Contacts of the helix formed by residues 2247 - 2252 (chain L) in PDB entry 6LTJ
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 ASN2247 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2182L ALA 3.6 9.9 + - - -
2183L ARG* 3.1 27.9 + - - -
2186L ALA* 3.2 28.6 - - + +
2241L LEU 2.6 31.6 + - - +
2242L ALA* 4.9 1.3 - - - -
2244L VAL* 3.2 24.5 - - + +
2245L ASP 3.6 1.2 - - - +
2246L GLU* 1.3 76.7 - - - +
2248L HIS* 1.3 57.8 + - - +
2249L SER 3.1 3.6 - - - -
2250L GLU* 2.9 26.5 + - - +
2251L PHE* 3.1 20.4 - - + -
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Residues in contact with HIS2248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2242L ALA* 3.1 31.6 + - + -
2245L ASP* 3.4 38.6 + - + +
2246L GLU* 3.4 2.2 - - - -
2247L ASN* 1.3 79.4 - - - +
2249L SER* 1.3 60.4 + - - +
2251L PHE* 3.3 20.2 + - - +
2252L THR* 3.7 14.4 + - - +
2281L LEU* 3.4 19.9 + - + -
2282L ILE* 4.9 12.1 - - + +
2284L GLN* 5.6 1.2 + - - -
2285L SER* 3.1 36.9 + - - -
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Residues in contact with SER2249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2246L GLU 4.5 5.2 + - - -
2247L ASN 3.1 0.6 - - - -
2248L HIS* 1.3 77.6 - - - +
2250L GLU* 1.3 73.8 + - - +
2251L PHE 3.4 0.2 - - - -
2252L THR* 3.2 15.1 + - - +
918O GLU* 3.2 34.0 + - - +
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Residues in contact with GLU2250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2183L ARG* 3.6 25.5 + - - -
2186L ALA* 3.8 17.7 - - + +
2187L VAL* 4.3 11.2 - - - +
2192L ILE* 3.6 21.7 - - + +
2246L GLU 3.5 1.9 - - - +
2247L ASN* 2.9 30.5 + - - +
2249L SER* 1.3 91.2 + - - +
2251L PHE* 1.3 57.9 + - - +
2252L THR 3.5 4.5 - - - +
2254L TYR* 3.2 26.0 - - - -
918O GLU* 5.2 0.9 - - - -
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Residues in contact with PHE2251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2192L ILE* 3.8 24.0 - - + -
2238L LEU* 3.8 28.3 - - + -
2241L LEU* 3.7 14.1 - - + -
2242L ALA* 3.6 37.5 - - + -
2247L ASN* 3.1 37.5 - - + -
2248L HIS* 3.3 11.8 + - - +
2250L GLU* 1.3 76.3 - - - +
2252L THR* 1.3 61.7 + - - +
2254L TYR* 2.8 24.8 + - + +
2255L GLU* 3.0 13.6 + - - -
2258L LEU* 4.2 8.7 - - + -
2278L VAL* 4.5 3.6 - - + -
2282L ILE* 3.5 40.8 - - + -
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Residues in contact with THR2252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2248L HIS 3.9 12.6 - - - +
2249L SER* 3.2 19.3 + - - +
2250L GLU 3.5 10.0 - - - +
2251L PHE* 1.3 79.7 - - - +
2253L LEU* 1.3 67.0 + - - +
2254L TYR* 3.4 3.3 + - - +
2255L GLU* 4.6 15.5 - - - +
2282L ILE* 5.7 1.5 - - + +
918O GLU* 3.5 23.1 - - + +
921O GLU* 4.9 9.6 - - - -
922O TYR* 5.9 11.0 - - + -
925O GLN* 5.4 9.6 - - - +
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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