Contacts of the strand formed by residues 346 - 351 (chain C) in PDB entry 1D1T
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 346 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLU* 3.1 28.0 - - + +
168C LYS* 3.8 26.2 - - + -
171C LEU* 3.5 24.2 - - + -
231C LYS* 6.2 0.2 - - - -
342C LEU 3.5 6.2 + - - +
343C ASP* 3.6 15.7 + - - +
344C GLN 4.9 0.4 - - - -
345C LEU* 1.3 72.3 - - - +
347C THR* 1.3 60.1 + - - +
348C HIS 3.7 12.6 - - - +
349C VAL* 3.7 28.5 - - + -
369C ARG* 3.5 7.6 - - + +
371C VAL* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C LYS* 4.3 17.5 - - - +
344C GLN 4.7 0.2 - - - +
345C LEU 3.2 3.3 + - - +
346C ILE* 1.3 74.1 - - - +
348C HIS* 1.3 75.6 + - - -
366C GLN 4.8 1.6 - - - +
367C SER* 3.2 16.5 - - - -
368C ILE* 2.8 49.5 + - + +
369C ARG 2.8 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C ILE* 3.4 5.8 + - - +
347C THR* 1.3 102.5 + - - +
349C VAL* 1.3 58.0 + - - +
350C LEU* 4.0 13.2 - - + -
357C GLU* 5.8 0.7 - - - -
361C LEU* 3.8 28.7 - - + +
366C GLN* 3.4 25.1 - - + -
367C SER* 3.5 10.3 - - - -
369C ARG 3.2 2.4 + - - -
370C THR* 3.1 22.0 - - + +
371C VAL 2.7 31.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
167C GLU* 5.3 15.0 - - + -
346C ILE* 3.7 21.5 - - + +
348C HIS* 1.3 75.2 - - - +
350C LEU* 1.3 72.4 + - - +
371C VAL* 3.3 17.7 - - + +
373C THR* 4.7 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C HIS* 4.5 10.1 - - + -
349C VAL* 1.3 87.8 - - - +
351C PRO* 1.3 75.2 - - + +
354C LYS* 4.1 20.6 - - + +
357C GLU* 3.0 32.1 - - + +
358C GLY 4.7 1.3 - - - +
361C LEU* 4.3 10.8 - - + -
370C THR* 4.2 19.3 - - + +
371C VAL 2.9 5.9 + - - -
372C LEU* 3.3 11.7 - - + -
373C THR* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C LEU* 1.3 94.6 - - + +
352C PHE* 1.3 68.0 + - - +
353C LYS* 3.5 26.7 - - - +
354C LYS* 2.8 37.7 + - + +
372C LEU* 3.9 2.8 - - - +
373C THR* 3.6 14.1 - - + +
----------------------------------------------------------
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