Contacts of the strand formed by residues 348 - 355 (chain A) in PDB entry 3DDN
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 348 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PRO* 3.2 7.5 - - - +
347A VAL* 1.3 88.7 - - - +
349A LEU* 1.3 64.7 + - - +
350A SER* 5.5 1.2 + - - -
396A VAL* 4.1 2.5 - - - -
397A THR* 3.1 25.6 - - - -
398A ALA* 5.2 0.2 - - - -
399A GLU* 6.4 1.3 - - - -
417A ALA* 3.6 0.2 - - - -
418A VAL* 2.8 53.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLY* 4.9 1.8 - - - -
338A ALA* 4.9 2.9 - - + -
346A PRO* 4.1 2.0 - - + -
348A SER* 1.3 76.7 - - - +
350A SER* 1.3 59.2 + - - +
351A VAL* 4.8 4.5 - - + -
369A ALA* 3.5 40.6 - - + +
370A LEU* 3.9 12.3 - - + +
373A LEU* 3.9 36.1 - - + -
397A THR 2.9 8.6 + - - +
398A ALA* 3.2 8.3 - - + +
399A GLU* 3.0 27.6 + - - +
415A VAL* 4.2 17.0 - - + -
416A ARG 3.2 2.0 - - - +
417A ALA* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A SER* 4.2 1.3 + - - -
349A LEU* 1.3 71.6 - - - +
351A VAL* 1.3 62.1 + - - +
352A GLN* 3.6 18.8 + - - -
399A GLU* 2.6 34.7 + - - +
401A CYS* 5.0 0.9 - - - -
414A ASP 3.5 1.9 - - - +
415A VAL* 3.6 0.4 - - - -
416A ARG* 2.6 55.4 + - - +
418A VAL* 4.7 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A VAL* 4.8 7.6 - - + -
349A LEU* 4.7 7.9 - - + +
350A SER* 1.3 75.6 - - - +
352A GLN* 1.3 59.2 + - - +
353A VAL* 4.4 3.6 - - + -
365A LEU* 4.8 3.6 - - + +
366A ARG* 4.2 12.3 - - + -
369A ALA* 3.8 26.9 - - + -
398A ALA* 5.2 0.2 - - + -
399A GLU 2.9 16.4 + - - +
400A ILE* 3.3 24.0 - - + +
401A CYS* 2.8 27.3 + - - +
413A VAL* 3.8 25.8 - - + -
414A ASP 3.5 4.0 - - - +
415A VAL* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A SER* 3.6 14.7 + - - -
351A VAL* 1.3 72.3 - - - +
353A VAL* 1.3 61.4 + - - +
354A ARG* 4.3 16.2 - - + +
401A CYS* 3.3 25.8 - - + +
412A VAL 4.0 0.3 - - - +
413A VAL* 3.3 6.8 - - - +
414A ASP* 2.8 61.9 + - - +
416A ARG* 2.7 46.1 + - - +
426A THR* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 4.4 3.4 - - + -
352A GLN* 1.3 76.0 - - - +
354A ARG* 1.3 63.8 + - - +
357A LEU* 3.7 35.4 - - + +
358A ALA* 3.8 19.6 - - - +
362A VAL* 4.0 17.7 - - + -
365A LEU* 4.4 7.0 - - + -
400A ILE* 3.9 27.4 - - + -
401A CYS 2.8 9.6 + - - +
402A LYS* 3.2 6.8 - - + -
403A ALA 2.9 24.9 + - - +
412A VAL 3.9 2.5 - - - -
413A VAL* 4.3 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLN* 4.3 18.3 - - + +
353A VAL* 1.3 85.8 - - - +
355A GLY* 1.3 65.4 + - - +
357A LEU* 4.4 2.4 + - - +
358A ALA* 4.4 1.1 - - - -
403A ALA* 3.3 19.1 - - + +
405A GLU 3.4 17.3 - - - +
406A SER* 3.8 8.7 - - - -
407A PRO* 3.9 31.2 - - - +
411A SER* 3.3 5.5 - - - -
412A VAL* 3.0 38.1 + - + +
414A ASP* 2.4 40.4 + - - +
442A GLN* 5.1 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ARG* 1.3 74.3 - - - +
356A GLU* 1.3 64.9 + - - -
358A ALA* 2.9 19.9 + - - +
359A ALA 4.4 0.2 + - - -
403A ALA 3.2 2.0 + - - -
404A SER* 3.0 28.0 + - - +
406A SER* 3.6 12.4 - - - +
410A ARG 3.2 11.9 - - - -
----------------------------------------------------------
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