Contacts of the strand formed by residues 297 - 300 (chain 0) in PDB entry 1O1F
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 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1510 ILE* 3.4 21.6 + - - +
1530 LEU* 4.5 13.7 - - - +
2780 THR* 3.2 33.6 + - - +
2820 ILE* 4.6 1.9 - - - +
2930 LEU 4.5 2.8 - - - +
2940 TYR 5.0 1.7 - - - +
2960 ASN* 1.3 70.7 - - - +
2980 VAL* 1.3 62.1 + - - +
2990 MET* 3.8 2.4 + - - -
3130 MET* 4.4 13.5 - - - +
3170 ILE* 3.9 9.9 - - - +
3280 LYS 2.9 15.6 + - - +
3290 ILE* 3.5 25.8 - - + +
3300 ILE* 2.7 31.1 + - - +
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Residues in contact with VAL 298 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1410 SER* 4.5 9.2 - - - +
1420 LEU* 3.7 34.5 - - + -
1450 SER* 3.5 27.1 - - - +
1470 ARG* 4.3 9.4 - - - -
1510 ILE 2.9 6.9 + - - +
1520 VAL* 3.1 20.4 - - + +
1530 LEU* 2.9 25.6 + - - +
2960 ASN 4.4 2.5 - - - +
2970 ASN* 1.3 76.8 - - - +
2990 MET* 1.3 71.6 - - - +
3300 ILE* 3.3 18.2 - - + +
3320 PRO* 5.3 4.3 - - + -
3380 SER* 5.9 1.1 - - - +
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Residues in contact with MET 299 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1530 LEU* 3.6 35.9 - - + +
2970 ASN* 4.8 5.6 - - - -
2980 VAL* 1.3 77.8 - - - +
3000 SER* 1.3 62.7 + - - +
3040 THR* 3.8 18.6 - - - +
3090 ILE* 4.3 13.2 - - + -
3100 ALA* 4.0 14.4 - - + -
3130 MET* 4.8 11.4 - - - -
3290 ILE* 3.6 31.6 - - + -
3300 ILE 2.8 11.0 + - - +
3310 ALA* 3.4 30.3 - - + -
3320 PRO* 3.9 11.4 - - - +
3350 ARG* 3.8 13.4 - - - +
3380 SER* 4.4 1.7 + - - -
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Residues in contact with SER 300 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1410 SER* 3.0 34.6 + - - -
1520 VAL* 3.6 5.0 - - - +
1530 LEU 3.1 10.1 + - - +
1540 ASP* 3.0 23.7 + - - +
1550 SER 3.1 21.3 + - - -
2980 VAL* 4.2 0.6 + - - -
2990 MET* 1.3 77.4 - - - +
3010 GLY* 1.3 60.4 + - - +
3040 THR* 3.3 10.8 - - - +
3350 ARG* 4.0 4.9 - - - -
3380 SER* 3.7 14.4 - - - -
3390 VAL* 4.5 2.6 - - - +
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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