Contacts of the helix formed by residues 142 - 154 (chain 3) in PDB entry 5LN3
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 CYS 142 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93 GLY 5.6 2.0 - - - -
103 ALA* 4.7 19.3 - - + -
1403 GLY 3.4 0.8 - - - -
1413 THR* 1.3 77.8 - - - +
1433 ALA* 1.3 62.6 + - - +
1443 GLU 3.2 3.4 - - - -
1453 GLN* 3.1 11.3 + - + +
1463 MET* 3.0 20.5 + - + +
1743 ALA* 5.0 1.8 - - - -
1773 ARG* 4.0 46.7 - - + +
1783 ASP* 4.5 14.6 - - - -
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Residues in contact with ALA 143 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652 GLU* 4.6 14.4 - - - +
682 VAL* 5.8 0.4 - - - -
1383 VAL* 3.7 25.6 - - + +
1393 SER* 5.0 1.3 - - - -
1403 GLY 3.6 19.2 + - - +
1413 THR 3.1 5.0 + - - +
1423 CYS* 1.3 76.7 - - - +
1443 GLU* 1.4 58.1 + - + +
1463 MET* 3.6 2.2 - - - +
1473 TYR* 2.8 32.2 + - - +
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Residues in contact with GLU 144 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652 GLU* 5.0 6.3 - - + +
662 GLY* 4.4 5.5 - - - -
672 MET* 4.1 21.0 + - - +
682 VAL* 4.1 34.9 - - + +
1413 THR 4.8 0.4 + - - -
1423 CYS 3.2 1.2 - - - -
1433 ALA* 1.4 77.0 - - + +
1453 GLN* 1.3 70.3 + - + +
1473 TYR* 3.5 4.3 - - - +
1483 GLY* 3.3 15.2 + - - -
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Residues in contact with GLN 145 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1423 CYS* 3.1 11.1 + - - +
1443 GLU* 1.3 83.4 - - + +
1463 MET* 1.4 55.7 + - - +
1483 GLY* 2.9 18.4 + - - -
1493 MET 3.0 9.9 + - - -
1773 ARG* 3.3 38.0 + - + +
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Residues in contact with MET 146 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 ALA* 3.9 18.4 - - + -
113 VAL 4.0 11.9 - - - +
123 MET* 3.8 17.3 - - + -
1383 VAL* 3.9 11.0 - - + -
1393 SER 3.8 22.4 - - - +
1423 CYS* 3.0 17.0 + - + +
1433 ALA* 3.2 8.9 + - - +
1453 GLN* 1.4 71.8 - - - +
1473 TYR* 1.3 59.3 + - - +
1493 MET* 3.2 24.4 + - + +
1503 CYS* 3.0 27.9 + - - +
1713 MET* 5.1 9.9 - - + -
1743 ALA* 3.5 31.9 - - + -
1773 ARG* 3.3 19.7 - - - +
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Residues in contact with TYR 147 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682 VAL* 3.8 23.3 - - + -
692 VAL* 2.9 40.4 + - + +
702 ALA* 5.0 4.9 - - - -
722 LYS* 3.5 18.9 - - - +
1363 PHE* 4.1 24.5 - + - -
1383 VAL* 4.1 10.5 - - + +
1433 ALA 2.8 16.7 + - - +
1443 GLU* 3.5 6.5 - - - +
1463 MET* 1.3 74.0 - - - +
1483 GLY* 1.4 61.1 + - - +
1503 CYS* 3.1 16.9 - - - -
1513 GLU* 3.0 67.0 + - + +
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Residues in contact with GLY 148 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682 VAL* 6.2 0.2 - - - -
1443 GLU 3.3 6.9 + - - -
1453 GLN* 2.9 9.3 + - - -
1473 TYR* 1.4 82.5 - - - +
1493 MET* 1.4 62.1 + - - +
1513 GLU* 3.5 7.7 + - - +
1523 SER* 3.3 24.8 + - - -
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Residues in contact with MET 149 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123 MET* 4.3 6.5 - - + -
1453 GLN 3.0 7.7 + - - -
1463 MET* 3.2 33.6 + - + +
1473 TYR 3.2 0.4 - - - -
1483 GLY* 1.4 75.3 - - - +
1503 CYS* 1.4 59.7 + - - +
1523 SER* 3.3 4.9 + - - -
1533 LEU* 2.9 45.2 + - + +
1703 ALA* 3.4 48.0 - - + +
1733 ASN* 4.2 12.3 - - - +
1773 ARG* 3.4 39.5 - - - +
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Residues in contact with CYS 150 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123 MET* 4.6 9.2 - - + -
143 MET* 3.6 26.6 - - + +
1363 PHE* 3.6 37.8 - - + -
1383 VAL* 3.9 10.5 - - - -
1463 MET 3.0 11.4 + - - +
1473 TYR* 3.1 36.3 + - - -
1493 MET* 1.4 80.8 - - - +
1513 GLU* 1.4 61.6 + - - +
1533 LEU* 5.1 0.4 - - - -
1543 TRP* 3.4 25.8 + - - +
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Residues in contact with GLU 151 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722 LYS* 3.7 16.5 + - - -
2382 LYS* 3.3 52.5 + - - +
2392 GLY* 5.9 3.4 - - - -
2402 THR 4.9 4.7 - - - +
1363 PHE* 5.4 6.7 - - + -
1473 TYR* 3.0 63.7 + - + +
1483 GLY* 4.0 7.0 - - - +
1503 CYS* 1.4 75.8 - - - +
1523 SER* 1.3 63.4 + - - +
1543 TRP* 4.4 7.2 + - - +
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Residues in contact with SER 152 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2402 THR 5.0 10.3 - - - +
2412 ARG* 5.7 1.7 - - - -
2422 LEU* 4.2 27.9 + - - +
2432 GLY 5.2 6.2 - - - +
2442 ARG* 5.5 0.3 - - - +
1483 GLY 3.3 11.7 + - - -
1493 MET* 3.3 8.9 + - - -
1503 CYS 3.2 0.4 - - - -
1513 GLU* 1.3 79.8 - - - +
1533 LEU* 1.4 72.6 + - - +
1543 TRP 3.8 5.2 - - - +
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Residues in contact with LEU 153 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2442 ARG* 3.2 49.6 + - + +
143 MET* 5.3 3.1 - - + -
1493 MET* 2.9 40.2 + - + +
1503 CYS* 4.7 2.9 - - - +
1523 SER* 1.4 77.0 - - - +
1543 TRP* 1.3 66.7 + - - +
1553 GLU* 4.0 2.9 - - - +
1663 THR* 4.2 22.2 - - + +
1693 GLN* 5.2 12.8 - - + -
1703 ALA* 4.3 28.5 - - + +
1733 ASN* 5.3 4.0 - - - +
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Residues in contact with TRP 154 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2382 LYS* 4.5 25.4 - - + -
2442 ARG* 5.4 0.2 - - - +
143 MET* 4.9 13.3 - - + +
153 LYS* 5.0 6.4 + - - +
1353 ASP* 3.6 56.5 + - + +
1363 PHE* 5.2 7.9 - + + -
1503 CYS 3.4 17.5 + - - +
1513 GLU* 4.7 5.0 - - - +
1523 SER 3.4 6.8 - - - +
1533 LEU* 1.3 84.1 - - - +
1553 GLU* 1.4 77.1 + - - +
1563 PRO* 3.7 31.6 + - + +
1583 MET* 5.1 10.2 - - + +
1663 THR* 5.0 7.3 - - - +
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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