Contacts of the helix formed by residues 147 - 159 (chain 5) in PDB entry 2JD6
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 SER 147 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1445 ALA 3.5 11.7 + - - +
1455 LYS 3.4 4.8 + - - -
1465 ASP* 1.3 77.1 - - - +
1485 PRO* 1.3 63.7 - - - +
1495 GLN* 3.4 11.8 + - - -
1505 ILE* 3.1 44.7 + - - +
1515 LEU* 3.3 19.8 + - - +
149J GLN* 3.6 11.7 + - - -
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Residues in contact with PRO 148 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1465 ASP* 3.8 7.9 - - - +
1475 SER* 1.3 86.0 - - - +
1495 GLN* 1.3 68.0 + - - +
1515 LEU* 3.2 5.8 + - + +
1525 PHE* 2.9 30.5 + - - +
143L PHE* 3.7 38.1 - - + +
147L SER* 6.4 1.1 - - - -
150L ILE* 4.0 12.8 - - + -
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Residues in contact with GLN 149 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475 SER* 3.4 13.2 + - - +
1485 PRO* 1.3 89.9 - - - +
1505 ILE* 1.3 62.5 + - - +
1525 PHE* 3.4 6.2 - - - +
1535 MET* 3.1 30.5 + - + +
149J GLN* 3.5 21.7 + - + +
147L SER* 3.2 22.4 + - - -
149L GLN* 3.4 34.0 - - + +
150L ILE* 3.7 25.1 - - + -
153L MET* 4.5 9.7 - - + +
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Residues in contact with ILE 150 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1405 LYS 4.9 2.5 - - - +
1435 PHE* 4.4 8.3 - - + +
1445 ALA* 3.3 31.6 - - + -
1475 SER* 3.1 25.6 + - - +
1495 GLN* 1.3 73.7 - - - +
1515 LEU* 1.3 60.6 + - - +
1535 MET* 3.1 8.0 + - - +
1545 LEU* 2.8 32.5 + - + +
148J PRO* 4.0 17.3 - - + +
149J GLN* 3.6 39.7 - - + +
152J PHE* 4.2 28.5 - - + -
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Residues in contact with LEU 151 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345 LEU* 6.3 0.2 - - + -
365 LEU* 4.4 14.8 - - + -
395 PHE* 3.7 28.5 - - + -
835 PRO* 4.4 23.8 - - + -
1415 LEU* 3.9 17.7 - - + -
1445 ALA* 4.6 6.1 - - + +
1475 SER 3.3 11.7 + - - +
1485 PRO* 3.2 10.2 + - + +
1505 ILE* 1.3 80.0 - - - +
1525 PHE* 1.3 57.0 + - - +
1545 LEU* 3.3 5.9 + - - +
1555 ASP* 2.9 30.9 + - - +
143L PHE* 4.2 19.7 - - + -
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Residues in contact with PHE 152 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365 LEU* 5.5 2.2 - - - -
1485 PRO 2.9 14.1 + - - +
1495 GLN* 3.4 11.9 - - - +
1515 LEU* 1.3 74.6 - - - +
1535 MET* 1.3 61.8 + - + +
1555 ASP* 3.1 13.0 - - - +
1565 LYS* 3.1 28.2 + - + +
140L LYS* 4.5 18.6 - - + -
143L PHE* 4.5 17.4 - + + -
150L ILE* 4.4 22.4 - - + -
153L MET* 3.9 45.5 - - + -
154L LEU* 4.8 7.4 - - + -
157L GLU* 3.2 38.4 - - - -
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Residues in contact with MET 153 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1495 GLN* 3.1 21.8 + - + +
1505 ILE* 3.1 9.2 + - - +
1525 PHE* 1.3 79.9 - - + +
1545 LEU* 1.3 66.0 + - - +
1565 LYS* 3.3 8.9 + - - +
1575 GLU* 3.0 26.2 + - - +
149J GLN* 5.2 4.9 - - + +
152J PHE* 3.9 36.8 - - + -
153J MET* 3.6 30.5 - - + -
153L MET* 3.8 29.4 - - + -
153Y MET* 4.1 10.1 - - + -
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Residues in contact with LEU 154 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395 PHE* 4.2 8.3 - - + -
1375 ILE* 4.7 5.4 - - + +
1405 LYS* 4.1 46.9 - - + +
1415 LEU* 3.6 35.7 - - + -
1445 ALA* 5.3 0.9 - - + -
1505 ILE* 2.8 24.5 + - + +
1515 LEU* 3.4 7.9 - - + +
1535 MET* 1.3 69.4 - - - +
1555 ASP* 1.3 65.6 + - - +
1575 GLU* 3.0 16.9 + - - +
1585 LEU* 2.9 44.4 + - + +
152J PHE* 4.6 9.3 - - + -
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Residues in contact with ASP 155 (chain 5).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355 GLY 5.2 1.0 - - - +
365 LEU* 3.3 29.3 - - + +
375 GLU* 4.5 2.1 + - - +
385 GLY* 3.1 33.8 + - - -
395 PHE* 3.3 25.0 + - + -
1515 LEU 2.9 14.0 + - - +
1525 PHE* 3.1 14.0 - - - +
1545 LEU* 1.3 76.3 - - - +
1565 LYS* 1.3 65.6 + - - +
1585 LEU* 3.3 1.3 + - - +
1595 SER* 3.1 17.2 + - - -
140L LYS* 5.7 2.6 + - - -
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Residues in contact with LYS 156 (chain 5).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1525 PHE* 3.1 17.1 + - + +
1535 MET* 3.6 11.0 - - - +
1545 LEU 3.3 0.2 - - - -
1555 ASP* 1.3 77.6 + - - +
1575 GLU* 1.3 66.1 + - + +
1595 SER* 2.9 30.0 + - - +
1605 ALA* 4.0 0.9 + - - +
156J LYS* 5.3 9.7 - - - +
157L GLU* 4.8 15.5 - - - +
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Residues in contact with GLU 157 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1405 LYS* 3.0 27.3 + - - -
1535 MET 3.0 10.9 + - - +
1545 LEU* 3.0 16.1 + - + +
1565 LYS* 1.3 77.6 - - + +
1585 LEU* 1.3 67.4 + - + +
1605 ALA* 2.9 25.6 + - - +
152J PHE* 3.1 31.4 - - - -
156J LYS* 4.1 25.9 - - - +
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Residues in contact with LEU 158 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385 GLY 3.9 15.1 - - - +
395 PHE* 3.3 51.6 - - + -
425 TRP* 3.9 18.4 - - + -
875 PHE* 5.0 0.9 - - + -
1375 ILE* 3.6 39.5 - - + -
1545 LEU* 2.9 23.5 + - + +
1555 ASP 3.7 4.9 - - - +
1575 GLU* 1.3 76.9 - - + +
1595 SER* 1.3 57.6 + - - +
1605 ALA 2.7 7.6 + - - -
1615 ARG* 2.9 23.8 + - - +
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Residues in contact with SER 159 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375 GLU 5.4 0.2 - - - -
385 GLY* 3.8 22.8 - - - -
415 ASN* 5.5 7.2 + - - +
1555 ASP* 3.1 6.7 + - - -
1565 LYS* 2.9 25.7 + - - +
1585 LEU* 1.3 74.7 - - - +
1605 ALA* 1.3 58.2 + - - +
1615 ARG 3.1 9.5 + - - +
1625 ALA* 4.6 5.7 + - - +
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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