Contacts of the strand formed by residues 297 - 300 (chain 9) 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 ASN 297 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1519 ILE* 3.4 20.6 + - - +
1539 LEU* 4.5 13.9 - - - +
2789 THR* 3.2 34.2 + - - +
2829 ILE* 4.6 1.6 - - - +
2939 LEU 4.5 3.5 - - - +
2949 TYR 5.0 1.5 - - - +
2969 ASN* 1.3 70.6 - - - +
2989 VAL* 1.3 62.4 + - - +
2999 MET* 3.8 2.7 + - - -
3139 MET* 4.4 12.5 - - - +
3179 ILE* 3.9 10.0 - - - +
3289 LYS 2.9 16.0 + - - +
3299 ILE* 3.5 26.5 - - + +
3309 ILE 2.7 30.3 + - - +
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Residues in contact with VAL 298 (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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1419 SER* 4.5 4.5 - - - +
1429 LEU* 3.7 24.9 - - + -
1459 SER* 3.5 21.3 - - - +
1479 ARG* 4.3 8.7 - - - -
1519 ILE 2.9 6.9 + - - +
1529 VAL* 3.1 20.8 - - + +
1539 LEU* 2.9 25.3 + - - +
2969 ASN 4.4 2.9 - - - +
2979 ASN* 1.3 75.3 + - - +
2999 MET* 1.3 71.5 + - - +
3309 ILE* 3.3 18.2 - - + +
3329 PRO* 5.3 3.8 - - + -
3389 SER* 5.9 0.7 - - - +
637D LYS* 3.6 22.4 - - - +
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Residues in contact with MET 299 (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* 3.6 35.7 - - + +
2979 ASN* 4.8 5.6 - - - -
2989 VAL* 1.3 77.5 - - - +
3009 SER* 1.3 61.9 + - - +
3049 THR* 3.8 19.1 - - - +
3099 ILE* 4.3 13.7 - - + -
3109 ALA* 4.0 15.0 - - - +
3139 MET* 4.8 11.0 - - - -
3299 ILE* 3.6 32.3 - - + -
3309 ILE 2.8 11.1 + - - +
3319 ALA* 3.4 29.6 - - + -
3329 PRO* 4.0 10.9 - - - +
3359 ARG* 3.8 13.9 - - - +
3389 SER* 4.4 1.6 + - - -
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Residues in contact with SER 300 (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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1419 SER* 3.0 34.0 + - - -
1529 VAL* 3.6 4.4 - - - +
1539 LEU 3.1 9.9 + - - +
1549 ASP* 3.0 23.2 + - - +
1559 SER 3.1 21.7 + - - -
2989 VAL* 4.2 1.3 + - - -
2999 MET* 1.3 78.2 - - - +
3019 GLY* 1.3 59.8 + - - +
3049 THR* 3.3 10.6 - - - +
3359 ARG* 4.0 4.9 - - - -
3389 SER* 3.7 14.6 - - - -
3399 VAL* 4.5 2.0 - - - +
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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