Contacts of the strand formed by residues 2243 - 2247 (chain C) in PDB entry 1B08
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 LYS2243 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2238C GLN 4.1 0.2 - - - +
2239C SER* 3.3 3.5 - - - -
2240C VAL* 2.8 39.1 + - + +
2242C GLU* 1.3 79.1 - - - +
2244C ILE* 1.3 64.8 + - - +
2245C PHE* 3.8 20.6 - - + +
2270C SER* 2.9 19.8 + - - -
2272C ARG* 4.1 9.4 - - - +
2276C GLU* 2.8 37.8 + - + +
2354C GLU* 3.0 38.1 + - + +
2355C PHE 3.5 11.9 - - - +
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Residues in contact with ILE2244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1227B GLN* 3.7 25.8 - - + +
1228B TYR* 3.5 35.4 - - + +
1231B VAL* 3.9 33.0 - - + -
2233C LEU* 3.7 21.1 - - + -
2238C GLN 3.4 5.8 - - - +
2239C SER* 4.1 13.5 - - - -
2242C GLU 4.6 1.1 - - - +
2243C LYS* 1.3 76.1 - - - +
2245C PHE* 1.3 74.8 + - - +
2246C LYS* 4.9 0.7 - - + -
2354C GLU* 3.1 3.7 - - - -
2355C PHE* 2.7 40.0 + - + +
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Residues in contact with PHE2245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2237C GLY* 3.0 4.0 - - - -
2238C GLN* 2.7 34.3 + - + +
2240C VAL* 3.7 24.9 - - + -
2243C LYS* 3.8 15.0 - - + -
2244C ILE* 1.3 77.2 - - - +
2246C LYS* 1.3 60.8 + - - +
2269C ALA* 4.0 21.3 - - + -
2270C SER 4.5 0.7 - - - -
2271C PRO* 4.6 6.3 - - + -
2276C GLU* 3.4 35.2 - - + -
2279C ALA* 4.1 4.0 - - + -
2280C LEU* 3.8 26.5 - - + -
2283C LEU* 3.8 17.7 - - + -
2352C VAL* 4.2 3.1 - - + -
2353C CYS 3.3 4.9 - - - +
2354C GLU* 3.6 36.1 - - + -
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Residues in contact with LYS2246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1231B VAL* 2.8 41.0 + - + +
1232B GLU 4.1 3.4 + - - -
1234B PHE* 2.9 37.6 + - + -
1235B PRO* 5.1 1.8 - - - -
2232C GLU* 2.8 29.6 + - - +
2233C LEU* 6.1 0.2 - - + -
2236C ASN* 3.4 28.9 - - - +
2237C GLY* 4.5 2.5 - - - +
2244C ILE 4.1 0.2 + - - -
2245C PHE* 1.3 75.6 - - - +
2247C THR* 1.3 73.2 + - - +
2283C LEU* 4.7 0.4 - - - -
2352C VAL* 4.1 3.3 - - - +
2353C CYS* 2.8 32.2 + - - +
2355C PHE* 4.3 10.1 - - + -
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Residues in contact with THR2247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1234B PHE* 3.9 3.6 - - - -
1235B PRO* 5.0 1.6 - - - +
2236C ASN* 3.0 46.4 + - + +
2246C LYS* 1.3 87.4 - - - +
2248C ALA* 1.3 60.8 + - - +
2249C GLY 3.2 12.3 + - - +
2283C LEU* 4.5 11.8 - - + +
2287C LYS* 4.3 18.8 - - + -
2350C LEU* 3.5 17.0 - - + +
2351C VAL 2.7 20.0 + - - -
2352C VAL* 4.0 12.8 - - - +
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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