Contacts of the strand formed by residues 150 - 155 (chain 9) 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 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429 LEU* 3.8 13.4 - - - +
1499 THR* 1.3 77.6 - - - +
1519 ILE* 1.3 62.0 + - - +
1639 VAL 4.9 0.2 - - - -
1649 PRO* 3.8 0.7 - - - +
1659 ILE* 2.9 28.7 + - - +
2939 LEU* 3.8 12.3 - - - +
2969 ASN* 3.2 22.0 - - - -
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Residues in contact with ILE 151 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429 LEU* 4.9 0.2 - - - -
1509 GLY* 1.3 74.4 - - - +
1529 VAL* 1.3 66.0 + - - +
1539 LEU 4.0 0.9 + - - -
1629 ASN* 4.5 5.8 - - + +
1639 VAL 3.7 8.5 - - - +
1649 PRO* 3.9 22.0 - - + -
2789 THR* 3.6 29.6 - - + +
2819 SER* 3.6 22.2 - - - +
2829 ILE* 3.7 12.8 - - + -
2939 LEU* 3.4 33.4 - - + +
2969 ASN 2.8 8.9 + - - +
2979 ASN* 3.4 20.9 - - - +
2989 VAL* 2.9 23.4 + - - +
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Residues in contact with VAL 152 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1389 ALA* 3.3 41.1 - - + +
1419 SER* 4.3 2.9 - - - -
1429 LEU* 3.8 30.3 - - + +
1519 ILE* 1.3 74.4 - - - +
1539 LEU* 1.3 67.9 + - - +
1549 ASP* 3.6 9.8 + - + -
1619 HIS 4.1 0.2 - - - -
1629 ASN* 3.2 7.2 - - - +
1639 VAL* 2.9 32.7 + - - +
1659 ILE* 4.5 1.6 - - + -
2989 VAL* 3.1 14.8 - - + +
3009 SER* 3.6 24.0 - - - +
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Residues in contact with LEU 153 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1519 ILE 4.0 1.0 + - - -
1529 VAL* 1.3 71.7 - - - +
1549 ASP* 1.3 60.0 + - - +
1559 SER* 5.1 2.2 - - - -
1609 THR* 4.4 8.5 - - + -
1619 HIS 3.4 8.1 - - - +
1629 ASN* 3.6 24.5 - - - +
2749 ILE* 3.6 40.8 - - + +
2789 THR* 3.9 9.9 - - - +
2979 ASN* 4.5 13.3 - - - +
2989 VAL 2.9 7.8 + - - +
2999 MET* 3.6 32.7 - - + -
3009 SER 3.1 24.6 + - - +
3049 THR* 4.0 13.5 - - + -
3099 ILE* 5.7 4.9 - - + -
3139 MET* 4.5 3.6 - - + -
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Residues in contact with ASP 154 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099 PRO* 5.9 3.1 - - + +
1379 GLN* 4.0 25.8 - - - +
1389 ALA* 4.1 11.8 + - + -
1529 VAL* 3.6 12.5 + - + +
1539 LEU* 1.3 73.8 - - - +
1559 SER* 1.4 64.5 + - - +
1569 GLY 5.1 0.4 + - - -
1599 VAL 4.0 1.1 - - - +
1609 THR* 3.2 3.4 - - - +
1619 HIS* 2.7 50.0 + - + +
3009 SER* 3.0 29.8 + - - +
3019 GLY* 4.0 4.2 + - - -
3399 VAL* 4.2 9.5 - - - +
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Residues in contact with SER 155 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539 LEU* 5.1 3.1 - - - -
1549 ASP* 1.4 76.3 + - - +
1569 GLY* 1.3 60.3 + - - +
1599 VAL 3.6 3.6 - - - -
1609 THR* 2.6 28.0 + - - +
1809 LEU 4.6 0.3 + - - -
1819 ALA* 4.5 1.9 - - - +
2619 LEU* 4.8 4.9 - - - +
2749 ILE* 5.5 1.1 - - - +
3009 SER 3.1 8.5 + - - -
3019 GLY* 3.2 13.6 - - - -
3039 THR* 3.1 38.4 + - - +
3049 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
------------------------------------------------------------
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