Contacts of the helix formed by residues 99 - 108 (chain D) in PDB entry 2ZNZ
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 LYS 99 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D VAL* 3.8 4.9 - - + -
96D LYS* 2.7 53.0 + - + +
97D ALA 5.6 0.4 - - - +
98D GLY* 1.3 74.9 - - - +
100D TYR* 1.3 63.8 + - - +
101D SER* 3.3 3.4 - - - -
102D GLU* 2.9 28.4 + - + +
103D VAL* 3.1 11.4 + - + +
148D PRO* 4.1 12.7 - - + +
149D GLY* 3.5 32.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D VAL* 3.5 30.5 + - + +
97D ALA* 3.5 17.8 - - - +
98D GLY* 3.3 27.6 - - - -
99D LYS* 1.3 74.6 - - - +
101D SER* 1.3 58.1 + - - +
103D VAL 3.5 0.2 + - - -
104D ALA* 3.0 27.0 + - - +
118D GLU* 3.6 29.6 - - - +
124D ASP* 3.9 35.2 + - + -
125D MET* 3.1 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C LYS* 5.8 4.9 - - - -
162C HIS* 4.7 9.9 + - - -
98D GLY 5.3 2.8 + - - -
99D LYS 4.6 2.1 + - - -
100D TYR* 1.3 77.2 - - - +
102D GLU* 1.3 66.0 + - - +
104D ALA* 3.9 5.5 - - - +
105D SER* 3.1 24.4 + - - -
118D GLU* 4.6 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LYS* 2.9 22.5 + - + +
101D SER* 1.3 78.6 + - - +
103D VAL* 1.3 66.0 + - + +
105D SER* 3.4 7.7 + - - -
106D ASN* 3.1 21.0 + - - +
147D ILE* 5.6 0.4 - - - -
148D PRO 5.2 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D VAL* 4.7 0.9 - - + -
95D VAL* 3.7 32.8 - - + -
99D LYS 3.1 11.3 + - - +
100D TYR 3.8 6.1 - - - +
102D GLU* 1.3 75.3 - - - +
104D ALA* 1.3 58.7 + - - +
106D ASN* 3.0 5.0 + - - +
107D LEU* 2.9 46.2 + - + +
125D MET* 4.2 1.3 - - - -
147D ILE* 4.3 9.2 - - + -
148D PRO 3.7 20.4 - - - +
149D GLY* 3.7 13.9 - - - -
150D VAL* 3.7 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C HIS* 3.4 46.1 - - + +
100D TYR 3.0 18.2 + - - +
101D SER 3.9 2.2 - - - +
102D GLU 3.4 0.2 - - - -
103D VAL* 1.3 76.5 - - - +
105D SER* 1.3 56.9 + - - +
107D LEU* 3.5 5.4 + - - +
108D ALA* 3.0 32.1 + - - +
116D VAL* 4.4 4.3 - - + +
125D MET* 3.7 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C HIS* 5.1 1.0 - - - -
101D SER 3.1 18.6 + - - -
102D GLU* 3.6 7.4 - - - -
104D ALA* 1.3 76.0 - - - +
106D ASN* 1.3 62.8 + - - +
108D ALA* 3.9 5.2 + - - +
109D LYS* 3.2 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D GLU 3.1 11.8 + - - +
103D VAL 3.0 8.5 + - - +
105D SER* 1.3 74.3 - - - +
107D LEU* 1.3 65.5 + - - +
109D LYS* 3.5 27.7 + - - +
110D TYR* 3.5 22.3 + - - -
147D ILE* 3.6 41.3 - - + +
148D PRO* 4.5 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D VAL* 4.6 7.4 - - + -
103D VAL* 2.9 35.9 + - + +
104D ALA* 3.8 4.9 - - - +
106D ASN* 1.3 72.6 - - - +
108D ALA* 1.3 55.1 + - - +
109D LYS 2.8 15.5 + - - -
110D TYR* 3.2 20.0 + - + +
113D ILE* 3.7 24.0 - - + +
116D VAL* 4.2 13.9 - - + -
125D MET* 3.9 19.3 - - - -
127D VAL* 3.9 20.4 - - + -
144D ILE* 3.8 37.5 - - + -
147D ILE* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C HIS* 4.3 11.7 - - + +
163C LYS* 3.3 48.5 + - + +
104D ALA 3.0 18.2 + - - +
105D SER* 4.3 7.2 - - - +
106D ASN 3.5 0.2 - - - -
107D LEU* 1.3 73.9 - - - +
109D LYS* 1.3 59.8 + - - +
110D TYR 3.4 0.9 - - - -
116D VAL* 4.1 6.0 - - + +
----------------------------------------------------------
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