Contacts of the strand formed by residues 3413 - 3417 (chain D) in PDB entry 1W21
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 SER3413 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3357D LYS* 3.3 16.8 + - - +
3358D GLY* 3.4 32.6 - - - +
3359D PHE* 3.8 6.7 - - - -
3381D TYR* 2.6 45.7 + - - -
3411D GLY 4.6 0.5 + - - -
3412D TYR* 1.3 75.4 - - - +
3414D GLY* 1.3 58.8 + - - +
3431D TYR* 3.3 22.9 - - - -
3432D VAL* 4.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY3414 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3235D SER* 4.6 0.7 - - - -
3286D SER* 3.5 12.8 - - - -
3357D LYS* 4.3 0.7 - - - -
3359D PHE* 3.9 9.7 - - - -
3413D SER* 1.3 76.6 - - - +
3415D ALA* 1.3 60.1 + - - -
3430D PHE* 3.1 6.8 - - - +
3431D TYR* 3.1 52.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA3415 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3128D LEU 4.9 0.2 - - - +
3235D SER* 4.6 9.9 + - - -
3236D GLU* 3.8 12.8 + - - +
3286D SER* 3.8 13.6 - - - +
3287D CYS 4.1 19.2 + - - +
3288D TYR* 4.6 7.6 - - + -
3359D PHE* 3.9 12.8 - - + +
3360D ALA 5.1 1.1 - - - +
3361D PHE* 3.5 28.7 - - + -
3414D GLY* 1.3 74.3 - - - -
3416D PHE* 1.3 64.6 + - - +
3429D CYS 3.6 4.5 - - - -
3430D PHE* 4.5 0.2 - - - +
3431D TYR* 4.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE3416 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3106D LEU* 3.6 28.3 - - + -
3128D LEU* 3.3 54.3 - - + +
3130D CYS* 4.0 25.6 - - - -
3135D CYS* 4.7 1.8 - - - -
3236D GLU* 3.3 14.6 - - - +
3287D CYS 5.1 2.0 - - - -
3288D TYR* 5.7 0.7 - - - -
3361D PHE* 4.2 0.2 - - - -
3415D ALA* 1.3 78.0 - - - +
3417D ILE* 1.3 77.1 + - - +
3429D CYS* 2.9 60.2 + - + +
3430D PHE* 3.6 24.0 - - - -
3431D TYR* 4.1 6.7 - + - -
3453D ALA* 4.1 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3417 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3097D LEU* 3.8 28.9 - - + -
3130D CYS* 4.0 14.0 - - - +
3236D GLU* 3.2 9.5 + - - +
3288D TYR* 3.9 13.5 - - + -
3289D GLY 4.2 2.7 - - - +
3361D PHE* 3.9 8.5 - - + -
3416D PHE* 1.3 87.8 - - - +
3418D ASP* 1.3 73.3 + - - +
3419D TYR* 3.0 58.7 + - + +
3420D TRP* 4.5 0.5 - - - -
3426D PHE* 4.0 13.5 - - + -
3427D ASN 3.4 25.1 - - - +
3428D PRO* 4.1 4.0 - - + -
3429D CYS* 4.8 1.1 - - - -
----------------------------------------------------------
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