Contacts of the strand formed by residues 1651 - 1655 (chain A) in PDB entry 3PXB
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 SER1651 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1650A MET* 1.3 75.8 - - - +
1652A MET* 1.3 65.0 + - - +
1675A THR* 3.5 26.4 - - - +
1677A THR* 4.2 14.7 - - - +
1683A GLU* 4.4 10.0 - - - +
1684A THR* 3.7 18.3 + - - -
1685A THR* 2.7 34.2 + - - +
1686A HIS 2.8 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1652 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1651A SER* 1.3 74.4 + - - +
1653A VAL* 1.3 70.1 + - - +
1665A VAL* 3.5 31.4 - - + -
1668A PHE* 4.4 13.2 - - + -
1669A ALA* 4.5 9.9 - - + -
1674A ILE* 3.5 29.2 - - + -
1675A THR 2.9 8.9 + - - +
1676A LEU* 3.4 13.4 - - + +
1677A THR* 2.9 28.8 + - - +
1684A THR* 4.6 0.4 - - - -
1686A HIS* 3.3 23.1 - - + +
1688A VAL* 3.9 11.7 - - + -
1718A TRP* 3.8 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1652A MET* 1.3 78.6 - - - +
1654A VAL* 1.3 68.2 + - - +
1676A LEU* 4.6 0.9 - - - -
1677A THR* 3.5 34.5 - - + +
1679A LEU 3.7 2.0 - - - +
1680A ILE* 3.7 27.1 - - + +
1684A THR* 4.0 7.6 - - + +
1686A HIS 3.2 11.8 + - - +
1687A VAL* 4.0 18.6 - - + -
1688A VAL* 3.1 24.3 + - - +
1702A LYS* 3.9 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1654 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SO4 4.1 1.9 + - - +
1653A VAL* 1.3 81.0 - - - +
1655A SER* 1.3 64.8 + - - +
1657A LEU* 3.4 32.5 - - + +
1662A PHE* 3.7 30.1 - - + -
1665A VAL* 3.8 27.4 - - + -
1676A LEU* 4.4 9.6 - - + -
1677A THR 4.8 0.8 + - - -
1687A VAL* 5.6 0.2 - - - -
1688A VAL* 3.4 12.3 - - + +
1702A LYS* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1655 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SO4 2.5 28.0 + - - -
1654A VAL* 1.3 76.8 - - - +
1656A GLY* 1.3 60.6 + - - +
1657A LEU* 3.1 19.0 - - - +
1687A VAL* 5.2 0.4 - - - -
1688A VAL 2.9 7.1 + - - -
1689A MET* 3.8 27.3 - - - +
1690A LYS* 3.2 14.6 + - - +
1700A ALA* 3.5 18.0 - - - +
1702A LYS* 4.2 10.3 - - - -
----------------------------------------------------------
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