Contacts of the strand formed by residues 3021 - 3025 (chain D) in PDB entry 1Y1S
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 LEU3021 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3019D ALA* 3.7 0.7 - - - +
3020D GLN* 1.3 82.0 - - + +
3022D ALA* 1.3 76.2 + - - +
3023D ILE* 4.5 2.5 - - + +
3061D ALA 5.0 0.2 + - - -
3062D VAL* 3.6 17.4 - - + +
3063D ILE 3.2 19.2 + - - -
3086D ILE* 3.9 3.7 - - - +
3088D THR* 3.4 28.0 - - + -
3090D LEU* 4.8 3.4 - - + -
3249D ALA* 3.8 34.8 - - + +
3252D LEU* 3.6 39.0 - - + +
3253D LEU* 3.8 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3022 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3021D LEU* 1.3 80.2 - - - +
3023D ILE* 1.3 66.7 + - - +
3024D VAL* 3.9 9.2 + - + +
3063D ILE* 3.1 29.6 - - + +
3065D CYS 5.3 0.2 - - - +
3081D LEU* 4.6 7.6 - - + -
3086D ILE* 3.8 18.8 - - + +
3088D THR 2.9 7.9 + - - +
3089D PHE* 3.5 6.2 - - + +
3090D LEU 3.0 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3023 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3021D LEU* 4.5 10.3 - - + -
3022D ALA* 1.3 74.1 - - - +
3024D VAL* 1.3 61.4 - - - +
3025D PRO* 3.3 3.9 - - + +
3034D ILE* 3.7 33.7 - - + -
3038D MET* 4.3 13.9 - - + -
3062D VAL* 4.6 2.5 - - + -
3063D ILE 2.7 13.7 + - - +
3064D VAL* 3.2 7.8 - - + -
3065D CYS 3.0 23.6 + - - -
3090D LEU* 3.3 18.2 - - + +
3092D ILE* 3.9 23.6 - - + -
3245D VAL* 4.2 12.6 - - + -
3246D VAL* 3.9 22.7 - - + -
3249D ALA* 4.6 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3024 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3022D ALA* 4.6 5.4 - - + +
3023D ILE* 1.3 75.9 - - - +
3025D PRO* 1.3 66.5 - - - +
3065D CYS 3.3 12.3 - - - +
3067D THR* 3.6 23.8 - - + +
3074D THR* 6.1 0.7 - - + -
3078D VAL* 5.3 4.3 - - + -
3081D LEU* 4.6 15.0 - - + -
3089D PHE* 4.3 24.0 - - + -
3090D LEU 2.9 26.0 + - - +
3091D ARG* 3.7 32.7 + - + +
3092D ILE* 3.8 2.0 + - - -
3202D LEU* 4.7 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO3025 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3023D ILE* 3.3 12.3 - - + +
3024D VAL* 1.3 89.5 - - - +
3026D GLY* 1.3 60.1 + - - +
3027D ASP 4.0 4.9 - - - +
3030D ARG* 3.9 16.2 - - + +
3031D VAL* 3.9 26.2 - - + +
3034D ILE* 4.0 16.8 - - + -
3064D VAL* 4.0 9.4 - - + -
3065D CYS 3.7 7.2 - - - +
3066D SER* 3.3 3.5 - - - -
3067D THR* 3.1 23.8 + - - -
3091D ARG* 4.5 0.4 - - - -
3092D ILE* 3.4 27.8 - - + +
----------------------------------------------------------
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