Contacts of the helix formed by residues 137 - 145 (chain 6) in PDB entry 1O1F
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 GLN 137 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116 ASP* 4.2 6.5 - - - +
126 ASN 4.1 13.8 + - - +
746 GLY* 5.0 5.5 + - - -
1066 THR* 3.8 23.6 + - - +
1076 GLU* 3.0 35.6 + - - +
1086 ALA* 3.4 12.2 - - - +
1096 PRO* 4.8 6.9 - - + +
1356 ALA 4.6 0.2 - - - -
1366 ILE* 1.3 72.5 - - - +
1386 ALA* 1.3 59.8 + - - +
1406 LEU* 2.9 24.0 + - - +
1416 SER* 3.1 11.1 + - - -
1546 ASP* 4.0 15.4 - - - +
3396 VAL* 4.0 21.9 - - + +
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Residues in contact with ALA 138 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096 PRO* 5.0 2.6 - - + +
1366 ILE* 3.6 3.5 - - + +
1376 GLN* 1.3 75.7 - - - +
1396 VAL* 1.3 63.3 + - + +
1416 SER* 3.2 2.9 + - - -
1426 LEU* 2.9 21.7 + - - +
1526 VAL* 3.3 34.2 - - + +
1546 ASP* 4.1 9.1 + - + +
1636 VAL* 3.4 43.5 - - + -
1656 ILE* 3.7 3.4 - - + -
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Residues in contact with VAL 139 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1356 ALA* 6.1 1.1 - - + -
1366 ILE* 3.3 38.1 - - + +
1376 GLN 3.1 0.6 - - - -
1386 ALA* 1.3 79.0 - - + +
1406 LEU* 1.3 60.7 + - + +
1426 LEU* 3.5 3.0 + - - +
1436 TYR* 3.3 24.7 + - + +
1656 ILE* 3.5 27.4 - - + -
1686 GLY* 4.2 19.7 - - - +
1706 ALA* 3.9 15.5 - - + +
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Residues in contact with LEU 140 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046 LEU* 4.4 1.3 - - + -
1066 THR* 3.4 33.7 - - + -
1356 ALA* 3.6 29.6 - - + -
1366 ILE 3.2 6.4 + - - +
1376 GLN 2.9 5.6 + - - +
1396 VAL* 1.3 75.6 - - + +
1416 SER* 1.3 66.8 + - - +
1436 TYR* 4.4 5.8 - - + -
1446 ALA* 3.1 25.1 + - - +
3386 SER 4.3 0.9 - - - -
3396 VAL* 3.3 26.7 - - + +
3426 GLY* 3.4 7.8 - - - +
3436 GLY* 3.8 21.3 - - - +
3466 LEU* 3.7 23.3 - - + -
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Residues in contact with SER 141 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376 GLN 3.1 7.3 + - - -
1386 ALA* 3.5 11.2 - - - -
1406 LEU* 1.3 77.1 - - - +
1426 LEU* 1.3 50.6 - - - +
1526 VAL* 4.3 5.8 - - - -
2986 VAL* 4.6 2.2 - - - -
3006 SER* 3.0 32.3 + - - -
3386 SER* 3.2 11.0 - - - -
3396 VAL* 3.1 27.4 + - - +
637G LYS* 2.0 44.4 + - - +
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Residues in contact with LEU 142 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386 ALA 2.9 16.7 + - - +
1396 VAL* 3.8 5.2 - - - +
1406 LEU 3.3 0.2 - - - -
1416 SER* 1.3 75.0 - - - +
1436 TYR* 1.3 60.0 + - - +
1456 SER* 2.9 23.2 + - - -
1476 ARG* 3.4 26.5 + - + +
1486 THR* 3.6 34.1 - - - +
1496 THR 3.8 2.7 - - - +
1506 GLY* 3.8 24.5 - - - +
1526 VAL* 3.8 16.3 - - + +
1656 ILE* 3.9 21.1 - - + -
2986 VAL* 3.7 26.9 - - + -
637G LYS* 3.1 5.2 + - - +
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Residues in contact with TYR 143 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1396 VAL* 3.3 17.7 + - + +
1406 LEU* 3.9 6.7 - - + +
1426 LEU* 1.3 78.4 - - - +
1446 ALA* 1.3 54.6 + - - +
1456 SER 3.0 0.2 - - - -
1476 ARG 3.4 10.1 - - - +
3426 GLY* 3.7 15.9 - - - -
3456 ILE* 3.5 15.0 - - + -
3466 LEU* 3.8 21.8 - - + -
541G MET* 1.9 55.9 - - - +
542G PHE* 2.3 67.6 + + + -
543G PRO* 2.1 47.0 - - + +
637G LYS* 3.7 0.5 - - - +
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Residues in contact with ALA 144 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1406 LEU 3.1 18.8 + - - +
1416 SER 3.4 1.6 - - - +
1436 TYR* 1.3 74.0 - - - +
1456 SER* 1.3 28.8 + - - -
1466 GLY 3.2 2.2 + - - -
3386 SER* 3.5 12.8 - - - +
3426 GLY* 3.5 13.5 - - - +
636G LYS* 2.8 11.1 - - - +
637G LYS* 0.7 236.7 + - + +
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Residues in contact with SER 145 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1426 LEU 2.9 5.1 + - - -
1446 ALA* 1.3 47.1 - - - +
1466 GLY* 1.3 54.3 + - - +
1476 ARG* 3.0 45.9 + - - -
2986 VAL* 3.5 15.0 - - - +
3306 ILE* 5.0 2.2 - - - -
3326 PRO* 4.7 13.9 - - - -
408G VAL* 6.3 0.2 - - - -
543G PRO* 3.7 0.2 - - - -
544G LYS* 5.2 0.7 - - - +
636G LYS* 5.0 5.2 - - - -
637G LYS* 1.2 92.6 + - - +
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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