Contacts of the strand formed by residues 297 - 300 (chain 3) 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 ASN 297 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1513 ILE* 3.4 19.9 + - - +
1533 LEU* 4.5 14.1 - - - +
2783 THR* 3.2 34.2 + - - +
2823 ILE* 4.6 1.6 - - - +
2933 LEU 3.7 3.3 + - - +
2943 TYR 5.0 1.7 - - - +
2963 ASN* 1.3 71.2 - - - +
2983 VAL* 1.3 61.7 + - - +
2993 MET* 3.8 2.7 + - - -
3133 MET* 4.4 12.7 - - - +
3173 ILE* 3.9 10.2 - - - +
3283 LYS 2.9 15.6 + - - +
3293 ILE* 3.5 26.4 - - + +
3303 ILE 2.7 30.5 + - - +
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Residues in contact with VAL 298 (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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1413 SER* 4.5 9.9 - - - +
1423 LEU* 3.7 34.5 - - + -
1453 SER* 3.5 27.4 - - - +
1473 ARG* 4.3 8.7 - - - -
1513 ILE 2.9 6.5 + - - +
1523 VAL* 3.1 20.5 - - + +
1533 LEU* 2.9 25.6 + - - +
2963 ASN 3.4 3.1 + - - +
2973 ASN* 1.3 75.1 + - - +
2993 MET* 1.3 71.6 - - - +
3003 SER* 5.3 0.2 - - - -
3303 ILE* 3.3 17.5 - - + +
3323 PRO* 5.3 4.0 - - + -
3383 SER* 5.9 1.3 - - - +
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Residues in contact with MET 299 (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* 3.6 35.9 - - + +
2973 ASN* 4.8 5.8 - - - -
2983 VAL* 1.3 78.1 - - - +
3003 SER* 1.3 61.9 + - - +
3043 THR* 3.8 19.3 - - - +
3093 ILE* 4.3 14.4 - - + -
3103 ALA* 4.0 15.0 - - - +
3133 MET* 4.8 11.0 - - - -
3293 ILE* 3.6 32.5 - - + -
3303 ILE 2.8 11.3 + - - +
3313 ALA* 3.4 28.9 - - + -
3323 PRO* 4.0 11.1 - - - +
3353 ARG* 3.8 13.8 - - - +
3383 SER* 4.4 1.6 + - - -
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Residues in contact with SER 300 (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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1413 SER* 3.0 34.1 + - - -
1523 VAL* 3.6 4.8 - - - +
1533 LEU 3.1 10.1 + - - +
1543 ASP* 3.0 23.0 + - - +
1553 SER 3.1 21.3 + - - -
2983 VAL* 4.2 1.1 + - - -
2993 MET* 1.3 78.0 - - - +
3013 GLY* 1.3 60.2 + - - +
3043 THR* 3.3 10.3 - - - +
3353 ARG* 4.0 4.9 - - - -
3383 SER* 3.7 14.1 - - - -
3393 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