Contacts of the strand formed by residues 150 - 155 (chain 6) in PDB entry 1O18
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 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1426 LEU* 3.8 13.4 - - - +
1496 THR* 1.3 77.1 - - - +
1516 ILE* 1.3 60.4 + - - +
1526 VAL 4.3 0.2 - - - -
1646 PRO* 3.7 0.5 - - - +
1656 ILE* 2.9 27.8 + - - +
2926 ASP 4.8 0.2 - - - -
2936 LEU* 3.8 13.2 - - - +
2966 ASN* 3.2 21.5 - - - -
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Residues in contact with ILE 151 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1426 LEU* 4.4 0.4 - - - +
1506 GLY* 1.3 74.7 - - - +
1526 VAL* 1.3 65.2 + - - +
1536 LEU 4.0 0.2 + - - -
1626 ASN* 4.5 6.3 - - + +
1636 VAL 3.7 8.5 - - - +
1646 PRO* 3.9 21.1 - - + -
2786 THR* 3.6 29.4 - - + +
2816 SER* 3.6 21.8 - - - +
2826 ILE* 3.7 13.7 - - + -
2936 LEU* 3.4 33.4 - - + +
2966 ASN 2.8 8.9 + - - +
2976 ASN* 3.4 20.8 - - - +
2986 VAL 2.9 23.7 + - - +
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Residues in contact with VAL 152 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386 ALA* 3.3 40.6 - - + +
1416 SER* 4.3 2.5 - - - -
1426 LEU* 3.8 29.6 - - + +
1516 ILE* 1.3 74.9 - - - +
1536 LEU* 1.3 67.6 + - - +
1546 ASP* 3.6 10.7 + - + -
1616 HIS 4.1 0.2 - - - -
1626 ASN* 3.2 6.5 - - - -
1636 VAL* 2.9 32.4 + - - +
1656 ILE* 4.5 1.3 - - + -
2986 VAL* 3.1 15.0 - - + +
3006 SER* 3.6 24.9 - - - +
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Residues in contact with LEU 153 (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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1516 ILE 4.0 1.0 + - - -
1526 VAL* 1.3 71.5 - - - +
1546 ASP* 1.3 58.1 + - - +
1556 SER* 5.1 2.2 - - - -
1606 THR* 4.4 9.2 - - + -
1616 HIS 3.4 8.1 - - - +
1626 ASN* 3.6 25.1 - - - +
2746 ILE* 3.6 40.6 - - + +
2786 THR* 3.9 10.5 - - - +
2976 ASN* 4.5 14.4 - - - +
2986 VAL 2.9 7.6 + - - +
2996 MET* 3.6 34.1 - - + -
3006 SER 3.1 24.6 + - - +
3046 THR* 4.0 13.9 - - + -
3096 ILE* 5.7 5.2 - - + -
3136 MET* 4.5 3.4 - - + -
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Residues in contact with ASP 154 (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* 5.9 1.7 - - - +
1376 GLN* 4.0 25.8 - - - +
1386 ALA* 4.1 10.6 + - + +
1526 VAL* 3.6 12.9 + - + +
1536 LEU* 1.3 73.8 - - - +
1556 SER* 1.4 64.4 + - - +
1596 VAL 4.0 1.3 - - - +
1606 THR* 3.2 3.0 - - - +
1616 HIS* 2.7 50.2 + - + +
3006 SER* 3.0 30.5 + - - +
3016 GLY* 4.0 4.7 + - - -
3396 VAL* 4.2 10.4 - - - +
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Residues in contact with SER 155 (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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1536 LEU* 5.1 3.8 - - - -
1546 ASP* 1.4 75.4 + - - +
1566 GLY* 1.3 60.4 + - - +
1596 VAL 3.6 4.0 - - - -
1606 THR* 2.6 27.3 + - - +
1806 LEU 4.6 0.7 + - - -
1816 ALA* 4.5 2.4 - - - +
2616 LEU* 4.8 4.8 - - - +
2746 ILE* 5.5 0.8 - - - +
3006 SER 3.1 8.3 + - - -
3016 GLY* 3.2 13.3 - - - -
3036 THR* 3.1 39.5 + - - +
3046 THR* 3.6 19.1 - - - -
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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