Contacts of the strand formed by residues 136 - 146 (chain E) in PDB entry 1ZMD
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 THR 136 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E ASP* 4.8 4.2 + - - +
3E GLN* 4.1 16.1 + - - -
128E THR* 4.2 14.4 - - + -
129E ALA 3.1 7.4 - - - -
130E THR* 3.8 19.1 - - + +
131E LYS* 5.3 3.2 + - - -
134E GLY 3.5 10.8 - - - +
135E GLY* 1.3 79.7 - - - +
137E GLN* 1.3 64.4 + - - +
138E VAL* 5.2 4.6 - - - +
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Residues in contact with GLN 137 (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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2E ASP 4.0 4.1 + - - -
3E GLN* 3.4 30.5 + - - +
4E PRO* 3.7 2.0 - - - +
5E ILE* 3.3 31.0 - - + +
115E VAL* 4.3 13.5 - - + -
128E THR* 3.4 2.2 - - - -
129E ALA* 2.7 43.9 + - + +
131E LYS* 4.1 18.8 + - - +
136E THR* 1.3 75.9 - - - +
138E VAL* 1.3 93.4 + - - +
139E ILE* 3.7 15.8 - - + +
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Residues in contact with VAL 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ASP* 4.7 3.7 + - - +
4E PRO* 3.4 14.3 - - + +
5E ILE 2.7 31.9 + - - +
126E GLN* 3.3 41.5 - - + +
127E VAL 3.5 3.4 - - - +
128E THR* 3.7 20.2 - - + +
136E THR* 5.2 4.5 - - - +
137E GLN* 1.3 89.1 + - - +
139E ILE* 1.3 56.5 + - - +
140E ASP* 4.3 10.5 - - - +
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Residues in contact with ILE 139 (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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5E ILE* 3.3 33.2 - - + +
7E ALA* 3.9 7.0 - - + -
10E THR* 3.5 27.8 - - + +
33E VAL* 4.3 11.7 - - + -
35E ILE* 4.0 22.0 - - + -
115E VAL* 4.8 4.0 - - + -
126E GLN* 3.4 2.8 - - - +
127E VAL* 2.7 58.8 + - + +
129E ALA 4.7 2.7 - - - +
137E GLN* 3.7 23.3 - - + +
138E VAL* 1.3 77.6 - - - +
140E ASP* 1.3 72.8 + - - +
141E THR* 3.8 1.4 + - - +
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Residues in contact with ASP 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E PRO* 4.3 15.1 - - - +
5E ILE 2.9 13.9 + - - +
6E ASP* 3.5 12.7 - - - +
7E ALA 3.0 23.2 + - - +
125E ASN 3.3 6.8 - - - +
126E GLN* 3.6 28.8 + - - +
138E VAL* 4.5 4.9 - - - +
139E ILE* 1.3 74.7 - - - +
141E THR* 1.3 60.1 + - - +
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Residues in contact with THR 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E ALA* 2.9 15.2 + - - -
8E ASP 3.2 8.1 + - - -
10E THR* 3.2 30.8 + - - +
125E ASN* 2.8 33.6 + - - +
127E VAL* 4.4 5.2 - - + -
139E ILE 4.3 7.2 - - - +
140E ASP* 1.3 75.7 - - - +
142E LYS* 1.3 65.4 + - - +
143E ASN 2.8 27.0 + - - +
144E ILE* 3.9 15.9 - - + -
314E ASN* 4.7 0.3 + - - -
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Residues in contact with LYS 142 (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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6E ASP* 5.5 6.1 - - - -
7E ALA 3.2 6.4 + - - +
8E ASP* 2.8 36.1 + - - +
125E ASN* 3.6 7.5 - - - +
141E THR* 1.3 73.9 + - - +
143E ASN* 1.3 76.3 + - - +
314E ASN* 3.0 25.1 + - - +
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Residues in contact with ASN 143 (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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8E ASP* 3.0 22.4 + - - +
9E VAL* 4.3 9.4 - - + +
10E THR 3.0 16.2 + - - -
30E PHE* 4.8 9.9 - - - -
141E THR* 2.8 21.2 + - - +
142E LYS* 1.3 91.9 - - - +
144E ILE* 1.3 64.5 + - - +
145E LEU 4.2 0.2 - - - -
314E ASN* 3.5 12.1 - - - +
316E TYR* 3.9 16.5 + - + -
342E MET* 3.9 28.6 - - - +
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Residues in contact with ILE 144 (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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10E THR 3.7 3.6 - - - +
12E ILE* 3.8 18.8 - - + -
121E ILE* 3.6 48.0 - - + -
123E GLY 3.8 5.4 - - - +
124E LYS 3.7 23.8 - - - +
125E ASN* 5.1 0.2 - - - -
126E GLN 4.3 2.9 - - - +
127E VAL* 3.9 19.5 - - + -
141E THR* 3.9 7.6 - - + -
143E ASN* 1.3 78.9 - - - +
145E LEU* 1.3 55.7 + - - +
146E ILE* 4.1 3.1 - - + -
314E ASN* 3.0 8.0 + - - +
315E ILE* 3.3 17.9 - - + -
316E TYR* 2.6 37.9 + - - +
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Residues in contact with LEU 145 (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 VAL* 5.0 4.9 - - + -
10E THR 3.0 13.4 + - - +
11E VAL* 3.4 18.7 - - + +
12E ILE* 2.9 27.5 + - - +
21E ALA* 3.6 30.3 - - + -
143E ASN 4.2 0.4 - - - -
144E ILE* 1.3 72.8 - - - +
146E ILE* 1.3 67.6 + - - +
147E ALA* 3.5 0.9 + - + -
316E TYR* 3.4 22.0 - - + +
318E ILE* 3.5 38.4 - - + -
335E GLY 4.8 0.7 - - - +
338E CYS* 4.0 14.1 - - - -
339E VAL* 4.2 13.5 - - + -
342E MET* 5.0 4.5 - - + -
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Residues in contact with ILE 146 (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 ILE* 4.3 7.0 - - + -
121E ILE* 3.9 22.7 - - + -
144E ILE* 4.4 2.9 - - + -
145E LEU* 1.3 71.9 - - - +
147E ALA* 1.3 61.6 + - - +
148E THR* 3.6 17.3 - - + +
287E LEU* 3.5 25.6 - - + -
289E LEU* 4.1 13.2 - - + -
302E ILE* 4.0 26.0 - - + -
310E THR* 4.7 6.5 - - + -
315E ILE* 3.8 25.1 - - + -
316E TYR 2.6 16.9 + - - +
317E ALA* 3.2 4.1 - - + +
318E ILE 3.1 27.0 + - - +
321E VAL* 3.9 3.6 - - + +
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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