASP 3.4 20.9 - - - +
316T ARG 4.2 1.3 - - - +
318T CYS* 3.6 16.7 + - - -
320T PHE* 1.3 99.5 - - + +
322T ASP* 1.3 55.4 + - - +
324T ILE* 3.3 2.7 + - + +
325T TYR* 2.7 62.3 + - + +
417T PHE* 3.9 28.3 - - + -
418T PHE* 5.5 2.5 - - + -
421T ILE* 4.8 10.3 - - + -
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Residues in contact with ASP 322 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316T ARG 3.7 14.2 + - - +
317T THR* 4.6 6.8 - - - +
318T CYS 3.1 21.0 + - - +
319T PRO* 4.1 4.7 - - + +
320T PHE 3.4 0.2 - - - -
321T LEU* 1.3 76.2 - - - +
323T LYS* 1.3 65.0 + - - +
325T TYR* 3.3 4.0 + - - +
326T GLN* 2.9 52.3 + - - +
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Residues in contact with LYS 323 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300T SER* 5.8 2.6 + - - -
301T LEU* 3.6 28.2 - - + +
304T GLU* 3.0 33.1 + - - +
319T PRO 3.6 5.2 + - - +
320T PHE 3.9 8.3 - - - +
321T LEU 3.3 0.2 - - - -
322T ASP* 1.3 81.6 + - - +
324T ILE* 1.3 54.4 + - + +
326T GLN* 3.7 2.4 - - - -
327T GLU* 2.7 73.1 + - - +
445T ARG* 4.0 11.2 - - - +
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Residues in contact with ILE 324 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320T PHE* 3.6 38.7 + - + +
321T LEU* 3.3 7.7 + - + +
323T LYS* 1.3 73.8 - - + +
325T TYR* 1.3 61.0 + - - +
328T ASP* 2.9 38.5 + - - +
329T ILE* 2.9 17.2 + - + -
417T PHE* 3.3 48.5 - - + -
441T VAL* 4.6 0.2 - - + -
445T ARG* 3.9 29.4 - - - +
448T MET* 4.0 13.5 - - + -
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Residues in contact with TYR 325 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314T MET 5.0 1.7 + - - -
316T ARG* 3.3 34.4 + - + +
321T LEU* 2.7 58.7 + - + +
322T ASP* 3.6 6.5 - - - +
324T ILE* 1.3 73.7 - - + +
326T GLN* 1.3 62.4 + - + +
329T ILE* 3.4 24.4 + - + -
330T PHE* 2.8 66.0 + + + -
345T LEU* 5.1 2.2 - - + -
349T GLU* 3.0 28.4 + - - -
418T PHE* 3.0 35.9 - + - -
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Residues in contact with GLN 326 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322T ASP* 2.9 40.0 + - - +
323T LYS* 3.8 3.6 - - - +
325T TYR* 1.3 79.2 - - + +
327T GLU* 1.3 64.3 + - + +
330T PHE* 3.3 30.7 - - - +
331T PRO* 3.4 15.8 - - - +
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Residues in contact with GLU 327 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323T LYS* 2.7 53.2 + - + +
326T GLN* 1.3 77.9 - - + +
328T ASP* 1.3 66.5 + - - +
331T PRO* 3.5 2.3 - - - +
445T ARG* 3.2 17.8 + - - +
452T LYS* 2.9 35.3 + - - +
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Residues in contact with ASP 328 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324T ILE* 2.9 17.4 + - - +
326T GLN 3.5 0.4 - - - -
327T GLU* 1.3 87.2 - - - +
329T ILE* 1.3 65.3 + - - +
331T PRO* 3.1 6.9 - - - +
332T CYS* 3.1 28.9 + - - +
445T ARG* 2.7 45.5 + - - +
448T MET* 3.6 36.9 - - + +
449T SER* 3.7 19.2 + - - -
452T LYS* 4.3 4.6 + - - +
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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