Contacts of the helix formed by residues 321 - 331 (chain C) in PDB entry 5I4A
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 321 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C GLU 3.2 26.9 - - - -
315C LEU* 2.4 30.1 + - - -
318C ASN* 2.9 14.5 + - - +
319C LYS 3.6 0.8 - - - -
320C HIS* 1.3 82.8 - - - +
322C VAL* 1.3 59.9 + - - +
323C PHE 3.3 10.2 + - - -
324C TYR* 3.2 8.7 + - - -
325C ARG* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 322 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LEU* 3.6 22.2 - - + -
321C SER* 1.3 72.9 - - - +
323C PHE* 1.3 60.4 + - - +
325C ARG* 3.5 28.7 - - + +
326C ALA* 3.0 28.1 + - - +
407C ILE* 4.6 7.9 - - + -
409C PRO* 4.1 26.0 - - + +
412C ILE* 4.1 13.2 - - + +
413C LYS* 4.0 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 323 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C LEU* 4.2 17.7 - - + -
315C LEU* 3.8 12.8 - - + +
316C PHE* 3.7 30.1 - + + -
321C SER* 3.1 10.8 + - - +
322C VAL* 1.3 82.8 - - - +
324C TYR* 1.3 71.7 + + - +
326C ALA* 4.0 2.4 - - - +
327C ALA* 3.2 20.3 + - - +
335C VAL* 4.1 14.6 - - + -
337C PHE* 3.9 23.8 - + - -
373C ILE* 4.9 2.9 - - + -
412C ILE* 3.9 20.2 - - + -
415C TYR* 4.6 9.4 - + - -
416C VAL* 3.5 28.0 - - + +
419C MET* 4.4 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 324 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LEU 3.3 18.6 - - - -
316C PHE* 2.6 26.0 + - - -
318C ASN 3.1 24.0 - - - -
319C LYS* 3.2 44.3 - - + +
320C HIS* 4.5 0.7 - - - -
321C SER* 3.2 16.6 + - - +
323C PHE* 1.3 78.9 - + - +
325C ARG* 1.3 60.7 + - - +
327C ALA* 3.7 5.4 - - - +
328C ALA* 3.0 28.2 + - - +
335C VAL* 3.8 38.4 - - + +
337C PHE* 3.2 22.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 325 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C HIS* 2.8 39.9 + - + +
321C SER* 2.9 28.1 + - - +
322C VAL* 3.5 28.3 - - - +
324C TYR* 1.3 75.2 - - - +
326C ALA* 1.3 60.2 + - - +
328C ALA* 3.3 5.5 + - - +
329C GLU* 2.8 46.5 + - - +
409C PRO* 6.3 0.2 - - - +
413C LYS* 5.3 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C PHE* 4.1 7.9 - - + -
322C VAL 3.0 19.2 + - - +
323C PHE 4.0 3.1 - - - +
325C ARG* 1.3 76.7 - - - +
327C ALA* 1.3 61.9 + - - +
329C GLU* 3.4 4.0 + - - +
330C LEU* 3.0 30.5 + - - +
413C LYS* 3.9 43.6 - - + +
416C VAL* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C LEU* 4.4 4.9 - - + -
323C PHE* 3.2 18.3 + - + +
324C TYR 3.7 2.9 - - - +
325C ARG 3.2 0.2 - - - -
326C ALA* 1.3 77.5 - - - +
328C ALA* 1.3 61.9 + - - +
330C LEU 3.4 0.5 + - - -
331C GLY 3.3 3.8 + - - -
332C PHE* 3.1 50.7 + - + -
335C VAL* 3.7 29.2 - - + -
416C VAL* 3.9 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C SER* 4.8 0.5 + - - -
324C TYR 3.0 17.4 + - - +
325C ARG* 3.7 6.7 - - - +
327C ALA* 1.3 76.4 - - - +
329C GLU* 1.3 62.9 + - + +
331C GLY* 3.1 13.7 + - - -
332C PHE 4.7 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C VAL 3.9 1.7 - - - +
282C PHE* 3.4 31.4 - - + +
283C LYS 5.5 0.2 - - - -
285C SER* 3.2 28.4 + - - -
325C ARG* 2.8 32.2 + - + +
326C ALA* 3.9 4.0 - - - +
327C ALA 3.3 0.2 - - - -
328C ALA* 1.3 76.6 - - + +
330C LEU* 1.3 59.6 + - - +
413C LYS* 2.9 32.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C VAL* 3.8 24.0 - - + +
282C PHE* 3.6 32.8 - - + -
285C SER* 3.1 6.3 - - - -
286C PHE* 3.0 49.9 + - + +
289C ASN* 3.0 11.8 + - - -
326C ALA 3.0 22.9 + - - +
327C ALA 3.4 3.8 + - - +
328C ALA 3.2 0.2 - - - -
329C GLU* 1.3 72.8 - - - +
331C GLY* 1.3 57.9 + - - +
332C PHE* 3.6 9.6 - - + -
416C VAL* 3.9 13.0 - - + +
417C TYR* 3.8 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C SER* 3.2 13.1 + - - -
289C ASN* 3.2 9.9 - - - -
290C GLU* 2.8 33.7 + - - +
328C ALA 3.1 13.2 + - - -
330C LEU* 1.3 76.9 - - - +
332C PHE* 1.3 65.1 + - - +
333C SER* 4.4 0.2 - - - -
----------------------------------------------------------
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