Contacts of the strand formed by residues 150 - 155 (chain 3) in PDB entry 1O19
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 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1423 LEU* 3.8 14.3 - - - +
1493 THR* 1.3 77.4 - - - +
1513 ILE* 1.3 60.8 + - - +
1643 PRO* 3.7 0.5 - - - +
1653 ILE* 2.9 29.1 + - - +
2923 ASP 4.8 0.2 - - - -
2933 LEU* 3.8 13.2 - - - +
2963 ASN* 3.2 20.6 - - - -
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Residues in contact with ILE 151 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1423 LEU* 4.4 0.6 - - - +
1503 GLY* 1.3 74.2 - - - +
1523 VAL* 1.3 65.7 + - - +
1533 LEU 4.0 0.3 + - - -
1623 ASN* 4.5 6.7 - - + +
1633 VAL 3.7 8.7 - - - +
1643 PRO* 3.9 22.7 - - + -
2783 THR* 3.6 29.6 - - + +
2813 SER* 3.6 21.3 - - - +
2823 ILE* 3.7 13.0 - - + -
2933 LEU* 3.4 33.0 - - + +
2963 ASN 2.8 8.6 + - - +
2973 ASN* 3.4 20.5 - - - +
2983 VAL 2.9 23.2 + - - +
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Residues in contact with VAL 152 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1383 ALA* 3.3 41.1 - - + +
1413 SER* 4.3 2.5 - - - -
1423 LEU* 3.8 29.8 - - + +
1513 ILE* 1.3 74.5 - - - +
1533 LEU* 1.3 67.8 + - - +
1543 ASP* 3.6 10.1 + - + -
1613 HIS 4.1 0.2 - - - -
1623 ASN* 3.2 6.3 - - - +
1633 VAL* 2.9 33.3 + - - +
1653 ILE* 4.5 1.6 - - + -
2973 ASN* 5.6 0.2 - - - -
2983 VAL* 3.1 15.0 - - + +
3003 SER* 3.6 24.5 - - - +
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Residues in contact with LEU 153 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1513 ILE 4.0 1.0 + - - -
1523 VAL* 1.3 72.2 - - - +
1543 ASP* 1.3 58.9 + - - +
1553 SER* 5.1 2.0 - - - -
1603 THR* 4.4 9.0 - - + -
1613 HIS 3.4 8.5 - - - +
1623 ASN* 3.6 23.8 - - - +
2743 ILE* 3.6 41.5 - - + +
2773 THR* 5.9 0.2 - - + -
2783 THR* 3.9 10.5 - - - +
2973 ASN* 4.5 13.9 - - - +
2983 VAL 2.9 7.8 + - - +
2993 MET* 3.6 35.5 - - + +
3003 SER 3.1 23.9 + - - +
3043 THR* 4.0 14.4 - - + -
3093 ILE* 5.7 4.5 - - + -
3133 MET* 4.5 3.6 - - + -
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Residues in contact with ASP 154 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093 PRO* 5.9 2.6 - - + +
1373 GLN* 4.0 25.8 - - - +
1383 ALA* 4.1 10.9 + - + +
1523 VAL* 3.6 12.5 + - + +
1533 LEU* 1.3 74.3 - - - +
1553 SER* 1.4 63.9 + - - +
1563 GLY 4.4 0.2 - - - -
1593 VAL 4.0 1.3 - - - +
1603 THR* 3.2 3.9 - - - +
1613 HIS* 2.7 50.7 + - + +
3003 SER* 3.0 31.4 + - - +
3013 GLY* 4.0 4.7 + - - -
3393 VAL* 4.2 9.2 - - - +
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Residues in contact with SER 155 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1533 LEU* 5.1 3.8 - - - -
1543 ASP* 1.4 75.4 + - - +
1563 GLY* 1.3 61.4 + - - +
1593 VAL 3.6 3.8 - - - -
1603 THR* 2.6 27.6 + - - +
1803 LEU 4.6 0.5 + - - -
1813 ALA* 4.5 2.3 - - - +
2613 LEU* 4.8 4.6 - - - +
2743 ILE* 5.5 0.8 - - - +
3003 SER 3.1 8.5 + - - -
3013 GLY* 3.2 13.6 - - - -
3033 THR* 3.1 39.0 + - - +
3043 THR* 3.6 19.5 - - - -
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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