Contacts of the strand formed by residues 445 - 449 (chain A) in PDB entry 5IYB
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 LYS 445 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ALA* 5.1 15.0 - - + -
392A GLU 3.4 8.7 - - - +
393A ILE* 4.1 25.1 - - + -
419A ILE* 3.5 3.3 - - - +
420A ILE* 2.7 71.5 + - + +
443A GLY 4.4 4.5 - - - +
444A TYR* 1.3 76.9 - - - +
446A VAL* 1.3 62.7 + - - +
447A GLU 4.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ALA* 4.5 0.2 - - - -
392A GLU* 2.7 36.1 + - - +
394A VAL* 3.7 14.8 - - + -
402A LEU* 4.7 19.3 - - + +
405A LEU* 5.6 0.7 - - + -
406A VAL* 4.4 11.0 - - + -
416A ALA* 3.8 26.2 - - + -
418A TYR 3.6 6.1 - - - +
419A ILE* 4.5 8.3 - - + -
440A LEU* 3.7 30.3 - - + -
444A TYR* 5.1 0.4 - - + -
445A LYS* 1.3 76.8 - - - +
447A GLU* 1.3 63.4 + - - +
448A ARG* 3.3 11.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PHE* 5.1 1.2 - - - -
389A THR* 3.1 20.9 - - - +
390A PHE 3.5 4.5 - - - +
391A ALA* 3.9 26.4 + - + +
416A ALA 3.7 0.3 - - - -
417A LYS* 2.7 35.0 + - - +
418A TYR* 2.8 37.3 + - + +
420A ILE* 4.0 18.8 - - + -
426A ARG* 3.9 2.9 + - - -
445A LYS 4.1 0.6 - - - -
446A VAL* 1.3 69.1 - - - +
448A ARG* 1.3 54.5 + - - +
507A GLN* 5.1 4.5 - - - +
1064B ARG* 3.0 44.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A THR* 3.2 5.6 + - - -
390A PHE* 3.1 54.8 + - - +
392A GLU* 2.7 32.2 + - + +
401A ARG* 5.0 1.7 - - - +
402A LEU* 5.1 1.6 - - + -
405A LEU* 3.9 24.5 - - + -
415A GLY 3.6 16.2 - - - +
416A ALA* 3.9 6.5 - - + +
446A VAL* 3.3 9.4 + - + +
447A GLU* 1.3 74.9 - - - +
449A HIS* 1.3 93.2 + - - +
450A MET* 3.5 3.6 - - - +
451A CYS* 3.5 16.5 - - - +
454A ASP* 2.8 44.0 + - - -
512A ARG* 4.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ALA 3.9 7.4 - - - +
386A ALA* 3.5 31.4 + - + +
388A MET 3.7 6.7 - - - -
410A ASN* 2.8 36.8 + - - -
412A GLN 4.6 0.7 - - - -
413A TYR* 2.9 32.3 + - + +
414A PRO* 5.0 2.2 - - + +
415A GLY* 3.4 12.0 + - - +
416A ALA 3.7 17.0 - - - -
417A LYS* 3.2 27.6 - - + +
448A ARG* 1.3 93.3 + - - +
450A MET* 1.3 68.6 + - - +
451A CYS* 3.5 2.4 + - - +
----------------------------------------------------------
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