Contacts of the helix formed by residues 120 - 136 (chain K) 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 VAL 120 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116K ILE* 2.7 43.3 + - + +
118K TYR 3.4 0.2 - - - -
119K LEU* 1.3 81.2 - - + +
121K ASP* 1.3 71.4 + - - +
122K LEU 3.4 0.7 - - - -
123K ASP* 3.3 2.1 + - - +
124K MET* 2.9 55.3 + - + +
170K PHE* 6.2 0.2 - - + -
296K PHE* 4.4 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 121 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K GLU* 4.3 13.2 - - - +
112K LYS* 2.8 45.9 + - - +
116K ILE* 3.2 20.3 + - - +
117K SER* 3.4 12.1 - - - +
120K VAL* 1.3 77.5 - - - +
122K LEU* 1.3 66.0 + - + +
124K MET* 3.3 7.5 + - - +
125K VAL* 3.0 32.2 + - + +
170K PHE* 3.7 17.7 - - - +
172K LEU* 5.6 1.1 - - + -
173K LEU* 4.7 8.2 + - + +
296K PHE* 5.4 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K ILE* 4.9 11.7 - - + +
99K ARG* 3.0 55.4 - - + +
102K LEU* 3.8 8.3 - - + -
103K ALA* 3.6 18.6 - - + +
106K GLU* 5.1 1.8 - - + -
117K SER 2.9 24.4 + - - +
118K TYR 3.7 8.1 - - - +
121K ASP* 1.3 77.5 - - + +
123K ASP* 1.3 66.3 + - - +
125K VAL* 3.2 5.3 + - + +
126K LEU* 3.0 30.2 + - + +
172K LEU* 3.4 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K ARG* 3.7 20.5 + - - +
118K TYR 3.8 4.0 + - - -
119K LEU 3.3 25.3 - - - +
120K VAL 3.3 3.0 + - - +
122K LEU* 1.3 77.3 - - - +
124K MET* 1.3 61.7 + - - +
126K LEU* 3.4 8.8 + - - +
127K LYS* 3.0 68.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 124 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120K VAL* 2.9 45.6 + - + +
121K ASP* 3.8 5.2 - - - +
123K ASP* 1.3 80.6 - - - +
125K VAL* 1.3 59.7 + - - +
127K LYS* 3.8 9.2 - - + +
128K CYS* 2.9 31.2 + - - +
170K PHE* 5.5 7.6 - - + -
173K LEU* 3.6 35.1 - - + +
177K TRP* 5.3 2.6 + - - -
296K PHE* 5.6 2.9 - - + -
459K PHE* 5.0 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K ILE* 4.1 24.5 - - + -
121K ASP 3.0 25.3 + - - +
122K LEU* 3.2 12.3 + - + +
124K MET* 1.3 75.7 - - - +
126K LEU* 1.3 64.9 + - - +
128K CYS* 3.2 2.1 + - - +
129K LEU* 3.0 42.9 + - + +
172K LEU* 3.8 21.8 - - + +
173K LEU* 3.8 28.5 - - - +
176K ALA* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K ALA* 3.2 35.4 - - + +
95K ILE* 3.8 16.4 - - + -
96K GLU* 3.7 42.6 - - + +
99K ARG* 4.5 19.5 - - + +
122K LEU* 3.0 18.5 + - + +
123K ASP* 3.6 10.8 - - - +
125K VAL* 1.3 78.1 - - + +
127K LYS* 1.3 57.7 + - + +
129K LEU* 3.5 1.1 + - - +
130K ARG* 3.0 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I ASP* 5.5 1.4 + - - -
82I SER* 5.3 5.8 - - - +
123K ASP* 3.0 51.2 + - - +
124K MET* 4.0 8.1 - - + +
125K VAL 3.3 0.2 - - - -
126K LEU* 1.3 77.9 - - + +
128K CYS* 1.3 57.8 + - - +
130K ARG* 4.0 6.8 - - - +
131K TYR* 3.0 29.6 + - - +
461K ALA* 3.8 8.9 - - + +
147L ASP* 3.7 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 128 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124K MET 2.9 18.7 + - - +
125K VAL 3.2 4.0 + - - +
127K LYS* 1.3 75.0 - - - +
129K LEU* 1.3 64.4 + - - +
131K TYR* 3.2 1.7 + - - +
132K TYR* 3.0 44.3 + - - -
173K LEU* 4.8 0.4 - - + -
176K ALA* 3.6 28.0 - - + -
177K TRP* 3.4 35.9 - - + +
461K ALA* 4.0 11.6 - - + +
477K LEU* 4.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K LEU* 4.1 20.2 - - + +
91K LEU* 4.1 24.9 - - + -
92K ALA* 4.1 18.8 - - + -
95K ILE* 3.5 32.5 - - + -
125K VAL* 3.0 25.4 + - + +
126K LEU* 4.0 2.7 - - - +
128K CYS* 1.3 76.7 - - - +
130K ARG* 1.3 57.8 + - - +
132K TYR* 3.9 3.6 - - - +
133K ALA* 3.0 28.7 + - - +
176K ALA* 4.1 28.0 - - + +
179K LEU* 4.8 5.2 - - + -
180K GLY* 4.5 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ARG* 3.4 49.4 - - - +
138I LYS* 4.9 0.7 + - - -
89K ASN* 3.8 21.9 + - - +
92K ALA* 3.8 31.3 + - + +
93K ASP* 3.3 23.4 + - - +
96K GLU* 2.6 31.7 + - - -
126K LEU* 3.0 41.3 + - - +
127K LYS* 4.2 5.3 - - - +
129K LEU* 1.3 73.2 - - - +
131K TYR* 1.3 65.2 + - - +
133K ALA* 3.6 3.0 + - - +
134K GLY* 3.5 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I ASP* 3.4 24.2 - - - +
138I LYS* 3.1 47.1 + - + +
140I HIS* 4.5 5.2 + - - -
127K LYS 3.0 20.2 + - - +
128K CYS 3.2 3.1 + - - +
130K ARG* 1.3 78.1 - - - +
132K TYR* 1.3 77.6 + + - +
134K GLY 3.1 10.9 + - - -
135K TRP* 2.8 36.6 + + - -
461K ALA* 3.5 29.8 - - + -
462K GLN* 3.5 33.3 + - + +
478K GLY* 3.6 22.2 - - - -
479K GLU 3.7 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 132 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K LEU* 3.9 3.6 - - + -
128K CYS* 3.0 42.1 + - - +
129K LEU 4.1 2.2 - - - +
131K TYR* 1.3 87.7 - + - +
133K ALA* 1.3 67.1 + - - +
135K TRP* 2.9 19.9 + + + +
136K ALA 3.3 7.8 + - - -
177K TRP 5.0 1.1 - - - -
180K GLY* 3.5 23.1 - - - +
181K PRO* 3.6 44.5 - - + +
184K ALA* 3.3 9.9 - - + +
461K ALA* 5.7 0.2 - - + -
477K LEU* 2.9 46.7 + - + -
478K GLY 3.1 16.0 + - - -
481K GLY* 4.1 4.5 - - - -
482K LEU* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85K GLY* 3.4 17.9 - - - +
88K LEU* 3.7 17.7 - - + +
89K ASN* 3.3 36.3 - - - +
129K LEU 3.0 19.1 + - - +
130K ARG 3.6 5.4 - - - +
131K TYR 3.2 0.2 - - - -
132K TYR* 1.3 76.1 - - - +
134K GLY* 1.3 62.4 + - - +
135K TRP 3.3 0.2 + - - -
136K ALA* 3.3 18.0 + - - +
137K ASP* 4.9 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 134 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I GLY* 3.9 22.7 - - - -
138I LYS* 3.7 8.7 - - - -
89K ASN* 5.2 0.2 - - - +
130K ARG 3.5 5.3 + - - -
131K TYR 3.1 10.1 + - - -
133K ALA* 1.3 80.8 - - - +
135K TRP* 1.3 57.8 + - - +
136K ALA 3.4 0.7 + - - -
137K ASP* 3.7 0.9 - - - +
138K LYS* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 135 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I TRP* 4.7 9.4 - + - -
138I LYS* 3.4 41.7 - - + +
140I HIS* 4.3 3.8 - + - -
131K TYR* 2.8 44.4 + + - -
132K TYR* 2.9 21.0 + + + +
134K GLY* 1.3 75.8 - - - +
136K ALA* 1.3 65.7 + - - +
137K ASP 3.2 1.6 - - - -
138K LYS* 3.0 47.3 + - + -
139K TYR* 3.7 15.8 + + - +
184K ALA* 4.8 2.0 - - + +
185K THR* 6.2 0.2 - - - +
478K GLY 4.8 0.2 - - - -
479K GLU* 3.6 48.8 - - + +
482K LEU* 3.6 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145J PRO* 5.1 1.4 - - - +
81K ALA* 3.3 23.6 - - - +
82K SER* 5.1 0.7 - - - -
84K ARG* 3.2 23.3 + - + -
85K GLY* 3.7 14.4 - - - +
132K TYR 3.3 4.8 + - - +
133K ALA 3.3 17.3 + - - +
135K TRP* 1.3 76.4 - - - +
137K ASP* 1.3 59.1 + - + +
138K LYS 4.0 0.2 + - - -
139K TYR* 5.0 2.9 + - - +
184K ALA* 3.4 28.2 - - - +
----------------------------------------------------------
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