Contacts of the helix formed by residues 120 - 136 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I ILE* 2.7 46.4 + - + +
119I LEU* 1.3 79.9 - - + +
121I ASP* 1.3 62.0 + - - +
122I LEU 3.5 0.2 - - - -
123I ASP* 3.2 2.8 + - - +
124I MET* 2.9 60.3 + - + +
296I PHE* 4.2 21.3 - - + -
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Residues in contact with ASP 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I GLU* 4.2 13.6 - - + +
112I LYS* 2.8 47.3 + - + +
116I ILE* 3.2 19.8 + - - +
117I SER* 3.4 10.3 - - - +
120I VAL* 1.3 78.0 - - - +
122I LEU* 1.3 63.3 + - + +
124I MET* 3.2 8.8 + - - +
125I VAL* 2.9 34.7 + - + +
170I PHE* 3.4 19.5 - - - +
172I LEU* 5.6 1.3 - - + -
173I LEU* 4.6 7.6 - - + +
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Residues in contact with LEU 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I ILE* 3.8 29.2 - - + -
99I ARG* 3.9 33.2 - - + +
102I LEU* 4.1 15.0 - - + -
103I ALA* 3.8 20.6 - - + +
106I GLU* 5.2 0.7 - - + -
117I SER* 2.9 30.0 + - - +
118I TYR 3.6 9.9 - - - +
121I ASP* 1.3 75.6 - - + +
123I ASP* 1.3 62.6 + - - +
125I VAL* 3.3 7.0 + - + +
126I LEU* 3.1 30.8 + - + +
172I LEU* 3.7 27.8 - - + -
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Residues in contact with ASP 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I ARG* 3.8 20.2 + - - +
118I TYR 3.9 2.6 + - - -
119I LEU 3.3 25.7 - - - +
120I VAL 3.2 3.2 + - - +
121I ASP 3.2 0.6 - - - -
122I LEU* 1.3 77.6 - - - +
124I MET* 1.3 63.6 + - - +
126I LEU* 3.3 8.9 + - - +
127I LYS* 3.0 63.3 + - - +
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Residues in contact with MET 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I VAL* 2.9 45.8 + - + +
121I ASP* 3.8 6.7 - - - +
123I ASP* 1.3 80.2 - - - +
125I VAL* 1.3 59.9 + - - +
127I LYS* 3.8 9.4 - - + +
128I CYS* 2.9 31.0 + - - +
170I PHE* 5.3 6.1 - - + -
173I LEU* 3.4 40.4 - - + +
177I TRP* 6.2 0.7 - - - -
296I PHE* 5.7 2.0 - - + -
459I PHE* 5.5 19.1 - - + +
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Residues in contact with VAL 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I ILE* 4.0 33.9 - - + -
121I ASP 2.9 19.8 + - - +
122I LEU* 3.6 11.9 - - + +
123I ASP 3.3 0.2 - - - -
124I MET* 1.3 76.4 - - - +
126I LEU* 1.3 63.6 + - - +
128I CYS* 3.3 2.1 + - - +
129I LEU* 3.1 27.1 + - + +
172I LEU* 3.6 46.2 - - + +
173I LEU* 3.7 12.3 - - - +
176I ALA* 4.0 15.0 - - + +
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Residues in contact with LEU 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92I ALA* 3.3 31.9 - - + +
95I ILE* 3.6 23.6 - - + -
96I GLU* 3.8 32.1 - - + +
99I ARG* 4.5 19.5 - - + +
122I LEU* 3.1 17.2 + - + +
123I ASP* 3.6 10.1 - - - +
124I MET 3.3 0.2 - - - -
125I VAL* 1.3 77.5 - - + +
127I LYS* 1.3 58.6 + - + +
129I LEU* 4.0 3.2 - - - +
130I ARG* 3.0 56.4 + - - +
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Residues in contact with LYS 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123I ASP* 3.0 49.9 + - - +
124I MET* 4.0 9.0 - - + +
126I LEU* 1.3 77.6 - - + +
128I CYS* 1.3 58.7 + - - +
130I ARG* 4.2 5.2 - - - +
131I TYR* 3.0 30.0 + - - +
461I ALA* 3.8 9.0 - - + +
147J ASP* 3.6 30.3 + - - +
80K ASP* 5.3 2.6 + - - -
82K SER* 5.3 7.9 - - - +
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Residues in contact with CYS 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I MET 2.9 18.9 + - - +
125I VAL 3.6 4.7 - - - +
126I LEU 3.2 0.2 - - - -
127I LYS* 1.3 75.4 - - - +
129I LEU* 1.3 65.6 + - - +
131I TYR* 3.2 1.6 + - - +
132I TYR* 3.0 48.5 + - - -
176I ALA* 3.4 31.0 - - + -
177I TRP* 3.7 30.3 - - + +
180I GLY* 5.1 0.2 - - - -
461I ALA* 3.9 12.5 - - + +
477I LEU* 4.4 2.5 - - - -
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Residues in contact with LEU 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88I LEU* 4.1 31.3 - - + +
91I LEU* 4.0 19.5 - - + -
92I ALA* 4.2 17.3 - - + -
95I ILE* 3.5 32.1 - - + -
125I VAL* 3.1 21.6 + - + +
126I LEU* 4.1 2.7 - - - +
128I CYS* 1.3 78.5 - - - +
130I ARG* 1.3 58.6 + - - +
132I TYR* 3.5 4.5 + - - +
133I ALA* 2.9 28.4 + - - +
176I ALA* 4.3 27.8 - - + +
179I LEU* 5.0 4.5 - - + -
180I GLY* 4.4 8.3 - - - +
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Residues in contact with ARG 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I ASN* 3.6 24.3 + - - +
92I ALA* 3.7 28.9 + - + +
93I ASP* 3.1 23.8 + - - +
96I GLU* 2.9 31.9 + - - -
126I LEU* 3.0 42.2 + - - +
127I LYS* 4.2 4.7 - - - +
129I LEU* 1.3 72.8 - - - +
131I TYR* 1.3 66.6 + - - +
133I ALA* 3.4 3.3 + - - +
134I GLY* 3.4 13.3 + - - -
86K ARG* 3.4 49.6 - - - +
138K LYS* 4.9 0.9 + - - -
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Residues in contact with TYR 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I LYS 3.0 20.3 + - - +
128I CYS 3.2 4.0 + - - +
130I ARG* 1.3 76.5 - - - +
132I TYR* 1.3 76.1 + + - +
134I GLY 3.0 15.8 + - - -
135I TRP* 3.0 34.8 + + - -
461I ALA* 3.3 28.5 - - + -
462I GLN* 3.4 38.9 + - + +
478I GLY* 3.5 17.1 - - - -
479I GLU 3.8 1.9 + - - -
137K ASP* 3.5 23.8 - - - +
138K LYS* 3.1 47.1 + - + +
140K HIS* 4.5 5.0 + - - -
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Residues in contact with TYR 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88I LEU* 4.0 3.6 - - + -
128I CYS* 3.0 43.5 + - - +
129I LEU 4.1 2.5 - - - +
131I TYR* 1.3 88.3 - + - +
133I ALA* 1.3 65.4 + - - +
134I GLY 3.1 0.2 - - - -
135I TRP* 3.1 18.6 + + + +
136I ALA 3.4 0.2 + - - -
180I GLY* 3.5 22.2 - - - +
181I PRO* 3.6 43.4 - - + +
184I ALA* 3.3 19.2 - - + +
461I ALA 5.3 0.4 - - - -
477I LEU* 2.7 49.8 + - + -
478I GLY 3.2 13.4 + - - -
481I GLY* 4.3 1.6 - - - -
482I LEU* 3.8 19.1 - - + -
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Residues in contact with ALA 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I GLY* 3.4 28.6 - - - +
88I LEU* 3.7 18.6 - - + +
89I ASN* 3.5 22.9 - - - +
129I LEU 2.9 18.8 + - - +
130I ARG 3.5 8.1 - - - +
131I TYR 3.2 0.2 - - - -
132I TYR* 1.3 77.4 - - - +
134I GLY* 1.3 61.5 - - - +
135I TRP 3.4 0.3 + - - -
136I ALA* 3.4 17.3 + - - +
137I ASP* 5.0 1.6 + - - +
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Residues in contact with GLY 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89I ASN* 5.3 0.4 - - - +
130I ARG 3.4 4.1 + - - -
131I TYR 3.0 10.3 + - - -
133I ALA* 1.3 81.7 - - - +
135I TRP* 1.3 56.9 + - - +
136I ALA 3.4 0.2 - - - -
137I ASP* 3.6 2.1 - - - +
138I LYS* 2.9 34.7 + - - +
134K GLY* 3.9 21.5 - - - -
138K LYS* 3.9 9.0 - - - -
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Residues in contact with TRP 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I TYR* 3.0 39.3 + + - -
132I TYR* 3.1 19.3 + + - +
134I GLY* 1.3 74.4 - - - +
136I ALA* 1.3 66.6 + - - +
137I ASP 3.2 2.9 - - - -
138I LYS* 3.0 50.3 + - + -
139I TYR* 3.6 15.7 + + - +
184I ALA* 4.7 2.2 - - + -
479I GLU* 3.6 46.0 - - + +
482I LEU* 3.6 34.9 - - + +
135K TRP* 4.7 9.4 - + - -
138K LYS* 3.3 45.0 - - + +
140K HIS* 4.0 6.5 - + - -
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Residues in contact with ALA 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I ALA* 3.2 25.8 - - - +
82I SER* 5.1 0.4 - - - -
84I ARG* 3.2 25.8 + - + -
85I GLY* 3.6 14.4 - - - +
88I LEU* 5.4 0.2 - - + -
132I TYR 3.4 5.2 + - - +
133I ALA 3.4 17.2 + - - +
134I GLY 3.4 1.0 - - - -
135I TRP* 1.3 77.3 - - - +
137I ASP* 1.3 57.2 + - + +
138I LYS 4.0 0.3 + - - -
139I TYR* 5.0 2.3 + - - +
184I ALA* 3.4 23.7 - - + +
145L PRO* 4.9 1.2 - - - +
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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) + - + + + + + -
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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