Contacts of the helix formed by residues 120 - 138 (chain D) in PDB entry 1Z10
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 ASN 120 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D SER 4.7 0.2 - - - +
100D GLY* 3.3 11.1 - - - -
101D ARG* 2.7 56.0 + - - +
102D GLY 5.2 0.2 + - - -
118D PHE 4.4 3.6 + - - -
119D SER* 1.3 74.1 + - - +
121D GLY* 1.3 72.5 + - - +
122D GLU 3.5 0.2 + - - -
123D ARG* 3.3 9.8 + - - +
124D ALA* 3.0 15.8 + - - -
373D ARG* 4.5 9.0 - - - +
375D LYS* 4.3 6.2 + - - +
437D ARG* 4.1 3.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ASN* 1.3 85.4 + - - +
122D GLU* 1.3 62.7 + - - -
124D ALA* 3.6 1.6 - - - +
125D LYS* 3.0 20.5 + - - +
375D LYS* 4.0 23.6 - - - +
437D ARG* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D ASN 3.5 0.2 + - - -
121D GLY* 1.3 68.7 - - - -
123D ARG* 1.3 67.3 + - - +
125D LYS* 3.6 23.1 + - - +
126D GLN* 2.9 52.9 + - + +
283D ASN 6.0 1.3 - - - +
285D GLU* 4.3 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D LYS 5.0 0.4 + - - -
113D GLY* 2.9 23.6 + - - -
114D TYR* 3.6 25.3 + - - +
119D SER* 3.5 23.3 - - - -
120D ASN 3.3 8.5 + - - +
121D GLY 3.2 0.6 - - - -
122D GLU* 1.3 80.9 - - - +
124D ALA* 1.3 57.8 + - - +
126D GLN* 3.7 1.0 - - - +
127D LEU* 2.8 47.4 + - + +
285D GLU* 3.0 35.8 + - - +
287D TYR* 3.0 22.5 + - - -
290D ASN* 3.7 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D VAL* 4.8 1.5 - - - +
119D SER* 2.9 25.5 + - - +
120D ASN 3.0 15.0 + - - +
121D GLY 3.6 3.8 - - - +
123D ARG* 1.3 75.6 - - - +
125D LYS* 1.3 65.4 + - - +
127D LEU* 4.6 1.6 - - - +
128D ARG* 2.9 29.7 + - - +
437D ARG* 3.4 37.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D GLY 3.0 12.7 + - - +
122D GLU* 3.2 26.9 + - - +
124D ALA* 1.3 75.5 - - - +
126D GLN* 1.3 66.7 + - - +
128D ARG* 4.3 2.0 - - - +
129D ARG* 3.3 49.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D GLU* 2.9 48.9 + - + +
123D ARG 3.7 2.5 - - - +
125D LYS* 1.3 78.6 - - - +
127D LEU* 1.3 65.5 + - + +
129D ARG* 3.4 33.3 + - - +
130D PHE* 3.0 26.5 + - - +
274D ARG* 4.2 8.0 + - - -
285D GLU* 4.2 19.7 - - + +
286D PHE* 3.6 26.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D GLY 3.5 28.3 - - - +
116D VAL* 3.8 17.3 - - + +
123D ARG* 2.8 35.6 + - + +
124D ALA 4.4 0.9 - - - +
126D GLN* 1.3 73.6 - - - +
128D ARG* 1.3 58.8 + - - +
130D PHE* 4.2 3.4 - - - +
131D SER* 2.7 34.2 + - - +
271D PHE* 3.8 34.8 - - + -
285D GLU* 4.0 11.2 - - + +
286D PHE* 4.5 8.5 - - + -
290D ASN* 3.6 29.2 - - + +
294D THR* 3.9 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D VAL* 3.6 15.1 - - + +
124D ALA* 2.9 19.7 + - + +
125D LYS* 4.3 2.5 - - - +
127D LEU* 1.3 76.1 - - - +
129D ARG* 1.3 67.3 + - - +
131D SER* 3.8 1.4 - - - -
132D ILE* 2.9 43.3 + - + +
435D GLY 4.9 0.2 + - - -
436D LYS 3.4 18.3 + - - -
437D ARG* 3.4 13.5 - - - +
438D ASN* 2.7 45.0 + - - -
440D PHE* 3.7 22.0 - - + +
500D HEM 2.7 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LYS* 3.3 44.7 + - - +
126D GLN* 3.4 31.7 + - - +
128D ARG* 1.3 80.6 - - - +
130D PHE* 1.3 64.9 + - - +
132D ILE* 4.0 5.8 - - - +
133D ALA* 3.1 24.7 + - + +
274D ARG* 5.9 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D GLN 3.0 19.3 + - - +
127D LEU 4.2 2.0 - - - +
129D ARG* 1.3 79.8 - - - +
131D SER* 1.3 58.7 + - - +
133D ALA* 3.1 6.5 + - + +
134D THR* 2.8 60.7 + - + -
267D PHE* 4.1 11.7 - + - -
270D SER* 3.7 8.3 - - - -
271D PHE* 3.4 59.7 - + + -
274D ARG* 3.6 42.6 - - + +
286D PHE* 3.6 18.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D VAL* 4.2 1.4 - - - +
127D LEU* 2.7 22.9 + - - +
128D ARG 3.8 0.4 - - - -
130D PHE* 1.3 77.5 - - - +
132D ILE* 1.3 58.8 + - - +
135D LEU* 2.9 35.8 + - - +
267D PHE* 3.8 18.6 - - - -
271D PHE* 5.9 0.3 - - - -
294D THR* 3.6 24.9 - - - +
298D LEU* 5.2 2.5 - - - -
440D PHE* 3.5 30.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D ARG* 2.9 46.7 + - + +
129D ARG* 4.0 4.7 - - - +
131D SER* 1.3 74.4 - - - +
133D ALA* 1.3 64.5 + - - +
135D LEU* 4.0 4.4 - - - +
136D ARG* 3.2 51.9 + - - +
440D PHE* 3.6 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D ARG* 3.1 21.1 + - + +
130D PHE* 3.7 4.9 - - + +
132D ILE* 1.3 80.3 - - - +
134D THR* 1.3 58.3 + - - +
136D ARG* 3.2 12.1 - - - +
137D ASP* 3.1 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D PHE* 2.8 46.1 + - + -
133D ALA* 1.3 70.9 - - - +
135D LEU* 1.3 63.0 + - - +
137D ASP* 3.3 11.5 + - - +
138D PHE* 3.1 49.8 + - + -
267D PHE* 3.4 33.7 - - + -
270D SER* 3.8 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D SER 2.9 19.4 + - - +
132D ILE* 4.0 4.5 - - - +
134D THR* 1.3 72.2 - - - +
136D ARG* 1.3 65.9 + - - +
138D PHE* 3.2 11.4 + - - +
139D GLY 3.4 1.0 + - - -
140D VAL* 3.1 44.8 + - + +
182D ILE* 5.0 3.8 - - + -
185D ILE* 4.0 20.5 - - + +
267D PHE* 3.8 26.0 - - + -
298D LEU* 4.3 18.6 - - + -
440D PHE* 3.9 32.1 - - + +
441D GLY* 5.7 0.2 - - - -
500D HEM 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ILE* 3.2 34.4 + - - +
133D ALA* 3.2 15.2 - - - +
135D LEU* 1.3 80.1 - - - +
137D ASP* 1.3 63.1 + - - +
139D GLY* 3.2 11.8 + - - -
140D VAL* 4.2 21.5 + - - +
142D LYS* 3.4 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ALA* 3.1 21.5 + - - +
134D THR* 3.5 16.8 + - - +
135D LEU 3.2 0.4 - - - -
136D ARG* 1.3 80.2 - - - +
138D PHE* 1.3 66.6 + - + +
139D GLY 3.2 0.2 - - - -
142D LYS* 3.0 20.3 + - - +
270D SER* 5.6 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D THR* 3.1 31.5 + - + +
135D LEU 3.2 6.3 + - - +
137D ASP* 1.3 84.2 - - + +
139D GLY* 1.3 56.2 + - - +
140D VAL 3.9 1.3 + - - -
142D LYS* 4.2 1.1 - - - -
144D GLY 5.6 0.5 - - - -
145D ILE* 4.8 4.9 + - - +
184D SER 6.0 0.4 - - - -
185D ILE* 4.1 37.8 - - + +
264D PRO* 4.1 12.3 - - + -
265D ARG 3.5 12.3 - - - -
266D ASP* 3.1 47.6 - - - -
267D PHE* 3.5 7.0 - - + -
270D SER* 3.4 19.7 - - - -
----------------------------------------------------------
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