Contacts of the helix formed by residues 144 - 155 (chain 9) in PDB entry 2J28
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 ALA 144 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1149 THR* 5.3 2.3 + - - -
1369 SER* 2.8 22.2 - - - +
1389 ASP* 3.8 19.7 - - + +
1399 VAL* 6.1 0.4 - - + -
1419 ARG* 3.9 7.4 - - - +
1429 PRO 2.2 27.2 + - - +
1439 ALA* 1.3 78.1 - - - +
1459 ILE* 1.3 72.7 - - + +
1469 LYS* 4.4 0.8 - - - +
1479 GLN* 4.4 0.5 - - - +
1489 LEU* 3.2 15.6 - - - +
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Residues in contact with ILE 145 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1369 SER* 3.6 3.6 - - - +
1449 ALA* 1.3 87.2 - - + +
1469 LYS* 1.3 73.2 + - - +
1489 LEU* 2.5 20.9 + - - +
1499 GLU* 2.6 31.7 + - + +
1599 PHE* 2.8 33.0 - - + -
1619 PRO* 1.8 61.5 - - + -
1629 SER 4.0 2.0 - - - +
1639 ASP* 4.3 18.6 - - - +
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Residues in contact with LYS 146 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1429 PRO* 5.9 2.2 - - - +
1439 ALA* 3.4 36.9 - - + +
1449 ALA 4.4 0.4 - - - +
1459 ILE* 1.3 92.4 - - - +
1479 GLN* 1.3 65.2 + - - +
1489 LEU 2.4 3.8 + - - -
1499 GLU* 2.4 38.1 + - - +
1509 THR* 3.3 4.0 + - - -
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Residues in contact with GLN 147 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1149 THR* 3.2 31.4 + - - +
1159 THR* 3.7 26.9 - - - +
1419 ARG* 5.3 1.0 + - - -
1439 ALA* 3.9 23.1 - - + +
1459 ILE 3.1 0.2 + - - -
1469 LYS* 1.3 85.7 - - + +
1489 LEU* 1.3 70.2 + - - +
1509 THR* 3.1 13.2 + - - -
1519 LEU* 3.0 16.8 - - + +
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Residues in contact with LEU 148 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1149 THR* 3.9 21.1 - - - +
1349 VAL* 5.0 6.1 - - + -
1359 VAL 5.4 1.3 - - - -
1369 SER* 4.3 19.7 - - - +
1449 ALA* 3.2 9.2 - - - +
1459 ILE* 2.5 32.3 + - + +
1469 LYS 2.4 5.3 + - - -
1479 GLN* 1.3 76.4 + - - +
1499 GLU* 1.3 83.0 + - - +
1509 THR 2.3 18.6 + - - -
1519 LEU* 2.6 38.4 - - + +
1529 ALA* 4.6 2.9 - - + -
1599 PHE* 4.0 24.7 - - + -
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Residues in contact with GLU 149 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459 ILE* 2.9 22.9 - - + +
1469 LYS* 2.4 31.1 + - - +
1489 LEU* 1.3 82.2 - - - +
1509 THR* 1.3 69.7 - - - +
1529 ALA* 2.7 18.6 - - - +
1539 GLU* 3.7 9.4 + - - +
1599 PHE* 2.7 35.4 - - + -
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Residues in contact with THR 150 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1469 LYS 3.3 2.3 + - - -
1479 GLN* 3.1 13.9 + - - -
1489 LEU 2.3 8.5 + - - -
1499 GLU* 1.3 84.4 - - - +
1519 LEU* 1.3 91.7 + - + +
1529 ALA 2.6 0.2 + - - -
1539 GLU* 2.9 12.1 + - - +
1549 GLN* 3.4 23.8 + - + +
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Residues in contact with LEU 151 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1149 THR* 5.6 2.2 - - - +
1159 THR* 5.4 6.3 - - - +
1189 GLY* 4.7 21.1 - - - +
1479 GLN* 3.0 19.5 - - + +
1489 LEU* 2.6 37.2 - - + +
1509 THR* 1.3 83.4 - - + +
1529 ALA* 1.3 58.6 + - - +
1549 GLN* 2.5 49.0 + - - +
1559 VAL* 2.5 22.7 + - + +
2799 THR* 5.5 5.6 - - + -
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Residues in contact with ALA 152 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349 VAL* 5.3 2.0 - - + -
1489 LEU* 4.6 3.4 - - + -
1499 GLU* 2.7 15.0 + - - +
1509 THR 2.6 3.0 + - - -
1519 LEU* 1.3 77.1 - - - +
1539 GLU* 1.3 49.4 + - - +
1559 VAL* 3.0 7.6 - - - +
1579 VAL* 2.4 51.9 + - - +
1599 PHE* 2.4 47.1 - - + -
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Residues in contact with GLU 153 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499 GLU* 4.9 8.6 - - - +
1509 THR 2.9 8.4 + - - +
1519 LEU 2.6 2.2 + - - -
1529 ALA* 1.3 73.7 - - - +
1549 GLN* 1.3 54.1 + - - +
1559 VAL 2.4 18.8 + - - -
1569 GLY* 2.4 17.2 + - - +
1579 VAL 4.3 2.2 - - - +
1589 ASP* 4.7 13.0 - - - +
1599 PHE* 4.7 14.2 - - + -
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Residues in contact with GLN 154 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1229 LYS* 4.5 2.3 + - - -
1509 THR* 3.4 16.5 + - + +
1519 LEU* 2.5 31.8 + - - +
1539 GLU* 1.3 72.7 - - - +
1559 VAL* 1.3 79.4 + - - +
2799 THR* 4.3 16.9 - - - +
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Residues in contact with VAL 155 (chain 9).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1229 LYS* 3.3 48.2 + - + +
1259 ARG* 5.5 3.6 - - - +
1519 LEU* 2.5 31.1 + - + +
1529 ALA* 3.0 17.3 - - - +
1539 GLU 2.4 14.3 + - - -
1549 GLN* 1.3 93.8 - - - +
1569 GLY* 1.3 57.6 + - - +
1579 VAL* 3.6 20.2 - - + +
2799 THR* 4.9 5.4 - - + -
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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