Contacts of the helix formed by residues 298 - 311 (chain H) 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 ASP 298 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B PRO 5.3 0.5 - - - +
334B THR* 3.9 8.2 - - - +
335B PHE* 5.5 0.9 - - - -
382B THR* 5.9 1.7 - - - +
406B PHE* 4.6 5.4 - - + -
410B ARG* 3.3 39.4 + - - +
452B LYS 4.4 6.6 - - - +
454B GLY* 4.9 1.5 - - - +
296H GLU 3.4 4.4 + - - -
297H ALA* 1.3 68.5 - - - +
299H LEU* 1.3 68.0 + - - +
300H SER* 3.4 16.3 + - - -
301H LEU* 2.8 48.9 + - + +
302H TYR* 2.8 20.5 + - - +
438H PHE* 4.6 3.5 - - - -
442H MET* 4.9 3.7 - - + +
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Residues in contact with LEU 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B SER* 3.9 22.9 - - - +
382B THR* 5.0 3.8 - - + -
383B GLY* 5.1 2.9 - - - +
384B GLN* 3.1 47.8 - - + +
297H ALA* 3.1 12.2 + - + +
298H ASP* 1.3 72.1 + - - +
300H SER* 1.3 64.0 + - - +
302H TYR* 4.0 13.9 - - + -
303H ASN* 2.8 41.3 + - - +
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Residues in contact with SER 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B THR* 3.8 23.5 - - - +
335B PHE 6.0 3.6 - - - -
298H ASP* 3.0 18.5 + - - -
299H LEU* 1.3 80.2 - - - +
301H LEU* 1.3 63.2 + - - +
303H ASN* 4.1 4.9 - - - +
304H GLU* 3.3 20.1 + - - +
323H LYS* 6.1 1.4 - - - -
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Residues in contact with LEU 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LYS* 4.0 16.8 - - + +
453B LEU* 4.2 2.5 - - + -
298H ASP* 2.8 31.2 + - + +
300H SER* 1.3 76.3 - - - +
302H TYR* 1.3 60.2 + - - +
304H GLU* 3.4 12.7 + - - +
305H PHE* 3.0 30.1 + - - +
320H PHE* 5.8 0.2 - - - -
323H LYS* 3.8 24.7 - - + -
438H PHE* 3.9 3.6 - - + -
442H MET* 3.2 35.7 - - + -
445H ARG* 3.8 27.6 - - - +
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Residues in contact with TYR 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297H ALA* 4.5 10.1 - - + -
298H ASP 2.8 11.5 + - - +
299H LEU* 3.6 19.5 - - + +
301H LEU* 1.3 78.8 - - - +
303H ASN* 1.3 69.5 + - - +
305H PHE* 3.4 2.7 + + - +
306H ARG* 2.9 66.3 + - + +
434H VAL* 4.3 11.9 - - + +
435H ASP* 2.4 35.0 + - - -
438H PHE* 3.5 46.2 - + + -
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Residues in contact with ASN 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299H LEU* 2.8 30.4 + - - +
300H SER* 4.1 4.3 - - - +
302H TYR* 1.3 84.5 - - - +
304H GLU* 1.3 66.4 + - - +
306H ARG* 3.3 11.2 + - - +
307H LEU* 3.0 33.9 + - + +
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Residues in contact with GLU 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300H SER 3.3 15.9 + - - +
301H LEU* 3.6 14.2 - - - +
303H ASN* 1.3 78.4 - - - +
305H PHE* 1.3 62.2 + - - +
307H LEU* 3.5 7.0 + - - +
308H TRP* 3.1 21.3 + - - +
319H PRO* 3.2 30.9 - - + +
320H PHE* 3.8 24.3 - - + +
323H LYS* 2.8 41.7 + - - +
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Residues in contact with PHE 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301H LEU 3.0 17.6 + - - +
302H TYR* 3.9 3.8 - + - +
304H GLU* 1.3 74.0 - - - +
306H ARG* 1.3 66.0 + - + +
308H TRP* 2.9 17.6 + + - +
309H LYS* 2.8 41.3 + - + +
320H PHE* 3.5 35.6 - + + -
424H ILE* 4.4 7.6 - - + -
434H VAL* 3.8 18.2 - - + -
437H MET* 3.9 26.0 - - + -
438H PHE* 3.6 46.2 - + + -
441H VAL* 3.8 19.5 - - + -
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Residues in contact with ARG 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302H TYR* 2.9 51.7 + - + +
303H ASN* 3.3 12.1 + - - +
305H PHE* 1.3 85.4 - - + +
307H LEU* 1.3 63.4 + - + +
309H LYS* 3.7 5.6 + - + +
310H ASP* 3.3 31.4 + - - +
434H VAL* 4.0 21.7 - - + +
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Residues in contact with LEU 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H ASN* 3.0 24.6 + - + +
304H GLU* 3.7 6.5 - - - +
306H ARG* 1.3 79.8 - - + +
308H TRP* 1.3 65.5 + - - +
310H ASP* 2.9 24.0 + - + +
311H GLU* 3.3 11.4 + - - +
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Residues in contact with TRP 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304H GLU 3.1 14.4 + - - +
305H PHE* 2.9 18.2 + + - +
307H LEU* 1.3 78.2 - - - +
309H LYS* 1.3 68.8 + - - +
311H GLU 3.1 6.9 + - - +
312H PRO* 3.0 32.1 - - + +
313H THR* 3.0 49.8 + - + +
318H CYS* 3.9 12.7 - - + -
320H PHE* 3.4 47.1 - + + -
321H LEU* 4.5 0.9 - - + +
421H ILE* 3.5 51.8 - - + -
424H ILE* 3.8 22.7 - - + -
425H GLN* 4.6 2.0 - - + -
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Residues in contact with LYS 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H PHE* 2.8 34.6 + - + +
306H ARG* 4.0 4.5 - - + +
308H TRP* 1.3 85.1 - - + +
310H ASP* 1.3 72.4 + - - +
312H PRO* 3.0 21.3 - - - +
424H ILE* 4.6 8.0 - - + +
434H VAL* 3.5 40.2 - - + -
437H MET* 4.2 25.6 - - + +
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Residues in contact with ASP 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ARG* 3.3 21.5 + - - +
307H LEU* 2.9 20.4 + - + +
309H LYS* 1.3 97.3 + - - +
311H GLU* 1.3 69.4 + - + +
312H PRO* 3.5 2.8 - - - +
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Residues in contact with GLU 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307H LEU 3.3 6.2 + - - +
308H TRP* 3.1 11.1 + - - +
310H ASP* 1.3 92.0 - - + +
312H PRO* 1.3 67.6 - - - +
313H THR* 3.6 9.4 + - - +
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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