Contacts of the strand formed by residues 120 - 135 (chain 1) in PDB entry 1D3I
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 120 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1191 PHE* 3.8 28.3 - - - +
1211 TYR* 3.9 27.8 - - - +
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Residues in contact with TYR 121 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1201 THR* 3.9 27.6 - - - +
1221 VAL* 3.8 28.7 - - - +
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Residues in contact with VAL 122 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211 TYR* 3.8 28.3 - - - +
1231 ARG* 3.8 28.7 - - - +
2521 ALA* 4.4 20.9 - - - +
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Residues in contact with ARG 123 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221 VAL* 3.8 28.7 - - - +
1241 PHE* 3.8 28.9 - - - +
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Residues in contact with PHE 124 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1231 ARG* 3.8 28.5 - - - +
1251 ASP* 3.8 28.7 - - - +
2501 VAL* 4.5 19.7 - - - +
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Residues in contact with ASP 125 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241 PHE* 3.8 28.3 - - - +
1261 SER* 3.8 28.9 - - - +
1891 PRO* 4.6 12.3 - - - -
1901 TYR* 4.6 18.8 - - - +
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Residues in contact with SER 126 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1251 ASP* 3.8 29.8 - - - +
1271 GLU* 3.7 29.8 - - - +
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Residues in contact with GLU 127 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261 SER* 3.7 30.7 - - - +
1281 TYR* 3.9 28.5 - - - +
1871 SER* 4.0 22.4 - - - +
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Residues in contact with TYR 128 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271 GLU* 3.9 28.0 - - - +
1291 THR* 3.8 28.9 - - - +
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Residues in contact with THR 129 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1281 TYR* 3.8 28.9 - - - +
1301 ILE* 3.8 28.7 - - - +
1851 ARG* 4.5 19.1 - - - +
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Residues in contact with ILE 130 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1291 THR* 3.8 28.9 - - - +
1311 LEU* 3.8 28.5 - - - +
2431 VAL* 4.6 20.0 - - - +
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Residues in contact with LEU 131 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1301 ILE* 3.8 28.7 - - - +
1321 ALA* 3.9 28.7 - - - +
1831 THR* 4.5 18.2 - - - +
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Residues in contact with ALA 132 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1311 LEU* 3.9 28.7 - - - +
1331 THR* 3.9 28.7 - - - +
2411 ILE* 4.6 18.8 - - - +
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Residues in contact with THR 133 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1321 ALA* 3.9 28.3 - - - +
1341 ALA* 3.8 28.7 - - - +
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Residues in contact with ALA 134 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1331 THR* 3.8 29.2 - - - +
1351 SER* 3.8 29.6 - - - +
2391 VAL* 4.4 20.4 - - - +
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Residues in contact with SER 135 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341 ALA* 3.8 29.6 - - - +
1361 GLN* 3.8 28.5 - - - +
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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
------------------------------------------------------------
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