Contacts of the strand formed by residues 136 - 146 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H THR* 3.6 25.7 - - + +
129H ALA 3.4 4.5 - - - -
130H THR* 3.9 11.4 + - - +
131H LYS* 3.5 12.8 + - - +
134H GLY 3.6 7.1 + - - -
135H GLY* 1.3 77.5 + - - -
137H GLN* 1.3 71.1 + - - +
138H VAL* 4.1 9.6 - - + -
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Residues in contact with GLN 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H PRO* 3.2 26.1 - - - +
5H ILE* 4.2 23.2 - - + +
115H VAL* 4.3 20.2 - - + -
129H ALA 2.8 36.0 + - - +
131H LYS* 4.5 10.5 - - + +
136H THR* 1.3 80.1 - - - +
138H VAL* 1.3 89.3 + - - +
139H ILE* 3.4 17.1 - - + +
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Residues in contact with VAL 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H PRO* 4.4 16.4 - - + +
5H ILE 3.3 13.7 + - - +
126H GLN* 4.7 18.6 - - + +
127H VAL 3.4 3.8 - - - +
128H THR* 3.4 28.0 - - + +
136H THR* 4.1 9.4 - - + -
137H GLN* 1.3 92.2 + - - +
139H ILE* 1.3 62.0 + - - +
140H ASP* 4.9 10.5 - - - +
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Residues in contact with ILE 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ILE* 3.1 35.7 - - + +
7H ALA* 4.2 4.5 - - + -
10H THR* 3.5 27.8 - - + +
33H VAL* 4.2 18.4 - - + -
35H ILE* 4.2 19.5 - - + -
115H VAL* 4.7 3.8 - - + -
126H GLN* 3.3 5.8 - - - +
127H VAL* 2.7 45.2 + - + +
129H ALA* 4.7 3.4 - - + +
137H GLN* 3.4 21.1 - - + +
138H VAL* 1.3 79.1 - - - +
140H ASP* 1.3 71.7 + - - +
141H THR* 3.8 1.4 + - - +
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Residues in contact with ASP 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H PRO* 5.5 4.5 - - - +
5H ILE 2.9 12.0 + - - +
6H ASP* 2.9 17.2 - - + +
7H ALA 2.8 23.9 + - - +
125H ASN* 3.3 6.7 - - + +
126H GLN* 3.7 27.4 + - - +
138H VAL* 4.9 9.9 - - - +
139H ILE* 1.3 73.1 - - - +
141H THR* 1.3 59.3 + - - +
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Residues in contact with THR 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H ALA 3.0 12.9 + - - -
8H ASP 3.5 3.5 + - - -
9H VAL 3.7 0.2 + - - -
10H THR* 3.0 36.5 + - + +
125H ASN* 2.8 41.5 + - - +
127H VAL* 4.4 4.5 - - + -
139H ILE* 4.2 8.1 - - - +
140H ASP* 1.3 75.5 - - - +
142H LYS* 1.3 64.7 + - - +
143H ASN 2.8 25.8 + - - +
144H ILE* 3.9 16.8 - - + -
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Residues in contact with LYS 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7H ALA 3.1 8.2 + - - +
8H ASP* 3.1 36.8 - - + +
30H PHE* 6.4 0.7 - - + -
125H ASN* 3.3 8.3 - - - +
141H THR* 1.3 74.3 + - - +
143H ASN* 1.3 71.5 + - - +
314H ASN* 2.9 30.0 + - - +
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Residues in contact with ASN 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H ASP* 2.9 18.1 + - - +
9H VAL* 3.5 9.8 - - + +
10H THR 2.9 15.9 + - - -
30H PHE* 5.2 6.1 - - - -
141H THR* 2.8 18.1 + - - +
142H LYS* 1.3 90.6 - - - +
144H ILE* 1.3 63.3 + - - +
314H ASN* 3.3 15.0 - - - +
316H TYR* 3.7 19.3 + - + -
342H MET* 4.0 30.7 - - + +
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Residues in contact with ILE 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H THR 3.5 6.1 - - - +
12H ILE* 3.8 19.1 - - + -
121H ILE* 3.6 47.8 - - + -
123H GLY 4.0 3.1 - - - +
124H LYS 3.6 23.8 - - - +
125H ASN* 5.1 0.4 - - - -
126H GLN 4.2 2.9 - - - +
127H VAL* 3.8 13.7 - - + -
141H THR* 3.9 16.2 - - + -
143H ASN* 1.3 77.4 - - - +
145H LEU* 1.3 59.9 + - - +
146H ILE* 4.5 0.7 - - + -
314H ASN* 2.9 7.7 + - - +
315H ILE* 3.3 17.8 - - + -
316H TYR* 2.7 36.8 + - - +
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Residues in contact with LEU 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 4.8 2.5 - - + -
10H THR 2.8 14.4 + - - +
11H VAL* 3.5 19.4 - - + +
12H ILE* 2.9 28.4 + - - +
21H ALA* 3.5 32.5 - - + -
143H ASN 4.2 0.2 - - - -
144H ILE* 1.3 74.8 - - - +
146H ILE* 1.3 66.2 + - - +
147H ALA 3.5 0.3 + - - -
316H TYR* 3.5 24.2 - - + -
317H ALA 3.9 1.1 - - - +
318H ILE* 3.9 33.4 - - + -
338H CYS* 4.0 7.2 - - + -
339H VAL* 4.1 17.0 - - + -
342H MET* 4.3 8.7 - - + -
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Residues in contact with ILE 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ILE* 4.3 6.5 - - + -
121H ILE* 3.8 30.7 - - + -
144H ILE* 4.5 2.5 - - + -
145H LEU* 1.3 73.8 - - - +
147H ALA* 1.3 60.1 + - - +
148H THR* 3.5 25.1 - - + +
287H LEU* 3.6 15.3 - - + -
289H LEU* 3.9 21.1 - - + -
294H ILE* 5.1 0.2 - - + -
302H ILE* 3.8 21.1 - - + -
310H THR* 4.7 4.9 - - + -
315H ILE* 3.8 15.7 - - + -
316H TYR 2.5 17.7 + - - +
317H ALA* 3.0 24.4 - - + +
318H ILE 3.0 10.0 + - - +
321H VAL* 3.8 2.6 - - + +
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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