Contacts of the strand formed by residues 355 - 360 (chain C) in PDB entry 3P3W
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 ILE 355 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PRO* 4.9 3.8 - - + -
116C ALA 3.8 18.6 - - - +
117C LEU* 5.4 2.0 - - - -
120C ALA* 4.3 17.5 - - + -
222C LEU* 5.0 9.2 - - + -
242C PHE* 4.2 25.4 - - + -
243C GLN 4.1 6.3 - - - +
244C ILE* 4.0 13.2 - - + -
353C TYR* 3.6 31.6 - - + -
354C THR* 1.3 73.4 - - - +
356C ASP* 1.3 76.3 + - - +
357C VAL* 3.9 3.5 + - + +
370C TYR* 3.3 3.3 - - - -
371C TRP* 2.7 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C PHE* 3.5 2.8 - - - -
243C GLN* 2.8 47.3 + - + +
244C ILE 4.8 2.4 - - - +
245C VAL 4.4 2.6 - - - +
246C ASN* 3.6 32.4 + - - +
354C THR* 5.1 6.2 - - - +
355C ILE* 1.3 75.2 - - - +
357C VAL* 1.3 60.1 + - - +
358C TYR* 4.3 16.3 + - + -
367C LYS* 3.3 33.4 + - - -
369C GLY 3.7 2.0 - - - -
370C TYR* 4.0 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ALA* 5.7 0.2 - - + -
124C LEU* 3.7 26.7 - - + -
240C THR* 3.9 15.9 - - + -
241C GLY 3.5 12.3 - - - +
242C PHE* 3.7 21.5 - - + -
355C ILE* 4.4 10.1 - - + +
356C ASP* 1.3 76.5 - - - +
358C TYR* 1.3 67.7 + - - +
359C GLU* 6.2 0.2 - - + -
367C LYS* 4.0 3.5 - - - +
368C ALA* 3.2 29.5 + - + +
369C GLY 3.0 17.6 + - - +
371C TRP* 4.9 6.5 - - + -
377C PHE* 4.4 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C PHE* 4.3 22.4 - + + -
239C ILE 3.9 0.5 - - - +
240C THR* 3.5 7.2 - - - +
241C GLY 2.8 38.3 + - - +
242C PHE 5.3 0.4 - - - -
243C GLN* 3.3 52.7 + - + -
245C VAL 4.9 4.7 + - - -
246C ASN* 5.4 2.4 + - - -
247C ASN* 5.1 12.8 + - - +
248C GLU* 6.0 1.6 - - - +
356C ASP* 4.3 14.8 + - + +
357C VAL* 1.3 77.3 - - - +
359C GLU* 1.3 59.5 + - - +
360C MET* 4.1 0.7 - - + -
366C ARG 3.5 17.0 - - - -
367C LYS* 4.0 32.1 + - + +
368C ALA* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C TYR* 5.0 10.1 - - - +
239C ILE 3.8 4.0 - - - -
240C THR* 4.8 3.6 - - + +
357C VAL 4.2 0.6 + - - -
358C TYR* 1.3 74.2 - - - +
360C MET* 1.3 62.2 + - - +
361C LYS* 3.9 25.8 + - + +
364C GLY 4.1 1.2 - - - +
365C SER* 3.8 1.2 - - - -
366C ARG* 3.2 40.3 + - + +
368C ALA* 4.5 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C PHE* 3.7 24.5 - - + -
229C LEU* 3.8 24.0 - - + -
230C GLU* 5.9 3.1 - - + -
233C MET* 3.6 40.0 - - + +
238C ASN* 3.7 3.8 - - - +
239C ILE* 2.9 40.0 + - + +
358C TYR* 4.1 0.6 - - + -
359C GLU* 1.3 73.0 - - - +
361C LYS* 1.3 64.0 + - - +
364C GLY 4.2 1.3 - - - -
365C SER* 3.9 25.6 - - - +
----------------------------------------------------------
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