Contacts of the strand formed by residues 150 - 155 (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 GLY 150 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1420 LEU* 3.8 14.1 - - - +
1490 THR* 1.3 77.6 - - - +
1510 ILE* 1.3 62.1 + - - +
1630 VAL 4.9 0.2 - - - -
1640 PRO* 3.7 0.9 - - - +
1650 ILE* 2.9 28.3 + - - +
2930 LEU* 3.8 12.8 - - - +
2960 ASN* 3.2 20.4 - - - -
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Residues in contact with ILE 151 (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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1420 LEU* 4.4 0.4 - - - +
1500 GLY* 1.3 75.3 - - - +
1520 VAL* 1.3 65.1 + - - +
1530 LEU 4.0 0.5 + - - -
1620 ASN* 4.5 5.8 - - + +
1630 VAL 3.7 8.5 - - - +
1640 PRO* 3.9 22.2 - - + -
2780 THR* 3.6 30.5 - - + +
2810 SER* 3.6 21.8 - - - +
2820 ILE* 3.7 11.9 - - + -
2930 LEU* 3.4 33.9 - - + +
2960 ASN 2.8 8.7 + - - +
2970 ASN* 3.4 21.0 - - - +
2980 VAL* 2.9 23.7 + - - +
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Residues in contact with VAL 152 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1380 ALA* 3.3 39.9 - - + +
1410 SER* 4.3 2.7 - - - -
1420 LEU* 3.8 31.0 - - + +
1510 ILE* 1.3 73.5 - - - +
1530 LEU* 1.3 67.0 + - - +
1540 ASP* 3.6 10.5 + - + -
1610 HIS 4.1 0.2 - - - -
1620 ASN* 3.2 7.2 - - - +
1630 VAL* 2.9 31.2 + - - +
1650 ILE* 4.5 1.8 - - + -
2970 ASN* 5.6 0.2 - - - -
2980 VAL* 3.1 14.1 - - + +
3000 SER* 3.6 24.9 - - - +
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Residues in contact with LEU 153 (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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1510 ILE 4.0 0.8 + - - -
1520 VAL* 1.3 70.9 - - - +
1540 ASP* 1.3 59.9 + - - +
1550 SER* 5.1 2.0 - - - -
1600 THR* 4.4 8.3 - - + -
1610 HIS 3.4 8.5 - - - +
1620 ASN* 3.6 24.5 - - - +
2740 ILE* 3.6 40.8 - - + +
2780 THR* 3.9 9.6 - - - +
2970 ASN* 4.5 13.9 - - - +
2980 VAL 2.9 7.8 + - - +
2990 MET* 3.6 32.7 - - + -
3000 SER 3.1 24.6 + - - +
3040 THR* 4.0 13.9 - - + -
3090 ILE* 5.7 4.9 - - + -
3130 MET* 4.5 3.1 - - + -
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Residues in contact with ASP 154 (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* 5.9 2.3 - - - +
1370 GLN* 4.0 26.0 - - - +
1380 ALA* 4.1 11.3 + - + +
1520 VAL* 3.6 13.6 + - + +
1530 LEU* 1.3 73.8 - - - +
1550 SER* 1.4 64.3 + - - +
1590 VAL 4.0 1.4 - - - +
1600 THR* 3.2 4.0 - - - +
1610 HIS* 2.7 50.8 + - + +
3000 SER* 3.0 29.4 + - - +
3010 GLY* 4.0 4.2 + - - -
3390 VAL* 4.2 9.5 - - - +
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Residues in contact with SER 155 (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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1530 LEU* 5.1 3.1 - - - -
1540 ASP* 1.4 76.1 + - - +
1560 GLY* 1.3 61.1 + - - +
1590 VAL 3.6 4.4 + - - -
1600 THR* 2.6 27.8 + - - +
1800 LEU 4.6 0.3 + - - -
1810 ALA* 4.5 2.3 - - - +
2610 LEU* 4.8 4.7 - - - +
2740 ILE* 5.5 1.2 - - - +
3000 SER 3.1 8.3 + - - -
3010 GLY* 3.2 13.3 - - - -
3030 THR* 3.1 38.3 + - - +
3040 THR* 3.6 18.8 - - - -
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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