Contacts of the helix formed by residues 136 - 148 (chain 1) in PDB entry 3SDI
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 GLY 136 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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01 THR* 5.8 1.3 - - - -
11 SER* 4.5 4.0 - - - -
451 SER* 5.3 0.2 + - - -
1351 THR* 1.3 73.7 - - - +
1371 PHE* 1.3 58.2 + - - -
1391 ALA* 3.0 25.7 + - - +
1401 HIS* 3.5 13.1 + - - -
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Residues in contact with PHE 137 (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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01 THR* 4.9 4.1 + - - -
11 SER* 3.4 10.8 + - - +
1361 GLY* 1.3 67.9 - - - -
1381 GLY* 1.3 61.2 + - - +
1401 HIS* 2.9 25.8 + - - +
1411 MET* 3.0 22.6 + - + +
1751 LEU* 4.1 11.2 - - + -
1781 ARG 4.9 1.3 - - - -
1791 ASP* 3.5 28.9 - - + +
132H LEU* 3.7 32.3 - - + -
24N ALA* 3.5 31.2 - - + -
25N TYR* 3.5 39.9 - + + -
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Residues in contact with GLY 138 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11 SER* 2.7 24.0 + - - -
31 ILE* 4.0 2.0 - - - -
1341 ALA* 3.3 14.4 - - - +
1351 THR 3.1 7.9 + - - -
1371 PHE* 1.3 73.4 - - - +
1391 ALA* 1.3 62.4 + - - +
1421 ALA* 2.9 32.5 + - - +
1431 ASN 3.0 10.2 + - - -
1751 LEU* 4.2 4.5 - - - +
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Residues in contact with ALA 139 (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* 3.6 18.6 - - - +
1351 THR* 3.6 3.6 + - - -
1361 GLY 3.0 16.3 + - - +
1381 GLY* 1.3 76.5 - - - +
1401 HIS* 1.3 67.5 + - + +
1431 ASN* 3.4 33.5 + - - +
1441 PRO* 3.8 1.6 - - - +
1471 ARG* 5.2 1.2 + - - -
25Z SER* 4.3 17.4 + - - +
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Residues in contact with HIS 140 (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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1361 GLY 3.5 19.1 + - - -
1371 PHE* 2.9 14.3 + + - +
1391 ALA* 1.3 82.8 - - + +
1411 MET* 1.3 58.7 + - - +
1441 PRO* 3.1 18.6 - - - +
132H LEU* 3.6 32.9 - - + +
133H ALA* 3.7 15.1 + - - +
24Z TYR 6.1 0.7 - - - -
25Z SER* 3.4 27.0 + - - -
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Residues in contact with MET 141 (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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1371 PHE* 3.0 16.3 + - + +
1401 HIS* 1.3 80.5 - - - +
1421 ALA* 1.3 65.8 + - - +
1441 PRO* 3.2 9.7 - - - +
1451 LEU* 3.6 9.0 - - - +
1741 VAL* 3.7 16.6 - - + +
1751 LEU* 3.9 17.5 - - + -
1781 ARG* 3.6 42.2 - - + -
1791 ASP* 6.3 0.2 - - - -
132H LEU* 3.4 34.1 - - + +
135H MET* 4.0 8.3 - - + -
136H ALA* 3.4 37.6 - - + +
25N TYR* 4.3 11.2 - - + -
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Residues in contact with ALA 142 (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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31 ILE* 3.6 31.0 - - + -
1341 ALA* 4.5 1.1 - - + -
1381 GLY* 2.9 20.6 + - - +
1411 MET* 1.3 71.8 - - - +
1431 ASN* 1.3 68.4 + - - +
1451 LEU* 3.0 3.9 + - - +
1461 LEU* 2.9 29.1 + - + +
1711 ALA* 4.1 24.9 - - + -
1751 LEU* 4.4 5.7 - - + +
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Residues in contact with ASN 143 (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 THR* 2.8 28.2 + - - -
1331 LEU* 3.8 11.9 + - - +
1341 ALA* 3.8 18.4 + - - +
1381 GLY 3.0 8.1 + - - -
1391 ALA* 3.4 29.8 + - - +
1421 ALA* 1.3 75.4 - - - +
1441 PRO* 1.4 63.1 - - + +
1461 LEU* 4.6 2.6 - - - +
1471 ARG* 2.8 67.8 + - - +
26Z ILE 4.5 4.9 + - - -
27Z ASN* 5.7 1.2 + - - +
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Residues in contact with PRO 144 (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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1391 ALA 3.8 1.3 - - - +
1401 HIS 3.1 27.6 - - - +
1411 MET 3.2 13.2 - - - +
1431 ASN* 1.4 95.0 - - + +
1451 LEU* 1.3 62.5 + - + +
1471 ARG* 3.7 2.6 + - + +
1481 LYS* 3.6 22.8 + - - +
133H ALA* 3.8 29.4 - - + +
136H ALA* 4.8 1.8 - - + -
137H VAL* 5.6 1.3 - - + -
161H ALA* 4.7 5.5 - - + +
165H ASN* 3.5 33.8 - - + +
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Residues in contact with LEU 145 (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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1411 MET 3.6 15.0 - - - +
1421 ALA* 3.0 7.2 + - - +
1441 PRO* 1.3 75.9 - - - +
1461 LEU* 1.3 65.5 + - + +
1481 LYS* 3.2 28.2 + - + +
1491 VAL* 3.9 7.3 + - - +
1671 ALA* 5.5 3.4 - - + +
1701 ASN* 4.0 11.0 - - - +
1711 ALA* 4.2 18.8 - - + -
1741 VAL* 3.8 22.0 - - + -
136H ALA* 3.4 29.8 - - + +
137H VAL* 4.0 14.8 - - + +
140H SER* 3.6 22.4 - - - +
141H HIS* 5.9 1.3 - - - +
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Residues in contact with LEU 146 (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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31 ILE* 4.4 7.9 - - + -
41 SER 3.9 17.0 - - - +
51 MET* 3.9 8.5 - - + +
1321 THR* 3.7 24.5 - - + +
1331 LEU 5.1 0.9 - - - +
1421 ALA* 2.9 33.9 + - + +
1431 ASN* 4.0 3.4 - - - +
1451 LEU* 1.3 76.3 - - - +
1471 ARG* 1.3 57.5 + - - +
1491 VAL* 3.0 22.2 + - - +
1501 VAL* 3.1 11.4 + - - +
1671 ALA* 3.6 42.2 - - + +
1681 ILE* 3.7 28.3 - - + -
1711 ALA* 4.4 4.7 - - + -
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Residues in contact with ARG 147 (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 SER* 4.9 8.1 + - - -
1321 THR* 3.8 16.5 + - + +
1391 ALA 5.2 1.2 + - - -
1431 ASN* 2.8 45.6 + - - +
1441 PRO* 4.1 4.5 - - - +
1461 LEU* 1.3 75.7 - - - +
1481 LYS* 1.3 59.1 + - - +
1501 VAL 3.5 14.1 - - - +
1511 ASP* 3.0 46.9 + - - +
165H ASN* 3.0 39.2 + - - +
26Z ILE* 2.9 48.2 + - - +
27Z ASN 4.0 9.5 + - - -
28Z SER* 5.3 0.4 - - - +
29Z ARG* 4.7 14.5 - - - +
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Residues in contact with LYS 148 (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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1441 PRO 3.6 16.0 + - - +
1451 LEU* 3.2 20.5 + - + +
1461 LEU 3.1 0.6 - - - -
1471 ARG* 1.3 79.2 - - - +
1491 VAL* 1.3 59.0 + - + +
1511 ASP* 5.7 1.1 - - - -
137H VAL* 4.8 20.5 - - + +
141H HIS* 4.4 20.0 + - - -
157H ASP* 4.6 25.3 + - - +
161H ALA* 6.2 0.9 - - + -
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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