Contacts of the helix formed by residues 137 - 145 (chain 0) 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 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110 ASP* 4.2 6.3 - - - +
120 ASN 4.1 13.0 + - - +
740 GLY* 5.0 5.3 + - - -
1060 THR* 3.8 23.6 + - - +
1070 GLU* 3.0 34.2 + - - +
1080 ALA* 3.4 11.5 - - - +
1090 PRO* 4.8 6.5 - - + +
1360 ILE* 1.3 71.7 - - - +
1380 ALA* 1.3 58.3 + - - +
1400 LEU* 2.9 23.8 + - - +
1410 SER* 3.1 11.3 + - - -
1540 ASP* 4.0 17.0 - - - +
3390 VAL* 4.0 21.1 - - + +
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Residues in contact with ALA 138 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090 PRO* 5.0 2.5 - - + +
1360 ILE* 3.6 3.7 - - + +
1370 GLN* 1.3 75.7 - - - +
1390 VAL* 1.3 63.1 + - + +
1410 SER* 3.2 3.3 + - - -
1420 LEU* 2.9 21.3 + - - +
1520 VAL* 3.3 33.4 - - + +
1540 ASP* 4.1 8.9 + - + +
1630 VAL* 3.4 43.5 - - + -
1650 ILE* 3.7 2.7 - - + -
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Residues in contact with VAL 139 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1350 ALA* 6.1 1.1 - - + -
1360 ILE* 3.3 39.3 - - + +
1370 GLN 3.1 0.4 - - - -
1380 ALA* 1.3 78.2 - - - +
1400 LEU* 1.3 61.1 + - + +
1420 LEU* 3.5 2.6 + - - +
1430 TYR* 3.3 24.6 + - + +
1650 ILE* 3.5 26.9 - - + -
1680 GLY* 4.2 19.3 - - - +
1700 ALA* 3.9 15.5 - - + -
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Residues in contact with LEU 140 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90 VAL* 6.0 0.4 - - + -
1040 LEU* 4.4 1.1 - - + -
1060 THR* 3.4 32.5 - - + -
1350 ALA* 3.6 29.8 - - + -
1360 ILE 3.2 8.2 + - - +
1370 GLN 2.9 7.0 + - - +
1390 VAL* 1.3 74.8 - - + +
1410 SER* 1.3 67.6 + - - +
1430 TYR* 4.4 5.2 - - + -
1440 ALA* 3.1 24.6 + - - +
3380 SER 4.3 1.1 - - - -
3390 VAL* 3.3 27.4 - - + +
3420 GLY* 3.4 7.3 - - - -
3430 GLY* 3.8 20.4 - - - +
3460 LEU* 3.7 24.0 - - + -
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Residues in contact with SER 141 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1370 GLN 3.1 6.8 + - - -
1380 ALA* 3.2 11.4 + - - -
1400 LEU* 1.3 81.8 - - - +
1420 LEU* 1.3 62.1 + - - +
1440 ALA* 3.3 10.4 + - - +
1450 SER* 3.4 10.7 + - - -
1520 VAL* 4.3 5.8 - - - -
2980 VAL* 4.5 6.7 - - - +
3000 SER* 3.0 31.1 + - - -
3380 SER* 3.2 13.9 + - - -
3390 VAL* 3.1 27.9 + - - +
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Residues in contact with LEU 142 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1380 ALA 2.9 16.1 + - - +
1390 VAL* 3.8 4.9 - - - +
1410 SER* 1.3 75.6 - - - +
1430 TYR* 1.3 59.6 + - - +
1450 SER* 2.9 26.7 + - - -
1470 ARG* 3.4 27.7 + - + +
1480 THR* 3.6 33.0 - - - +
1490 THR 3.8 2.7 - - - +
1500 GLY* 3.8 24.2 - - - +
1520 VAL* 3.8 16.1 - - + +
1650 ILE* 3.9 21.5 - - + -
2980 VAL* 3.7 29.4 - - + -
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Residues in contact with TYR 143 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1390 VAL* 3.3 17.5 + - + +
1400 LEU* 3.9 6.1 - - + +
1420 LEU* 1.3 78.6 - - - +
1440 ALA* 1.3 59.5 + - - +
1450 SER 3.0 0.2 - - - -
1460 GLY* 2.9 28.4 + - - -
1470 ARG 3.4 14.6 - - - +
1480 THR* 5.0 10.5 - - + -
3420 GLY* 3.7 15.9 - - - -
3450 ILE* 3.5 34.0 - - + +
3460 LEU* 3.8 30.0 - - + +
3490 LEU* 4.2 17.8 - - - +
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Residues in contact with ALA 144 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400 LEU 3.1 19.1 + - - +
1410 SER 3.4 6.3 - - - +
1430 TYR* 1.3 76.1 - - - +
1450 SER* 1.3 55.8 + - - +
1460 GLY 3.2 3.1 + - - -
3340 GLU* 5.2 8.0 - - - +
3380 SER* 3.5 16.4 - - - +
3410 ILE* 4.3 11.2 - - + +
3420 GLY* 3.5 21.3 - - - +
3450 ILE* 4.4 13.4 - - - +
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Residues in contact with SER 145 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1410 SER 3.4 8.0 + - - -
1420 LEU 2.9 11.7 + - - -
1440 ALA* 1.3 75.2 - - - +
1460 GLY* 1.3 54.9 + - - +
1470 ARG* 3.0 45.1 + - - -
2980 VAL* 3.5 22.2 - - - +
3300 ILE* 4.9 2.4 - - - +
3320 PRO* 4.7 18.2 - - - -
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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