Contacts of the strand formed by residues 19 - 25 (chain E) in PDB entry 1ZM9
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 19 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E LEU 4.4 6.3 - - - +
13E MET* 5.0 0.2 - - - -
15E LYS 3.3 20.0 - - - +
16E VAL* 2.9 18.2 + - + +
18E ASN* 1.3 80.8 - - - +
20E ARG* 1.3 89.2 + - - +
21E ASN* 3.5 28.3 - - - +
99E LEU* 3.2 23.1 - - + +
101E ASN* 3.7 7.2 - - - +
344E SER* 3.4 14.9 - - - -
345E PRO* 4.1 6.7 - - + -
451E GLY 4.8 2.9 - - - +
452E ASN* 4.6 17.3 - - - +
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Residues in contact with ARG 20 (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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17E THR 3.4 15.4 + - - -
18E ASN* 3.7 3.8 - - - +
19E VAL* 1.3 112.9 + - - +
21E ASN* 1.3 65.5 + - - +
22E MET* 3.7 3.0 + - + -
89E ILE* 4.5 2.0 - - - +
91E GLN* 2.9 25.3 + - - -
93E THR* 4.2 10.3 - - - +
98E PHE* 4.3 12.7 - - + -
99E LEU 2.7 12.5 + - - +
100E ILE* 3.3 14.2 - - + +
101E ASN 2.8 26.4 + - - +
338E ILE* 3.9 28.7 - - + +
339E VAL* 3.2 28.6 + - + -
342E LEU* 2.7 30.2 + - + -
343E PRO 3.6 10.3 - - - -
344E SER* 3.7 4.5 - - - -
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Residues in contact with ASN 21 (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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19E VAL* 3.5 5.5 - - - +
20E ARG* 1.3 71.0 - - - +
22E MET* 1.3 60.5 + - - +
101E ASN* 2.9 38.2 + - + +
103E ILE* 4.7 2.2 - - + -
121E VAL 4.4 8.5 - - - +
122E THR* 4.1 2.9 - - - -
123E ASP* 2.9 37.8 + - - +
124E GLY 3.2 6.9 + - - -
343E PRO 4.7 1.5 + - - +
345E PRO* 3.0 34.6 - - - +
399E ARG* 4.6 4.2 - - - -
451E GLY 3.3 11.3 + - - +
453E ILE* 3.6 28.6 + - + +
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Residues in contact with MET 22 (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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20E ARG 4.2 8.7 - - - +
21E ASN* 1.3 76.4 - - - +
23E SER* 1.3 80.5 + - - +
24E VAL* 4.2 7.2 - - + -
39E LEU* 5.7 6.1 - - + -
77E LEU* 6.3 0.2 - - - -
100E ILE* 4.2 15.3 - - + -
101E ASN 3.1 14.3 + - - +
102E LEU* 3.8 25.6 - - + -
103E ILE* 2.9 28.1 + - - +
122E THR* 3.6 8.1 - - - +
124E GLY* 3.2 27.8 - - - +
126E LEU* 4.3 10.3 - - + +
338E ILE* 4.1 21.1 - - + -
342E LEU* 3.7 18.6 - - + -
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Residues in contact with SER 23 (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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22E MET* 1.3 81.4 - - - +
24E VAL* 1.3 71.5 + - - +
25E ILE* 4.0 8.9 - - - +
102E LEU* 4.7 0.9 - - - -
103E ILE* 3.3 16.6 + - - +
104E ASP 5.0 0.4 - - - -
105E SER* 2.3 30.4 + - - -
118E ALA* 4.9 6.7 - - - +
119E LEU* 5.3 5.1 - - - +
122E THR* 4.2 14.4 - - - -
124E GLY 3.4 5.0 + - - -
125E ALA* 3.3 6.4 - - - -
126E LEU 3.0 22.7 + - - -
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Residues in contact with VAL 24 (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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22E MET* 4.2 8.3 - - + -
23E SER* 1.3 81.6 + - - +
25E ILE* 1.3 60.1 + - - +
26E ALA* 3.5 1.7 + - + -
32E LYS* 3.4 46.1 + - + +
35E LEU* 6.0 1.1 - - + -
36E THR* 3.6 30.1 - - + -
102E LEU* 3.7 16.5 - - + +
103E ILE 4.6 1.6 + - - -
105E SER* 3.9 8.1 + - - -
126E LEU* 3.6 24.7 - - + +
128E VAL* 4.0 18.4 - - + -
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Residues in contact with ILE 25 (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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23E SER* 4.7 7.2 - - - +
24E VAL* 1.3 70.1 - - - +
26E ALA* 1.3 60.6 + - - +
105E SER* 5.5 1.3 - - - +
119E LEU* 3.9 22.7 - - + -
125E ALA* 3.5 28.3 - - + -
126E LEU 3.1 5.8 + - - +
127E VAL* 3.3 18.9 - - + -
128E VAL 2.9 24.4 + - - -
139E THR* 3.7 23.8 - - + +
142E VAL* 3.4 44.9 - - + -
143E LEU* 4.4 4.5 - - + +
146E ALA* 4.9 6.1 - - + -
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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