Contacts of the helix formed by residues 347 - 363 (chain C) in PDB entry 4U0Z
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 HIS 347 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C PHE* 3.5 47.9 + + + +
198C ILE* 4.7 1.6 - - - +
199C ASP* 3.0 37.1 + - - -
345C ASN 4.0 0.4 + - - -
346C LEU* 1.3 72.5 - - - +
348C PRO* 1.4 75.3 - - + +
349C VAL* 3.2 42.8 - - + +
350C GLU* 2.9 18.5 + - + +
351C PHE* 3.1 10.0 + - - +
386C TYR* 3.2 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C LEU 3.6 4.9 - - - +
347C HIS* 1.4 96.2 - - + +
349C VAL* 1.3 55.7 + - - +
351C PHE* 3.5 7.8 + - + +
352C ALA* 3.0 30.5 + - - +
380C ILE* 4.1 7.0 - - + +
381C LEU* 4.1 5.3 - - + +
384C ALA* 3.8 24.5 - - + +
386C TYR* 3.5 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C PHE* 4.1 8.5 - - + -
198C ILE* 4.4 5.6 - - + -
347C HIS* 3.1 24.4 + - + +
348C PRO* 1.3 74.3 - - - +
350C GLU* 1.4 57.6 + - - +
352C ALA* 3.5 1.9 + - - +
353C ALA* 3.0 28.1 + - - +
381C LEU* 4.3 10.1 - - + -
386C TYR* 4.2 16.2 - - + -
415C ILE 4.4 3.4 - - - +
418C ILE* 4.2 9.7 - - + +
419C ALA* 3.8 38.6 - - + +
422C THR* 3.7 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C PHE* 4.1 21.4 - - + -
346C LEU* 3.4 27.0 - - + +
347C HIS* 2.9 17.5 + - - +
349C VAL* 1.4 74.1 - - - +
351C PHE* 1.3 64.4 + - - +
353C ALA* 3.6 1.6 + - - +
354C LEU* 3.1 36.1 + - + +
415C ILE* 3.6 35.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C TRP* 3.5 28.5 - + - -
338C LEU* 3.6 38.6 - - + -
343C ALA* 3.5 44.6 - - + +
344C MET* 5.2 4.7 - - - -
346C LEU* 4.0 10.9 - - + +
347C HIS 3.1 11.9 + - - +
348C PRO* 3.9 9.0 - - + +
350C GLU* 1.3 75.1 - - - +
352C ALA* 1.3 52.0 + - - +
354C LEU* 3.2 2.7 + - - -
355C ALA* 2.8 32.3 + - + +
380C ILE* 3.3 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C PRO 3.0 17.5 + - - +
349C VAL 3.8 4.0 - - - +
351C PHE* 1.3 76.0 - - - +
353C ALA* 1.4 60.3 + - - +
355C ALA* 3.6 2.1 + - - +
356C HIS* 3.1 23.9 + - - +
377C MET* 3.6 35.9 - - + +
380C ILE* 3.7 19.2 - - + +
381C LEU* 3.9 14.8 - - + -
418C ILE* 5.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C VAL 3.0 18.0 + - - +
350C GLU 4.0 3.8 - - - +
351C PHE 3.4 0.2 - - - -
352C ALA* 1.4 73.7 - - - +
354C LEU* 1.4 51.6 + - - +
356C HIS* 3.3 3.9 + - - +
357C TYR* 2.8 29.8 + - - +
377C MET* 5.0 0.2 - - - -
414C PHE* 3.2 19.1 - - + -
415C ILE* 4.0 25.1 - - + -
418C ILE* 3.8 32.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C TRP* 3.7 19.1 - - + -
346C LEU* 3.8 23.6 - - + -
350C GLU* 3.1 37.7 + - + +
351C PHE 3.7 3.4 - - - +
353C ALA* 1.4 71.5 - - - +
355C ALA* 1.3 60.0 + - - +
357C TYR* 3.2 7.2 + - + +
358C LYS* 2.8 49.8 + - - +
411C VAL* 3.9 36.3 - - + -
415C ILE* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C PHE* 3.4 14.8 - - + -
337C TRP* 3.6 13.7 - - + -
338C LEU* 4.0 24.2 - - + -
351C PHE* 2.8 20.7 + - + +
352C ALA 3.7 4.7 - - - +
354C LEU* 1.3 70.9 - - - +
356C HIS* 1.3 63.3 + - - +
359C LEU* 3.0 21.3 + - - +
376C LEU* 4.7 9.0 - - + -
377C MET* 5.6 0.7 - - - -
380C ILE* 4.3 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C ALA 3.1 12.2 + - - +
353C ALA 3.4 8.7 - - - +
355C ALA* 1.3 76.0 - - - +
357C TYR* 1.3 69.6 + - - +
359C LEU 3.5 0.2 + - - -
360C VAL* 3.2 36.3 + - + +
373C SER* 3.7 20.2 + - - +
374C ARG* 3.8 17.2 + - + -
376C LEU* 5.9 0.4 - - - -
377C MET* 3.4 32.6 - - + +
391C ILE* 4.1 4.5 - - + -
399C TYR* 2.7 45.2 + + - -
403C LEU* 4.8 1.8 - - + +
414C PHE* 3.7 15.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ALA 2.8 20.0 + - - +
354C LEU* 3.2 8.5 + - + +
356C HIS* 1.3 76.7 - - - +
358C LYS* 1.3 64.1 + - + +
360C VAL* 3.2 6.3 + - + +
361C TYR* 2.8 62.1 + + + +
403C LEU* 3.9 21.1 - - + -
406C ALA* 3.3 31.3 + - + -
407C ASN* 2.9 40.0 + - - -
411C VAL* 4.0 23.8 - - + -
414C PHE* 3.9 15.5 - + + -
501C APC 5.5 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C PHE* 3.7 20.0 - - + -
337C TRP* 3.8 52.3 - - + +
354C LEU* 2.8 35.3 + - - +
357C TYR* 1.3 81.5 - - + +
359C LEU* 1.4 60.7 + - - +
361C TYR* 3.3 9.1 + - - +
362C ILE* 3.1 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C VAL* 4.3 15.7 - - + -
331C MET* 4.0 18.6 - - + -
334C PHE* 3.8 17.3 - - + -
355C ALA 3.0 17.6 + - - +
356C HIS 4.0 0.7 - - - +
358C LYS* 1.4 73.3 - - - +
360C VAL* 1.3 57.3 + - - +
362C ILE* 3.0 13.4 + - - +
363C HIS 3.0 23.9 + - - -
364C PRO* 3.7 28.6 - - + +
365C PHE* 4.9 2.5 - - + -
369C ASN* 5.0 3.4 - - + +
372C THR* 4.4 8.7 - - - +
373C SER* 3.4 31.0 - - - +
376C LEU* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C HIS* 4.4 0.5 - - - -
356C HIS* 3.2 25.6 + - + +
357C TYR* 3.5 5.2 - - + +
359C LEU* 1.3 77.7 - - - +
361C TYR* 1.3 61.9 + - - +
363C HIS* 3.1 28.0 + - - +
369C ASN* 4.3 4.7 - - + +
370C GLY* 4.3 6.1 - - - +
373C SER* 3.2 20.4 + - - +
403C LEU* 4.2 15.9 - - + -
501C APC 3.0 64.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C HIS* 2.8 59.3 + + - -
320C ILE 5.6 1.6 + - - -
321C PRO* 3.6 4.7 - - - +
322C PRO* 3.7 15.4 - - + +
330C GLN* 5.8 3.1 - - + -
357C TYR* 2.8 45.6 + + + +
358C LYS* 3.4 14.6 - - - +
360C VAL* 1.3 76.0 - - - +
362C ILE* 1.3 72.6 + - + +
363C HIS 3.4 0.5 + - - -
407C ASN* 3.7 7.9 - - + -
501C APC 5.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ARG* 3.4 6.8 + - - -
322C PRO* 3.3 24.0 - - + +
327C VAL* 4.5 8.5 - - + +
330C GLN* 3.9 46.4 - - + +
331C MET* 4.2 27.1 - - + -
334C PHE* 3.9 20.4 - - + -
358C LYS* 3.1 22.8 + - + +
359C LEU* 3.0 7.4 + - - +
361C TYR* 1.3 80.3 - - + +
363C HIS* 1.3 69.8 + - - +
364C PRO* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ARG* 2.7 33.4 + - - -
314C VAL* 3.9 18.8 - - + -
316C VAL* 3.5 27.3 - - + +
319C HIS* 5.3 0.2 - - + -
321C PRO* 3.6 16.2 - - + -
359C LEU 3.0 10.8 + - - -
360C VAL 3.1 21.2 + - - +
361C TYR 3.3 1.0 - - - +
362C ILE* 1.3 76.7 - - - +
364C PRO* 1.4 56.1 - - - +
365C PHE 3.2 12.0 + - - -
366C ILE 5.1 1.3 + - - -
369C ASN* 3.1 33.0 + - + +
501C APC 3.0 52.6 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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