Contacts of the helix formed by residues 4012 - 4024 (chain D) in PDB entry 1D1Z
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 SER4012 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3104C LYS* 4.4 14.8 - - - -
4011D ILE* 1.3 78.3 - - - +
4013D ARG* 1.3 65.6 + - - +
4014D GLU* 3.2 10.4 + - - +
4015D THR* 3.0 28.3 + - - -
4016D GLY 3.1 17.7 + - - -
4032D ARG* 4.0 6.9 - - - -
4035D GLU* 3.7 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4013 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2013B ARG* 3.1 47.1 - - - +
2017B GLU* 4.8 1.2 + - - -
2035B GLU* 5.6 0.2 + - - -
2053B THR* 4.3 14.3 + - - -
2055B ARG* 5.2 1.2 - - - +
5002B SO4 3.2 32.7 + - - -
4012D SER* 1.3 70.0 - - - +
4014D GLU* 1.3 63.9 + - - +
4016D GLY* 3.2 1.9 + - - -
4017D GLU* 2.9 56.7 + - - +
4032D ARG* 3.4 35.8 + - - +
4035D GLU* 2.9 21.5 + - - +
4051D ILE 5.8 0.6 + - - -
4053D THR* 4.0 13.8 + - - +
4055D ARG* 5.0 2.6 - - - +
5004D SO4 3.6 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4014 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4012D SER* 3.2 8.8 + - - +
4013D ARG* 1.3 79.2 - - - +
4015D THR* 1.3 58.8 + - - +
4017D GLU* 3.3 5.7 + - - +
4018D LYS* 2.9 62.5 + - + +
4035D GLU* 4.7 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR4015 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3025C LEU* 3.8 23.3 - - + -
3100C TYR* 3.8 33.0 - - + +
3101C PRO* 4.9 12.0 + - - +
4011D ILE* 4.1 10.7 - - + -
4012D SER* 3.0 26.6 + - - -
4014D GLU* 1.3 78.3 - - - +
4016D GLY* 1.3 64.5 + - - +
4018D LYS* 3.3 6.7 + - - +
4019D LEU* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4016 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4011D ILE* 3.9 17.9 - - - +
4012D SER 3.1 10.3 + - - -
4013D ARG 3.8 2.2 - - - -
4015D THR* 1.3 80.6 - - - +
4017D GLU* 1.3 57.9 + - - +
4019D LEU* 3.5 3.5 + - - +
4020D LEU* 3.0 35.8 + - - +
4030D LEU* 3.8 18.1 - - - +
4032D ARG* 4.9 3.1 - - - -
4044D CYS* 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4017 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2013B ARG* 2.8 24.9 + - - -
4013D ARG* 2.9 54.1 + - + +
4014D GLU* 3.9 5.4 - - - +
4016D GLY* 1.3 74.3 - - - +
4018D LYS* 1.3 61.2 + - + +
4020D LEU* 3.8 2.1 - - + +
4021D LEU* 2.8 43.7 + - + +
4032D ARG* 4.9 2.6 + - - +
4044D CYS* 6.0 2.0 - - + -
4051D ILE* 3.9 42.2 - - + +
4053D THR* 4.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS4018 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3100C TYR* 4.8 12.8 - - + -
4014D GLU* 2.9 49.8 + - + +
4015D THR* 3.3 6.7 + - - +
4017D GLU* 1.3 76.0 - - - +
4019D LEU* 1.3 63.6 + - - +
4021D LEU* 3.4 9.4 + - + +
4022D ALA* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4019 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3025C LEU* 3.4 43.3 - - + -
3100C TYR* 3.4 30.0 + - + +
4015D THR 3.1 15.8 + - - +
4016D GLY* 3.6 5.4 - - - +
4018D LYS* 1.3 78.1 - - - +
4020D LEU* 1.4 65.4 + - - +
4022D ALA* 3.2 17.9 + - + +
4023D THR* 3.3 16.7 + - + +
4030D LEU* 4.7 6.7 - - + -
4102D VAL* 3.7 26.0 - - + -
4104D LYS 4.4 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4020 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4016D GLY 3.0 23.3 + - - +
4019D LEU* 1.4 76.2 - - - +
4021D LEU* 1.3 64.2 + - - +
4023D THR* 2.7 26.5 + - - -
4028D SER* 3.7 10.5 - - - +
4029D TYR* 3.7 33.9 - - - +
4030D LEU* 4.0 8.1 - - + -
4044D CYS* 3.6 38.4 - - + +
4045D VAL 4.2 0.4 - - - +
4046D LEU* 3.4 12.8 - - + +
4051D ILE* 3.5 29.8 - - + -
4102D VAL* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4021 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4017D GLU* 2.8 36.8 + - + +
4018D LYS* 3.9 8.3 - - + +
4020D LEU* 1.3 73.1 - - - +
4022D ALA* 1.3 63.2 + - - +
4024D GLY* 3.1 14.6 + - - -
4046D LEU* 3.8 16.8 - - + +
4049D GLY* 3.2 29.2 - - - +
4050D TYR* 4.9 0.2 - - - -
4051D ILE* 4.4 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4022 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3100C TYR* 5.3 3.1 - - - +
4018D LYS 3.0 14.8 + - - +
4019D LEU* 3.4 16.6 - - + +
4021D LEU* 1.3 78.0 - - - +
4023D THR* 1.3 62.0 + - - +
4024D GLY* 3.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR4023 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4019D LEU* 3.6 18.4 - - + +
4020D LEU* 2.7 20.6 + - - +
4022D ALA* 1.3 77.7 - - + +
4024D GLY* 1.3 64.5 + - - +
4025D LEU* 3.1 20.6 + - - +
4028D SER* 2.9 29.7 + - - +
4046D LEU* 3.9 0.5 - - - +
4102D VAL* 4.5 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4024 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4020D LEU 3.5 1.2 + - - -
4021D LEU 3.1 15.8 + - - -
4022D ALA 4.4 0.9 - - - -
4023D THR* 1.3 78.9 + - - +
4025D LEU* 1.3 62.8 + - - +
4026D ASP* 4.3 1.5 + - - +
4046D LEU* 3.8 10.8 - - - -
----------------------------------------------------------
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