Contacts of the strand formed by residues 413 - 420 (chain A) in PDB entry 4DGX
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 413 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A VAL 4.3 1.4 + - - -
346A PHE* 3.4 53.9 + - - +
349A ASN* 3.4 31.6 + - - +
350A SER 4.9 0.6 + - - -
351A ARG* 3.7 36.9 - - - +
402A LYS* 3.5 3.1 - - - -
403A LEU* 2.8 60.8 + - - +
411A THR* 3.3 16.2 + - - +
412A GLU* 1.3 76.4 - - - +
414A THR* 1.3 62.1 + - - +
415A VAL* 3.7 9.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ARG* 3.8 26.7 + - - +
400A GLU* 3.6 25.6 + - + +
401A LEU 3.3 6.7 - - - +
402A LYS* 3.8 22.7 - - + +
413A ARG* 1.3 74.6 - - - +
415A VAL* 1.3 64.8 + - - +
416A TRP* 3.4 40.1 + - + -
449A ILE* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A TRP* 4.7 5.6 - - + -
345A VAL* 4.3 4.7 - - + -
350A SER 3.8 18.4 - - - +
351A ARG* 3.4 15.5 - - - -
352A VAL 4.2 0.4 - - - +
353A ILE* 3.6 33.9 - - + -
399A ARG 3.6 0.9 - - - +
401A LEU* 2.6 49.8 + - + +
403A LEU* 4.1 33.7 - - + -
413A ARG* 4.3 6.1 - - + -
414A THR* 1.3 77.0 - - - +
416A TRP* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ARG 2.8 22.1 + - - +
352A VAL* 3.3 4.8 - - + +
353A ILE 2.8 26.3 + - - +
398A LEU* 4.1 22.9 - - + -
399A ARG 3.6 3.1 - - - -
400A GLU* 3.6 42.6 - - + -
414A THR* 3.4 28.4 - - + +
415A VAL* 1.3 73.8 - - - +
417A GLN* 1.3 61.7 + - - +
418A TYR* 3.7 18.9 + - + -
445A LYS* 3.6 50.6 - - + +
449A ILE* 3.9 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ILE* 3.6 22.2 - - + +
355A MET* 4.3 11.2 - - + +
370A TYR* 3.3 21.9 + - - +
371A TRP* 3.6 30.3 - - - -
397A THR 3.4 2.9 - - - +
398A LEU* 3.3 7.5 - - - +
399A ARG* 2.7 78.6 + - - +
401A LEU* 4.0 19.6 - - + +
415A VAL 3.6 0.6 + - - -
416A TRP* 1.3 73.2 - - - +
418A TYR* 1.3 61.5 + - - +
419A HIS* 4.6 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 4.2 9.4 - - + -
353A ILE 2.8 12.3 + - - +
354A VAL* 3.5 3.2 - - - -
355A MET 2.8 25.8 + - - -
396A TYR* 3.8 24.2 - + - -
397A THR 3.9 1.6 - - - -
398A LEU* 3.8 28.1 - - + +
416A TRP* 4.0 20.9 - - + -
417A GLN* 1.3 69.7 - - - +
419A HIS* 1.3 60.0 + - - +
420A PHE 3.9 0.2 - - - -
438A PHE* 3.3 25.9 - + + -
441A GLU* 3.9 34.5 + - + +
442A VAL* 3.7 23.1 - - + -
445A LYS* 3.1 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A MET* 3.7 34.6 - - + -
357A THR 2.8 27.9 + - - -
358A LYS* 4.3 5.8 - - - -
359A GLU* 5.0 4.9 - - + -
371A TRP* 4.1 11.3 - + - -
396A TYR* 2.9 6.5 - - - +
397A THR* 2.8 50.2 + - - +
399A ARG* 3.2 25.4 + - - +
417A GLN* 3.5 9.5 + - - +
418A TYR* 1.3 71.9 - - - +
420A PHE* 1.3 66.2 + - - +
421A ARG* 3.4 27.6 + - - +
438A PHE* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A MET 2.7 20.4 + - - +
356A THR* 4.2 17.6 - - - -
357A THR* 4.2 4.2 + - - +
358A LYS 5.0 0.3 + - - -
395A ASP* 3.6 25.4 - - + -
396A TYR* 3.8 2.0 - - - -
418A TYR 3.8 1.2 + - - -
419A HIS* 1.3 77.5 + - - +
421A ARG* 1.3 61.3 + - - +
422A THR* 3.5 32.3 - - - -
423A TRP* 3.8 24.8 + + + +
429A PRO* 5.3 2.0 - - + -
434A GLY* 3.9 16.4 - - - -
435A VAL* 4.0 22.4 - - + -
438A PHE* 3.7 37.0 - + + -
469A PHE* 4.0 18.8 - + + -
----------------------------------------------------------
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