Contacts of the helix formed by residues 350 - 355 (chain C) in PDB entry 4U1D
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 ARG 350 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 3.6 30.6 + - + +
345B TYR* 4.9 24.8 - - - -
257C TYR* 5.7 4.9 - - - +
261C GLU* 3.2 37.4 + - - -
347C PRO 5.6 5.6 - - - +
348C HIS 3.3 0.6 - - - -
349C LEU* 1.3 79.9 - - + +
351C MET* 1.3 63.4 + - + +
352C TYR 3.1 1.6 + - - -
353C ARG* 3.2 29.0 + - - +
354C LEU* 3.6 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C TYR* 2.9 51.6 - - + +
260C ILE* 3.7 31.0 - - + -
290C PHE* 3.7 13.9 - - + -
298C LEU* 3.7 20.4 - - + -
348C HIS* 3.5 12.5 - - + +
349C LEU 3.1 1.8 - - - -
350C ARG* 1.3 75.2 - - + +
352C TYR* 1.3 65.1 + - - +
353C ARG 3.2 0.2 - - - -
354C LEU* 3.0 34.3 + - + +
355C LEU* 3.1 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ASP* 5.6 3.8 + - - +
296C PRO* 6.2 0.2 - - - +
297C LEU* 4.6 19.1 - - + +
298C LEU* 3.8 31.9 - - + +
346C ASP* 4.4 10.8 + - - -
348C HIS 3.9 13.5 - - - -
349C LEU* 3.2 32.3 - - + +
350C ARG 3.1 1.4 + - - -
351C MET* 1.3 75.8 - - - +
353C ARG* 1.3 61.1 + - + +
355C LEU* 3.2 6.6 + - - +
357C LEU* 2.9 43.3 + - + +
359C ALA* 4.3 3.4 - - - -
360C LYS* 3.6 29.4 - - + +
361C PRO* 3.5 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 2.4 38.2 + - - -
219A LYS* 3.3 29.3 - - - +
264C PHE* 3.8 13.7 - - + -
349C LEU 5.8 1.9 + - - +
350C ARG* 3.2 25.8 + - - +
352C TYR* 1.3 80.7 - - + +
354C LEU* 1.3 61.2 + - + +
356C ASN* 3.1 18.9 + - - +
357C LEU 3.3 13.9 - - - +
358C ASP* 4.7 10.0 + - - +
359C ALA* 6.2 0.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
260C ILE* 4.7 6.5 - - + +
261C GLU* 3.6 44.4 - - + +
264C PHE* 3.4 52.0 - - + +
265C HIS* 5.3 1.6 - - + -
282C TYR* 5.4 1.9 + - - -
350C ARG* 4.0 23.6 - - + +
351C MET* 3.0 40.4 + - + +
353C ARG* 1.3 81.2 - - + +
355C LEU* 1.3 59.8 + - - +
356C ASN* 3.2 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ILE* 4.9 1.1 - - + -
286C LEU* 4.3 16.4 - - + -
290C PHE* 3.5 42.6 - - + -
298C LEU* 3.8 22.9 - - + +
301C THR* 3.6 25.8 - - + -
302C ALA* 4.4 4.5 - - - +
305C LYS* 3.2 24.8 - - + +
351C MET* 3.1 26.5 + - + +
352C TYR 3.2 5.6 + - - +
353C ARG 3.2 0.8 - - - -
354C LEU* 1.3 77.9 - - + +
356C ASN* 1.3 67.2 + - - +
357C LEU* 3.1 17.5 + - + +
----------------------------------------------------------
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