Contacts of the strand formed by residues 136 - 146 (chain D) in PDB entry 1ZMC
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D ALA 3.3 12.5 - - - +
2D ASP* 3.3 28.0 + - - +
128D THR* 4.6 11.7 - - + -
129D ALA 3.2 6.7 - - - -
130D THR* 3.5 18.6 - - + +
131D LYS* 4.3 4.1 + - - +
134D GLY 3.5 10.3 - - - +
135D GLY* 1.3 80.0 - - - +
137D GLN* 1.3 61.8 + - - +
138D VAL* 5.4 5.0 - - - +
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Residues in contact with GLN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D ALA* 3.6 27.9 + - - +
2D ASP* 5.6 0.4 - - - +
3D GLN* 3.2 28.0 + - - +
4D PRO* 3.9 0.4 - - - +
5D ILE* 3.6 11.0 - - - +
115D VAL* 4.1 31.0 - - + -
127D VAL 3.9 0.5 - - - +
128D THR* 3.5 1.7 - - - -
129D ALA* 2.7 41.4 + - - +
131D LYS* 3.8 17.0 - - - +
136D THR* 1.3 75.9 - - - +
138D VAL* 1.3 95.2 + - - +
139D ILE* 4.4 5.1 - - + +
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Residues in contact with VAL 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN 5.6 0.2 - - - -
4D PRO* 4.4 17.5 - - + -
5D ILE* 3.0 15.5 + - - +
126D GLN* 3.2 37.9 - - + +
127D VAL 3.7 2.9 - - - +
128D THR* 4.4 14.1 - - + +
136D THR* 5.4 5.2 - - - +
137D GLN* 1.3 102.1 + - - +
139D ILE* 1.3 65.8 + - - +
140D ASP* 4.4 8.1 - - - +
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Residues in contact with ILE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 3.3 26.7 - - + +
7D ALA* 4.1 15.3 - - + -
10D THR* 3.5 25.8 - - + +
33D VAL* 4.1 13.7 - - + -
35D ILE* 3.3 39.3 - - + -
115D VAL* 4.5 6.3 - - + -
126D GLN* 3.3 4.0 - - - -
127D VAL* 2.8 49.3 + - + +
129D ALA* 4.6 4.7 - - + -
137D GLN* 4.4 10.8 - - + +
138D VAL* 1.3 78.7 - - - +
140D ASP* 1.3 61.4 + - - +
141D THR* 3.6 1.9 + - - +
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Residues in contact with ASP 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PRO* 3.9 20.6 - - - +
5D ILE 2.8 10.9 + - - +
6D ASP* 3.2 15.9 - - - +
7D ALA* 2.8 24.1 + - - +
125D ASN 3.4 7.0 - - - +
126D GLN* 3.3 31.5 - - - +
138D VAL* 4.1 2.6 - - - +
139D ILE* 1.3 73.7 - - - +
141D THR* 1.3 58.5 + - - +
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Residues in contact with THR 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ALA* 2.9 14.0 + - - -
8D ASP 3.3 9.7 + - - -
9D VAL 3.5 0.3 + - - -
10D THR* 3.0 27.0 + - - +
124D LYS 4.9 0.3 - - - +
125D ASN* 3.0 35.2 + - - +
127D VAL* 4.4 2.9 - - + -
139D ILE* 4.4 7.0 - - - +
140D ASP* 1.3 75.9 - - - +
142D LYS* 1.3 62.2 + - - +
143D ASN 2.8 27.9 + - - +
144D ILE* 3.7 19.7 - - + -
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Residues in contact with LYS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ALA 3.1 7.8 + - - +
8D ASP* 2.5 39.5 + - + +
125D ASN* 3.2 10.1 + - - +
141D THR* 1.3 73.0 + - - +
143D ASN* 1.3 73.6 + - - +
314D ASN* 3.0 24.0 + - - +
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Residues in contact with ASN 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ASP* 2.8 25.2 + - - +
9D VAL* 4.2 16.4 - - + +
10D THR 3.1 12.0 + - - -
30D PHE* 5.2 5.3 - - - -
141D THR* 2.8 26.0 + - - +
142D LYS* 1.3 93.5 - - - +
144D ILE* 1.3 66.4 + - - +
314D ASN* 3.5 21.1 - - - +
316D TYR* 4.0 14.7 + - + -
342D MET* 4.4 18.5 - - - +
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Residues in contact with ILE 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D THR 3.5 4.9 - - - +
12D ILE* 4.0 19.5 - - + -
121D ILE* 4.0 40.2 - - + -
123D GLY 4.0 3.4 - - - +
124D LYS 3.8 21.5 - - - +
126D GLN 4.1 4.5 - - - +
127D VAL* 3.6 27.4 - - + -
141D THR* 3.7 6.5 - - + -
143D ASN* 1.3 82.8 - - - +
145D LEU* 1.3 61.5 + - - +
146D ILE* 4.4 4.7 - - + -
314D ASN 3.1 6.2 + - - +
315D ILE* 3.3 16.4 - - + -
316D TYR* 2.7 35.0 + - - -
342D MET* 5.7 0.2 - - - -
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Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.7 3.1 - - + -
10D THR 2.8 13.7 + - - +
11D VAL* 3.3 20.6 - - + +
12D ILE* 2.8 32.0 + - - -
21D ALA* 3.6 31.6 - - + -
144D ILE* 1.3 74.6 - - - +
146D ILE* 1.3 62.9 + - - +
147D ALA* 3.5 1.0 + - + -
316D TYR* 3.5 24.5 - - + +
318D ILE* 3.9 32.3 - - + -
335D GLY 5.0 0.9 - - - +
338D CYS* 4.0 5.8 - - - -
339D VAL* 4.2 15.7 - - + -
342D MET* 4.5 8.7 - - + -
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Residues in contact with ILE 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ILE* 4.3 6.1 - - + -
121D ILE* 4.1 5.2 - - + -
144D ILE* 4.4 8.3 - - + -
145D LEU* 1.3 72.5 - - - +
147D ALA* 1.3 60.7 + - - +
148D THR* 3.4 25.4 - - + +
287D LEU* 3.4 27.8 - - + -
289D LEU* 4.0 15.0 - - + -
294D ILE* 5.3 0.2 - - + -
302D ILE* 3.7 28.3 - - + -
310D THR* 4.8 3.8 - - + -
315D ILE* 4.0 22.7 - - + -
316D TYR 2.7 18.7 + - - +
317D ALA* 3.1 6.5 - - + +
318D ILE 3.0 28.1 + - - +
321D VAL* 4.3 2.7 - - + -
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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