Contacts of the strand formed by residues 499 - 503 (chain A) in PDB entry 1YC0
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 VAL 499 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A VAL 3.7 0.2 - - - +
443A VAL* 3.5 5.5 - - - +
444A SER* 3.0 53.0 + - - +
445A ALA 3.4 20.6 - - - +
446A ALA* 3.9 7.4 - - - -
449A PHE* 3.9 19.1 - - + -
482A TYR* 4.1 12.6 - - + -
483A ILE 3.4 23.3 - - - +
484A PRO* 3.8 7.4 - - + -
498A LEU* 1.3 77.8 - - - +
500A LEU* 1.3 75.0 + - - +
501A ILE* 4.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A TRP* 4.0 21.3 - - + -
442A VAL 3.5 5.4 - - - +
443A VAL* 4.5 8.7 - - + -
482A TYR* 3.2 4.0 - - - -
483A ILE* 2.7 46.9 + - + +
498A LEU* 3.7 13.5 - - + -
499A VAL* 1.3 77.1 - - - +
501A ILE* 1.3 62.2 + - - +
502A ARG 4.1 0.4 + - - -
640A TRP* 3.4 27.1 - - + -
641A ILE* 3.8 30.5 - - + +
644A ARG* 3.4 39.0 - - + -
645A ILE* 5.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ILE* 3.6 23.6 - - + -
440A CYS 3.5 0.2 - - - +
441A TRP* 3.2 8.4 - - - -
442A VAL* 2.7 50.0 + - + +
444A SER* 4.0 9.6 - - - -
449A PHE* 3.3 37.7 - - + -
460A VAL* 4.3 8.7 - - + -
479A ILE* 3.5 35.9 - - + -
481A LYS 3.7 7.9 - - - +
482A TYR* 4.2 6.5 - - + -
499A VAL* 4.5 4.7 - - + +
500A LEU* 1.3 78.1 - - - +
502A ARG* 1.3 62.7 + - - +
503A LEU* 3.7 3.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A CYS* 3.2 27.6 - - - +
441A TRP* 3.5 47.8 - - + +
479A ILE* 3.5 6.1 - - - +
480A GLU* 2.8 57.4 + - + +
481A LYS* 3.1 28.2 + - + +
501A ILE* 1.3 71.4 - - - +
503A LEU* 1.3 63.8 + - - +
505A LYS* 5.4 9.1 - - - +
644A ARG 5.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU* 4.4 1.8 - - + -
439A THR 3.8 19.5 - - - +
440A CYS* 2.8 19.9 + - - +
442A VAL* 3.9 20.6 - - + -
460A VAL* 3.8 34.8 - - + -
462A LEU* 4.3 16.4 - - + -
477A PHE* 4.1 28.9 - - + -
478A GLY 3.6 5.2 - - - +
479A ILE* 4.3 1.6 - - + +
480A GLU* 3.6 5.2 - - - +
501A ILE* 4.5 5.6 - - + +
502A ARG* 1.3 88.2 + - - +
504A LYS* 1.3 62.1 + - - +
505A LYS* 3.7 1.4 + - - +
510A CYS* 3.6 22.0 - - + -
511A ALA 4.6 0.4 - - - +
----------------------------------------------------------
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