Contacts of the helix formed by residues 137 - 145 (chain 4) 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 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114 ASP* 4.2 6.3 - - - +
124 ASN 4.1 13.1 + - - +
744 GLY* 5.0 5.1 + - - -
1064 THR* 3.8 23.4 + - - +
1074 GLU* 3.0 34.2 + - - +
1084 ALA* 3.4 11.5 - - - +
1094 PRO* 4.8 6.7 - - + +
1364 ILE* 1.3 72.2 - - - +
1384 ALA* 1.3 58.2 + - - +
1404 LEU* 2.9 23.8 + - - +
1414 SER* 3.1 11.3 + - - -
1544 ASP* 4.0 17.5 - - - +
3394 VAL* 4.0 20.6 - - + +
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Residues in contact with ALA 138 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094 PRO* 5.0 2.3 - - + +
1364 ILE* 3.6 3.7 - - + +
1374 GLN* 1.3 76.1 - - - +
1394 VAL* 1.3 62.9 + - + +
1414 SER* 3.2 3.4 + - - -
1424 LEU* 2.9 21.0 + - - +
1524 VAL* 3.3 31.9 - - + +
1544 ASP* 4.1 8.9 + - + +
1634 VAL* 3.4 44.4 - - + -
1654 ILE* 3.7 3.1 - - + +
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Residues in contact with VAL 139 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1354 ALA* 6.1 1.1 - - + -
1364 ILE* 3.3 39.5 - - + +
1374 GLN 3.1 0.2 - - - -
1384 ALA* 1.3 78.8 - - - +
1404 LEU* 1.3 61.6 + - + +
1424 LEU* 3.5 2.7 + - - +
1434 TYR* 3.3 24.6 + - + +
1654 ILE* 3.5 26.9 - - + -
1684 GLY* 4.2 19.1 - - - +
1704 ALA* 3.9 15.7 - - + -
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Residues in contact with LEU 140 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94 VAL* 6.0 0.2 - - + -
1044 LEU* 4.4 0.7 - - + -
1064 THR* 3.4 33.0 - - + -
1354 ALA* 3.6 28.7 - - + -
1364 ILE 3.2 8.6 + - - +
1374 GLN 2.9 6.8 + - - +
1394 VAL* 1.3 74.4 - - + +
1414 SER* 1.3 68.0 + - - +
1434 TYR* 4.4 5.2 - - + -
1444 ALA* 3.1 24.6 + - - +
3384 SER 4.3 0.9 - - - -
3394 VAL* 3.3 27.8 - - + +
3424 GLY* 3.4 7.7 - - - +
3434 GLY* 3.8 21.3 - - - +
3464 LEU* 3.7 24.0 - - + -
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Residues in contact with SER 141 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1374 GLN 3.1 7.6 + - - -
1384 ALA* 3.2 11.9 + - - -
1404 LEU* 1.3 77.5 - - - +
1424 LEU* 1.3 49.5 - - - +
1444 ALA* 3.4 0.2 - - - +
1524 VAL* 4.3 5.8 - - - -
2984 VAL* 4.6 2.7 - - - -
3004 SER* 3.0 30.7 + - - -
3384 SER* 3.2 11.3 - - - -
3394 VAL* 3.1 27.7 + - - +
637A LYS* 2.0 43.4 + - - +
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Residues in contact with LEU 142 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1384 ALA 2.9 16.3 + - - +
1394 VAL* 3.8 5.2 - - - +
1414 SER* 1.3 76.0 - - - +
1434 TYR* 1.3 59.4 + - - +
1454 SER* 2.9 24.1 + - - -
1474 ARG* 3.4 27.1 + - + +
1484 THR* 3.6 33.0 - - - +
1494 THR 3.8 3.1 - - - +
1504 GLY* 3.8 24.2 - - - +
1524 VAL* 3.8 16.3 - - + +
1654 ILE* 3.9 21.3 - - + -
2984 VAL* 3.7 26.2 - - + -
637A LYS* 3.1 5.5 + - - +
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Residues in contact with TYR 143 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1394 VAL* 3.3 17.0 - - + +
1404 LEU* 3.9 6.1 - - + +
1424 LEU* 1.3 79.5 - - - +
1444 ALA* 1.3 55.8 + - - +
1454 SER 3.0 0.4 - - - -
1474 ARG 3.4 10.1 - - - +
3424 GLY* 3.7 15.5 - - - -
3454 ILE* 3.5 14.1 - - + -
3464 LEU* 3.8 22.9 - - + -
541A MET* 1.9 55.0 - - - +
542A PHE* 2.3 69.2 + + + -
543A PRO* 2.1 47.4 - - + +
637A LYS* 3.7 0.3 - - - +
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Residues in contact with ALA 144 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1404 LEU 3.1 18.2 + - - +
1414 SER 3.4 1.8 - - - +
1434 TYR* 1.3 73.8 - - - +
1454 SER* 1.3 28.5 + - - -
1464 GLY 3.2 2.7 + - - -
3384 SER* 3.5 13.0 - - - +
3424 GLY* 3.5 13.9 - - - +
543A PRO* 4.8 0.2 - - - +
636A LYS* 2.8 11.0 - - - +
637A LYS* 0.7 236.7 + - + +
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Residues in contact with SER 145 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1424 LEU 2.9 5.5 + - - -
1444 ALA* 1.3 46.8 - - - +
1464 GLY* 1.3 54.4 + - - +
1474 ARG* 3.0 44.9 + - - -
2984 VAL* 3.5 15.4 - - - +
3304 ILE* 4.9 2.9 - - - +
3324 PRO* 4.7 13.7 - - - -
543A PRO* 3.7 0.2 - - - -
544A LYS* 5.1 0.5 - - - +
636A LYS* 5.0 5.2 - - - -
637A LYS* 1.2 90.7 + - - +
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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