Contacts of the helix formed by residues 120 - 138 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLY* 3.6 9.0 - - - -
101A ARG* 2.9 50.7 + - - +
113A GLY 5.0 0.2 + - - -
118A PHE 4.6 3.2 + - - -
119A SER* 1.3 77.7 + - - +
121A GLY* 1.3 70.3 + - - +
123A ARG* 3.4 9.7 + - - +
124A ALA* 3.2 14.9 + - - -
373A ARG* 4.4 9.9 - - - +
375A LYS* 4.1 9.4 - - - +
437A ARG* 4.1 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ASN* 1.3 77.7 + - - +
122A GLU* 1.3 63.3 + - - -
124A ALA* 3.2 3.4 + - - +
125A LYS* 2.9 24.2 + - - +
375A LYS* 4.1 23.8 - - - +
437A ARG* 5.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ASN 3.6 0.2 + - - -
121A GLY* 1.3 71.4 - - - -
123A ARG* 1.3 65.5 + - - +
125A LYS* 3.3 12.9 + - - +
126A GLN* 2.7 50.0 + - - +
283A ASN 6.1 1.1 - - - +
285A GLU* 4.4 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS 4.9 0.4 + - - -
113A GLY* 2.9 32.5 + - - -
114A TYR* 3.5 27.4 + - - +
119A SER* 3.7 8.1 - - - -
120A ASN 3.4 9.6 + - - +
121A GLY 3.2 0.6 - - - -
122A GLU* 1.3 79.8 - - - +
124A ALA* 1.3 63.0 + - - +
126A GLN* 3.7 0.5 - - - +
127A LEU* 3.1 45.3 + - + +
285A GLU* 3.1 37.0 + - - +
287A TYR* 3.3 20.5 + - - -
290A ASN* 3.7 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 4.6 3.4 - - - +
119A SER* 3.0 25.7 + - - +
120A ASN 3.2 8.8 + - - -
121A GLY 3.6 6.3 - - - +
123A ARG* 1.3 78.2 - - - +
125A LYS* 1.3 55.3 + - - +
127A LEU* 4.1 1.5 - - - +
128A ARG* 2.7 40.3 + - + +
437A ARG* 3.5 35.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLY 2.9 15.8 + - - +
122A GLU* 3.6 17.0 - - - +
123A ARG 3.3 0.2 - - - -
124A ALA* 1.3 78.7 - - - +
126A GLN* 1.3 58.1 + - - +
128A ARG* 4.0 3.5 - - - +
129A ARG* 3.1 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 2.7 43.7 + - - +
123A ARG 3.7 3.6 - - - +
125A LYS* 1.3 77.3 - - - +
127A LEU* 1.3 60.5 + - - +
129A ARG* 3.4 14.1 + - - +
130A PHE* 3.0 30.8 + - - +
274A ARG* 5.3 7.7 - - - +
285A GLU* 4.1 18.8 - - + +
286A PHE* 3.5 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY* 3.4 33.4 - - - +
116A VAL* 4.0 15.7 - - + -
119A SER* 4.5 0.2 - - - +
123A ARG* 3.1 25.8 + - + +
124A ALA 4.1 1.1 - - - +
126A GLN* 1.3 80.0 - - + +
128A ARG* 1.3 63.4 + - - +
130A PHE* 4.0 3.9 - - - +
131A SER* 2.9 30.2 + - - +
271A PHE* 3.8 34.8 - - + -
285A GLU* 4.0 9.6 - - + +
286A PHE* 4.2 8.7 - - + -
290A ASN* 3.6 27.6 - - + +
294A THR* 3.8 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 3.7 13.4 - - + +
124A ALA* 2.7 24.6 + - + +
125A LYS* 4.0 3.8 - - - +
127A LEU* 1.3 76.1 - - - +
129A ARG* 1.3 62.8 + - - +
131A SER* 3.2 2.2 + - - -
132A ILE* 3.0 38.9 + - + +
436A LYS 3.5 16.9 + - - -
437A ARG* 3.5 12.9 - - - +
438A ASN* 2.7 47.1 + - - -
440A PHE* 3.6 32.8 - - + +
500A HEM 2.9 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LYS* 3.1 42.0 + - - +
126A GLN* 4.0 14.1 - - - +
128A ARG* 1.3 78.1 - - - +
130A PHE* 1.3 64.1 + - - +
132A ILE* 4.1 5.8 - - - +
133A ALA* 3.1 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLN 3.0 17.5 + - - +
127A LEU 4.0 3.4 - - - +
129A ARG* 1.3 81.2 - - - +
131A SER* 1.3 62.1 + - - +
133A ALA* 3.3 5.3 + - + +
134A THR* 2.8 57.9 + - + -
267A PHE* 3.8 15.9 - + - -
270A SER* 3.8 10.1 - - - -
271A PHE* 3.5 55.2 - + + -
274A ARG* 4.1 29.8 - - + +
286A PHE* 3.6 24.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 4.5 0.9 - - - +
127A LEU 2.9 22.1 + - - -
128A ARG 3.8 0.4 - - - -
130A PHE* 1.3 74.6 - - - +
132A ILE* 1.3 68.2 + - - +
134A THR* 4.1 0.3 - - - -
135A LEU* 2.9 29.8 + - - +
267A PHE* 3.6 19.1 - - - -
294A THR* 3.5 26.1 - - - +
298A LEU* 5.0 2.0 - - - -
440A PHE* 3.6 27.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ARG* 3.0 43.6 + - + +
129A ARG* 4.1 5.8 - - - +
131A SER* 1.3 77.0 - - - +
133A ALA* 1.3 64.4 + - - +
135A LEU* 3.4 7.2 + - - +
136A ARG* 3.1 57.7 + - - +
440A PHE* 3.6 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 3.1 17.7 + - + +
130A PHE* 3.7 6.1 - - + +
132A ILE* 1.3 81.7 - - - +
134A THR* 1.3 63.9 + - - +
136A ARG* 3.2 9.8 + - - +
137A ASP* 3.0 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 2.8 40.9 + - + -
133A ALA* 1.3 73.7 - - - +
135A LEU* 1.3 67.4 + - - +
137A ASP* 3.1 10.6 + - + +
138A PHE* 3.1 39.6 + - + -
267A PHE* 3.7 26.5 - - + -
270A SER* 3.6 30.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER 2.9 23.0 + - - +
132A ILE* 3.8 4.7 - - - +
134A THR* 1.3 74.7 - - - +
136A ARG* 1.3 63.5 + - + +
138A PHE* 3.0 14.5 + - - +
139A GLY 3.4 0.5 + - - -
140A VAL* 3.1 43.1 + - + +
182A ILE* 4.4 10.5 - - + -
185A ILE* 3.7 25.6 - - + -
267A PHE* 4.3 5.2 - - + -
298A LEU* 4.1 28.7 - - + -
440A PHE* 3.8 32.1 - - + +
441A GLY* 5.8 0.2 - - - -
444A LEU* 5.8 0.2 - - + -
500A HEM 4.5 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 3.1 40.3 + - - +
133A ALA* 3.5 10.3 - - - +
135A LEU* 1.3 76.8 - - - +
137A ASP* 1.3 60.9 + - - +
139A GLY* 2.9 17.8 + - - -
140A VAL* 3.8 22.0 - - + +
142A LYS* 2.9 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ALA* 3.0 22.4 + - - +
134A THR* 3.1 12.6 + - + +
136A ARG* 1.3 79.1 - - - +
138A PHE* 1.3 69.6 + - + +
139A GLY 3.2 0.9 + - - -
142A LYS* 4.2 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 3.1 30.6 + - + +
135A LEU 3.0 9.7 + - - +
136A ARG 3.0 1.4 - - - -
137A ASP* 1.3 84.5 - - + +
139A GLY* 1.3 57.9 + - - +
140A VAL* 3.6 0.8 + - - -
144A GLY 5.2 0.9 - - - -
145A ILE* 4.0 16.1 + - - +
185A ILE* 4.1 28.5 - - + +
264A PRO* 4.4 15.0 - - + -
265A ARG 3.7 11.7 - - - -
266A ASP* 3.3 40.8 - - - -
267A PHE* 3.6 6.1 - - - -
270A SER* 3.4 22.9 - - - -
----------------------------------------------------------
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