Contacts of the strand formed by residues 414 - 418 (chain I) in PDB entry 4CDC
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 TYR 414 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H ARG* 3.4 50.5 - - - +
222H VAL* 3.7 19.8 - - - +
223H SER 4.4 2.6 + - - -
225H VAL* 3.4 21.0 + - + +
359H TYR* 4.0 0.2 - - - -
386I VAL* 3.8 17.0 - - + -
400I ILE* 4.3 5.8 - - + -
401I VAL 3.2 9.4 - - - +
402I LYS* 3.4 38.7 - - + +
409I TRP* 3.8 3.5 - - - -
410I GLY* 3.8 1.4 - - - -
411I GLU* 2.8 40.7 + - + +
412I ASN* 3.6 12.6 - - + -
413I GLY* 1.3 82.4 - - - +
415I PHE* 1.3 68.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 415 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350H PHE* 3.8 25.6 - + - -
356H PHE* 3.7 24.0 - + + -
359H TYR* 3.3 31.4 - - + -
364H TYR* 5.0 0.4 - - + -
383I VAL* 4.3 3.4 - - + -
400I ILE* 3.7 2.6 - - - -
401I VAL* 2.8 73.3 + - + +
403I ASN* 4.1 17.3 - - + -
409I TRP* 3.6 22.0 - + + -
411I GLU* 4.5 1.6 - - - -
414I TYR* 1.3 75.3 - - - +
416I ARG* 1.3 73.6 + - - +
417I ILE* 4.0 24.2 - - + -
426I ILE* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 416 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359H TYR* 3.3 6.2 + - - -
361H LYS* 5.5 0.2 - - - +
362H GLY* 3.5 29.4 + - - +
363H ILE* 4.2 11.7 - - - +
364H TYR* 2.8 28.7 + - - +
391I ASP* 5.3 5.1 + - - -
398I TYR* 3.5 48.0 + - + -
399I TRP 3.1 11.4 - - - +
400I ILE* 4.3 11.9 - - + -
411I GLU* 3.1 34.3 + - - +
415I PHE* 1.3 81.1 - - - +
417I ILE* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 417 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350H PHE* 4.5 10.1 - - + -
363H ILE* 3.8 4.3 - - - -
364H TYR* 3.5 34.1 - - + +
398I TYR* 3.2 2.1 - - - +
399I TRP* 2.8 46.4 + - + -
401I VAL* 3.9 10.1 - - + -
415I PHE* 4.0 12.8 - - + -
416I ARG* 1.3 75.3 - - - +
418I ARG* 1.3 67.0 + - - +
423I GLU* 3.6 36.8 - - + +
424I CYS* 4.8 0.2 - - + -
426I ILE* 3.8 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 418 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363H ILE* 3.6 12.7 + - + +
364H TYR 3.1 16.1 + - - +
365H HIS* 3.4 52.9 + - + +
396I MET* 3.5 37.2 - - + +
397I ASP 3.7 4.9 - - - -
399I TRP* 3.7 8.7 + - - -
417I ILE* 1.3 76.6 - - - +
419I ARG* 1.3 60.0 + - - +
421I THR* 4.1 13.6 + - - +
423I GLU* 3.6 27.7 + - + +
426I ILE* 4.5 0.7 - - - +
427I GLU* 4.2 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