Contacts of the helix formed by residues 98 - 111 (chain D) in PDB entry 1ZUM
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 ASP 98 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D LEU 3.1 9.3 + - - +
95D ILE 3.3 4.5 - - - +
96D GLU 3.2 0.2 - - - -
97D ARG* 1.3 114.8 + - - +
99D ARG* 1.3 58.0 + - - +
100D THR 3.4 2.2 - - - -
101D TYR* 3.3 13.9 + - + -
102D LEU* 2.8 33.6 + - + +
203D TYR* 2.7 43.2 + - + -
207D LEU* 3.7 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ILE 3.0 9.4 + - - +
96D GLU* 3.1 30.9 + - - +
97D ARG 3.3 1.6 + - - -
98D ASP* 1.3 76.9 - - - +
100D THR* 1.3 58.3 + - - +
102D LEU* 3.3 1.2 + - - +
103D ALA* 2.9 32.4 + - - +
118D TYR* 3.0 66.6 + - + +
119D LEU* 4.2 8.1 + - - +
122D LEU* 3.8 26.8 - - + +
123D ASP* 3.8 28.5 + - - +
126D LEU* 4.3 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D PRO* 3.8 17.0 - - + +
10D ALA 4.1 16.4 - - - +
11D PRO* 4.9 3.8 - - + -
12D ASN* 5.5 2.5 - - + +
97D ARG 5.1 1.0 + - - -
98D ASP 3.4 0.4 - - - -
99D ARG* 1.3 77.3 - - - +
101D TYR* 1.3 65.0 + - - +
103D ALA* 3.4 2.3 + - - +
104D ALA* 3.2 22.5 + - - +
114D TYR* 3.7 18.1 - - + +
118D TYR* 3.7 21.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ASN* 6.2 3.4 - - + -
15D PRO* 4.0 20.2 - - + -
16D GLU 2.7 30.8 + - - -
18D PHE* 3.2 28.5 + + - -
98D ASP* 3.3 15.0 + - + +
100D THR* 1.3 79.7 - - - +
102D LEU* 1.3 66.3 + - + +
104D ALA* 3.2 6.5 + - - +
105D LEU* 3.0 45.9 + - + +
203D TYR* 3.8 46.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ILE* 4.2 28.9 - - + +
98D ASP* 2.8 24.6 + - + +
99D ARG 3.9 2.9 - - - +
101D TYR* 1.3 77.9 - - + +
103D ALA* 1.3 57.7 + - - +
105D LEU* 3.3 4.0 + - + +
106D GLU* 2.9 30.4 + - - +
122D LEU* 4.3 8.1 - - + -
172D LEU* 4.2 14.9 - - + +
200D THR* 3.8 39.3 - - + +
203D TYR* 3.8 34.5 - - + -
204D VAL* 4.5 5.8 - - + -
207D LEU* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ARG 2.9 21.2 + - - +
100D THR 3.9 0.4 - - - +
101D TYR 3.3 0.2 - - - -
102D LEU* 1.3 72.7 - - - +
104D ALA* 1.3 57.0 + - - +
106D GLU* 3.5 0.8 - - - +
107D THR* 3.1 29.6 + - - -
114D TYR* 3.8 16.4 - - + -
117D SER* 3.3 10.4 - - - -
118D TYR* 3.7 38.1 - - + +
122D LEU* 3.9 11.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
12D ASN* 3.6 31.6 - - + +
15D PRO* 4.1 7.6 - - + -
100D THR 3.2 17.1 + - - +
101D TYR* 3.7 4.9 - - - +
103D ALA* 1.3 74.9 - - - +
105D LEU* 1.3 60.1 + - - +
107D THR* 3.2 4.0 + - - -
108D LEU* 2.8 28.2 + - - +
114D TYR* 3.8 15.2 - - + -
335D PHE* 3.6 13.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PRO* 3.9 20.3 - - + +
16D GLU 5.0 0.7 - - - +
17D VAL* 4.6 11.7 - - + -
101D TYR* 3.0 47.7 + - + +
102D LEU* 3.8 6.3 - - + +
104D ALA* 1.3 73.8 - - - +
106D GLU* 1.3 66.3 + - - +
108D LEU* 3.2 9.5 + - + -
109D ASP* 3.0 23.4 + - - +
199D LEU* 3.8 35.9 - - + +
200D THR* 3.7 29.1 - - + +
203D TYR* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D LEU 2.9 18.0 + - - +
103D ALA* 3.5 8.7 - - - +
104D ALA 3.2 0.2 - - - -
105D LEU* 1.3 76.7 - - - +
107D THR* 1.3 56.6 + - - +
109D ASP* 4.0 1.5 - - - +
110D ASN* 2.8 37.1 + - + +
112D LYS* 4.5 12.1 - - + -
117D SER* 3.6 15.0 - - - +
121D ASP* 4.0 12.5 - - + +
122D LEU* 5.3 0.4 - - + -
171D PRO* 3.4 23.8 - - + +
172D LEU* 3.0 38.3 + - + +
200D THR* 2.7 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ASN* 5.1 1.4 - - - +
103D ALA 3.1 6.1 + - - -
104D ALA 3.5 7.4 - - - -
106D GLU* 1.3 79.5 - - - +
108D LEU* 1.3 58.4 + - - +
111D GLY* 2.8 27.9 + - - +
112D LYS 2.8 29.6 + - - +
114D TYR* 3.1 22.9 - - - +
117D SER* 3.2 8.6 + - - -
334D PRO* 3.6 26.2 - - + +
335D PHE* 3.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLN 3.7 22.7 - - - +
14D GLN* 4.4 6.5 - - - +
15D PRO* 4.0 27.1 - - + +
41D ASN* 3.3 53.0 - - - +
42D PRO* 3.5 1.2 - - - +
48D ILE* 3.5 33.4 - - + +
104D ALA 2.8 14.0 + - - +
105D LEU* 3.2 16.4 + - + +
107D THR* 1.3 80.0 - - - +
109D ASP* 1.3 60.9 + - - +
335D PHE* 4.2 9.6 - - + -
3117D EDO 3.7 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D THR* 2.6 14.4 + - - -
42D PRO* 3.4 9.3 - - - +
48D ILE* 3.5 11.8 - - + +
105D LEU 3.0 14.8 + - - +
106D GLU* 4.3 2.0 - - - +
108D LEU* 1.3 77.0 - - - +
110D ASN* 1.3 60.3 + - - +
196D GLN 3.5 5.6 - - - +
197D THR* 3.2 25.2 - - + +
198D PRO* 3.3 12.8 - - - +
199D LEU* 3.5 27.1 + - + +
200D THR* 5.8 1.8 - - + +
345D VAL* 5.6 0.5 - - - +
3704D NA 2.5 47.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PRO* 3.6 12.3 - - - +
106D GLU* 2.8 24.4 + - + +
109D ASP* 1.3 76.1 - - - +
111D GLY* 1.3 54.9 + - - +
112D LYS* 2.9 37.1 + - - +
168D TRP 2.9 28.3 + - - -
169D ASN* 3.3 15.6 + - - +
171D PRO* 3.8 9.3 - - + +
197D THR* 3.9 13.0 - - + -
297D ASN* 4.5 1.0 - - - +
298D GLN* 4.6 3.3 + - - -
300D GLN* 5.0 2.6 + - - +
343D PRO 4.5 3.3 - - - +
345D VAL* 3.7 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PRO* 4.4 4.4 - - - +
43D SER* 4.6 4.5 - - - -
107D THR 2.8 21.4 + - - -
109D ASP 3.8 0.2 - - - -
110D ASN* 1.3 74.4 - - - +
112D LYS* 1.3 64.3 + - - +
334D PRO* 3.3 15.5 - - - +
342D GLY* 3.5 4.3 - - - -
343D PRO* 3.3 36.2 - - - +
----------------------------------------------------------
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