Contacts of the helix formed by residues 98 - 111 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94E LEU 3.1 9.3 + - - +
95E ILE 3.2 5.4 - - - +
97E ARG* 1.3 120.0 + - - +
99E ARG* 1.3 57.2 + - - +
100E THR 3.4 2.5 - - - -
101E TYR* 3.3 11.0 + - + -
102E LEU* 2.9 32.7 + - + +
203E TYR* 2.9 33.3 + - + -
207E LEU* 3.6 8.6 - - + +
14I GLN* 5.7 0.5 + - - -
3119I EDO 4.3 12.9 + - - -
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Residues in contact with ARG 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ILE 2.9 10.5 + - - +
96E GLU* 3.2 30.4 + - - +
97E ARG 3.4 1.2 + - - -
98E ASP* 1.3 77.3 - - - +
100E THR* 1.3 64.3 + - - +
102E LEU* 3.3 0.9 + - - +
103E ALA* 2.9 26.9 + - - +
118E TYR* 2.8 65.3 + - + +
119E LEU* 4.0 8.9 + - - +
122E LEU* 3.9 25.1 - - + +
123E ASP* 3.8 30.0 + - - +
126E LEU* 4.4 18.3 - - + +
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Residues in contact with THR 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E PRO* 3.9 4.9 - - + +
10E ALA 4.1 17.5 - - - +
11E PRO* 4.2 7.2 - - + -
12E ASN 5.2 1.8 - - - +
97E ARG 5.1 0.2 + - - -
98E ASP 3.4 0.6 - - - -
99E ARG* 1.3 76.9 - - - +
101E TYR* 1.3 64.1 + - - +
103E ALA* 3.4 2.3 + - - +
104E ALA* 3.1 22.9 + - - +
114E TYR* 3.7 17.3 - - - +
118E TYR* 3.8 20.8 + - - -
16I GLU* 2.6 38.3 + - - +
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Residues in contact with TYR 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ASN* 6.5 0.7 - - + -
15E PRO* 3.9 18.7 - - + +
16E GLU 2.6 32.3 + - - -
17E VAL* 4.1 3.1 - - - -
18E PHE* 3.4 25.1 + + - -
98E ASP* 3.3 9.5 + - + +
100E THR* 1.3 81.4 - - - +
102E LEU* 1.3 62.2 + - + +
104E ALA* 3.2 6.5 + - - +
105E LEU* 2.9 54.5 + - + +
203E TYR* 3.8 38.6 - + - -
3119I EDO 3.7 27.8 - - - -
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ILE* 3.9 39.0 - - + +
98E ASP* 2.9 22.8 + - + +
99E ARG 4.0 0.2 - - - +
101E TYR* 1.3 79.0 - - + +
103E ALA* 1.3 57.2 + - - +
105E LEU* 3.4 2.1 + - + -
106E GLU* 2.8 30.3 + - - +
122E LEU* 3.9 17.0 - - + +
172E LEU* 4.3 5.6 - - + +
200E THR* 3.7 39.8 - - + +
203E TYR* 3.8 27.8 - - + -
204E VAL* 4.3 8.5 - - + -
207E LEU* 4.3 13.0 - - + -
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Residues in contact with ALA 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ARG 2.9 18.7 + - - +
100E THR 3.7 0.7 - - - +
102E LEU* 1.3 75.6 - - - +
104E ALA* 1.3 58.4 + - - +
106E GLU* 3.3 4.1 + - - +
107E THR* 3.0 31.0 + - - -
114E TYR* 3.7 20.6 - - + -
117E SER* 3.4 4.0 - - - -
118E TYR* 3.7 32.5 - - + +
122E LEU* 3.5 13.1 - - + +
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Residues in contact with ALA 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E PRO* 4.2 9.9 - - + -
12E ASN* 3.6 26.7 - - + +
15E PRO* 4.1 7.2 - - + -
100E THR* 3.1 16.8 + - + +
101E TYR* 3.6 5.6 - - - +
103E ALA* 1.3 74.7 - - - +
105E LEU* 1.3 61.0 + - - +
107E THR 3.2 1.6 + - - -
108E LEU* 2.9 26.7 + - - +
114E TYR* 3.9 2.6 - - - -
335E PHE* 3.4 27.2 - - + -
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E PRO* 3.9 22.3 - - + +
17E VAL* 4.3 15.3 - - + -
101E TYR* 2.9 48.1 + - + +
102E LEU* 3.8 5.2 - - + +
104E ALA* 1.3 75.7 - - - +
106E GLU* 1.3 63.0 + - - +
108E LEU* 3.7 6.5 - - + +
109E ASP* 3.1 24.9 + - - +
199E LEU* 4.0 49.4 - - + +
200E THR* 3.8 15.9 - - + -
203E TYR* 4.5 6.5 - - + -
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Residues in contact with GLU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LEU 2.8 18.3 + - - +
103E ALA* 3.4 9.0 - - - +
104E ALA 3.2 0.2 - - - -
105E LEU* 1.3 76.8 - - - +
107E THR* 1.3 57.0 + - - +
109E ASP* 4.3 2.5 - - - +
110E ASN* 2.8 37.4 + - + +
112E LYS* 4.3 13.5 - - + -
117E SER* 3.7 15.0 - - - +
121E ASP* 4.3 12.1 - - + +
122E LEU* 5.1 0.4 - - + -
170E PHE 4.3 0.2 - - - -
171E PRO* 3.4 24.4 - - - +
172E LEU* 3.0 37.4 + - + +
197E THR* 5.6 0.3 - - - -
200E THR* 2.7 30.7 + - + +
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Residues in contact with THR 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ASN* 5.1 1.2 + - - -
103E ALA 3.0 8.3 + - - -
104E ALA 3.2 7.6 + - - -
106E GLU* 1.3 75.4 - - - +
108E LEU* 1.3 61.6 + - - +
111E GLY* 2.8 28.3 + - - +
112E LYS 2.8 28.4 + - - +
114E TYR* 3.2 19.8 - - - +
117E SER* 3.1 14.6 + - - -
334E PRO* 3.6 23.8 - - + +
335E PHE* 3.8 24.9 - - + -
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Residues in contact with LEU 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E GLN 3.7 22.2 - - - +
14E GLN* 4.9 4.5 - - + -
15E PRO* 3.8 29.4 - - + +
41E ASN* 3.3 53.0 + - - +
42E PRO* 3.5 1.0 - - - +
48E ILE* 3.8 33.7 - - + -
104E ALA 2.9 16.3 + - - +
105E LEU* 3.7 11.7 - - + +
107E THR* 1.3 78.3 - - - +
109E ASP* 1.3 58.7 + - - +
335E PHE* 4.3 8.9 - - + -
3118E EDO 3.6 10.3 - - - +
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Residues in contact with ASP 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E THR* 2.6 13.7 + - - -
42E PRO* 3.4 9.6 - - - +
48E ILE* 3.5 11.5 - - + +
105E LEU* 3.1 15.9 + - + +
106E GLU* 4.3 2.7 - - - +
108E LEU* 1.3 77.9 - - - +
110E ASN* 1.3 58.0 + - - +
196E GLN 3.6 7.2 - - - +
197E THR* 3.4 16.5 - - + +
198E PRO* 3.4 1.7 - - - +
199E LEU* 3.2 47.5 + - + +
200E THR* 4.8 2.4 + - + +
345E VAL* 4.9 1.9 - - - +
3705E NA 2.4 46.8 - - - -
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Residues in contact with ASN 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E PRO* 3.5 10.9 - - - +
106E GLU* 2.8 25.3 + - + +
109E ASP* 1.3 76.2 - - + +
111E GLY* 1.3 54.6 + - - +
112E LYS* 2.9 37.2 + - - +
168E TRP* 2.8 29.5 + - - -
169E ASN* 3.3 15.8 + - - +
171E PRO* 3.8 8.7 - - + +
197E THR* 3.9 13.3 - - + +
297E ASN* 4.5 1.4 + - - +
298E GLN* 4.7 2.8 + - - -
300E GLN* 5.1 5.7 + - - +
343E PRO 4.6 2.1 - - - +
345E VAL* 4.0 21.7 + - - +
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Residues in contact with GLY 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E PRO* 3.7 13.8 - - - +
43E SER* 4.7 2.9 - - - -
107E THR 2.8 20.9 + - - -
110E ASN* 1.3 74.4 - - - +
112E LYS* 1.3 65.0 + - - +
298E GLN* 4.6 0.9 - - - -
334E PRO* 3.3 15.1 - - - +
342E GLY* 3.5 5.1 - - - -
343E PRO* 3.3 28.1 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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