Contacts of the helix formed by residues 2335 - 2349 (chain L) in PDB entry 2BT4
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 VAL2335 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2220L LEU* 4.3 10.1 - - + -
2228L TYR 4.3 17.0 - - - +
2229L GLY* 6.0 0.7 - - - -
2231L ASP* 3.6 27.6 - - + +
2236L VAL* 3.7 26.7 - - + -
2239L LEU* 3.5 30.0 - - + +
2307L ILE* 4.3 7.6 - - + +
2334L GLY* 1.3 67.8 - - - -
2336L GLN* 1.3 63.9 + - - +
2337L GLY 3.0 6.4 + - - -
2338L TYR* 3.1 27.8 + - + +
2339L VAL 3.9 0.5 + - - -
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Residues in contact with GLN2336 (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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943E GLU* 3.4 23.4 + - - +
944E ARG* 2.8 36.3 + - - +
947E ALA* 3.3 15.9 - - - +
2239L LEU* 5.0 2.2 - - - -
2333L CYS 3.4 9.2 + - - +
2334L GLY* 3.0 1.4 - - - -
2335L VAL* 1.3 81.3 - - - +
2337L GLY* 1.3 61.3 + - - +
2338L TYR 3.2 0.2 - - - -
2339L VAL* 3.0 27.2 + - + +
2340L PHE* 3.1 39.4 + - + -
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Residues in contact with GLY2337 (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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2305L VAL* 3.7 18.4 - - - +
2306L HIS 5.8 0.2 - - - -
2330L VAL* 4.0 24.5 - - - +
2333L CYS* 3.4 5.5 + - - -
2334L GLY 2.9 15.0 + - - -
2336L GLN* 1.3 79.2 - - - +
2338L TYR* 1.3 56.2 + - - +
2340L PHE* 3.2 9.3 + - - +
2341L GLY 2.9 23.2 + - - -
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Residues in contact with TYR2338 (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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2211L ILE* 4.1 17.0 - - + -
2213L ASN* 2.7 29.7 + - - -
2217L LEU* 4.1 3.5 - - - +
2233L LEU* 4.8 3.1 - - - +
2236L VAL* 3.7 31.0 - - + +
2239L LEU* 5.7 1.8 - - + -
2240L CYS* 3.8 22.4 - - - -
2277L VAL* 4.5 10.7 - - + +
2279L ASN* 3.1 31.3 + - + +
2305L VAL* 3.9 17.9 - - + +
2307L ILE* 3.9 27.2 - - + +
2335L VAL* 3.1 21.0 + - - +
2337L GLY* 1.3 77.3 - - - +
2339L VAL* 1.3 62.8 + - + +
2341L GLY* 3.2 1.6 + - - -
2342L VAL* 3.0 27.2 + - - +
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Residues in contact with VAL2339 (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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2239L LEU* 4.3 39.5 - - + +
2240L CYS* 5.9 0.2 - - - -
2243L ALA* 4.1 18.2 - - + -
2335L VAL 4.6 1.1 - - - +
2336L GLN* 3.0 26.5 + - + +
2338L TYR* 1.3 75.3 - - - +
2340L PHE* 1.3 64.5 + - + +
2342L VAL* 3.1 4.3 + - - +
2343L GLU* 2.8 54.0 + - - +
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Residues in contact with PHE2340 (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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930E VAL* 5.1 0.7 - - + -
940E PHE* 3.4 58.8 - + + -
943E GLU* 3.4 28.5 - - + -
944E ARG* 3.9 6.7 - - + -
2303L VAL* 5.4 0.7 - - - -
2330L VAL* 4.2 11.9 - - + -
2333L CYS* 3.8 33.2 - - + -
2336L GLN* 3.1 48.4 + - + -
2337L GLY* 3.2 11.9 + - - +
2339L VAL* 1.3 76.6 - - + +
2341L GLY* 1.3 62.5 + - - +
2343L GLU* 3.1 7.7 + - - -
2344L ARG* 2.8 22.8 + - - +
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Residues in contact with GLY2341 (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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2277L VAL* 3.8 17.5 - - - -
2303L VAL* 3.9 25.4 - - - +
2330L VAL* 5.2 0.2 - - - +
2337L GLY 2.9 14.6 + - - -
2338L TYR 3.2 4.0 + - - -
2339L VAL 3.2 0.6 - - - -
2340L PHE* 1.3 75.3 - - - +
2342L VAL* 1.3 61.3 + - - +
2344L ARG* 3.2 2.6 + - - +
2345L ILE* 3.0 27.4 + - - +
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Residues in contact with VAL2342 (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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2204L LEU* 5.6 0.4 - - + -
2209L ILE* 3.8 26.1 - - + +
2211L ILE* 4.1 25.6 - - + -
2240L CYS* 4.5 15.0 - - + +
2243L ALA* 3.9 12.3 - - + +
2244L ALA* 3.8 28.7 - - - +
2247L HIS* 5.2 2.5 - - + -
2251L VAL* 4.8 0.7 - - + -
2277L VAL* 4.5 2.9 - - + -
2338L TYR 3.0 14.5 + - - +
2339L VAL 3.1 6.3 + - - +
2341L GLY* 1.3 75.7 - - - +
2343L GLU* 1.3 59.2 + - - +
2345L ILE* 3.3 2.1 + - - +
2346L ALA* 2.8 29.5 + - + +
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Residues in contact with GLU2343 (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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936E GLN* 3.5 15.5 + - - +
940E PHE* 3.2 18.9 - - + -
943E GLU* 2.6 37.4 - - - +
2243L ALA* 5.4 2.2 - - + -
2247L HIS* 4.0 28.5 + - + +
2339L VAL* 2.8 37.3 + - + +
2340L PHE* 3.1 7.0 + - - +
2342L VAL* 1.3 76.3 - - + +
2344L ARG* 1.3 61.8 + - - +
2346L ALA* 3.4 7.1 + - - +
2347L ALA* 3.1 17.2 + - - +
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Residues in contact with ARG2344 (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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932E GLY 4.3 5.3 + - - -
933E CYS* 3.1 53.3 + - - +
934E GLY* 3.7 7.1 - - - +
936E GLN* 2.9 34.3 + - - +
940E PHE* 3.9 7.6 - - + -
2303L VAL* 4.0 21.8 - - + -
2327L ASP* 6.2 1.0 - - + +
2328L GLY* 5.9 0.9 - - - -
2340L PHE 2.8 16.3 + - - +
2341L GLY 3.7 4.0 - - - +
2343L GLU* 1.3 75.7 - - - +
2345L ILE* 1.3 59.8 + - - +
2347L ALA* 3.1 9.2 + - - +
2348L LEU* 2.9 61.5 + - + +
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Residues in contact with ILE2345 (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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2204L LEU* 4.4 7.2 - - + -
2209L ILE* 4.0 28.0 - - + -
2274L CYS* 4.2 7.9 - - - +
2275L GLY* 4.1 14.4 - - - -
2276L ILE 3.8 13.9 - - - +
2277L VAL* 3.9 15.3 - - + -
2301L PRO* 3.6 38.6 - - + +
2303L VAL* 4.0 13.9 - - + -
2341L GLY 3.0 19.0 + - - +
2342L VAL 3.7 5.6 - - - +
2344L ARG* 1.3 75.6 - - - +
2346L ALA* 1.3 58.9 + - - +
2348L LEU* 4.4 4.0 - - - +
2349L ALA* 2.7 30.6 + - + +
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Residues in contact with ALA2346 (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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2204L LEU* 3.8 30.5 - - + +
2247L HIS* 3.8 28.9 - - + +
2342L VAL* 2.8 17.8 + - + +
2343L GLU 3.6 5.6 - - - +
2344L ARG 3.2 0.2 - - - -
2345L ILE* 1.3 78.2 - - - +
2347L ALA* 1.3 61.9 + - - +
2348L LEU 3.5 0.2 + - - -
2349L ALA 3.7 4.2 - - - +
2350L GLY* 3.7 14.2 + - - -
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Residues in contact with ALA2347 (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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936E GLN* 3.4 28.3 - - - +
2343L GLU 3.1 9.7 + - - +
2344L ARG* 3.1 15.5 + - - +
2346L ALA* 1.3 78.4 - - - +
2348L LEU* 1.3 64.0 + - - +
2350L GLY* 3.5 15.4 + - - +
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Residues in contact with LEU2348 (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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2301L PRO* 3.5 35.4 - - + +
2302L VAL 5.4 0.2 - - - +
2303L VAL* 5.6 1.1 - - + -
2327L ASP* 4.8 16.4 - - + -
2344L ARG* 2.9 58.9 + - + +
2345L ILE* 3.9 3.4 - - + +
2347L ALA* 1.3 75.8 - - - +
2349L ALA* 1.3 56.6 + - - +
2350L GLY 2.7 17.4 + - - +
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Residues in contact with ALA2349 (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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2202L ARG 3.8 21.8 - - - +
2203L SER* 4.2 6.9 - - - -
2204L LEU* 3.6 30.3 + - + +
2274L CYS* 4.1 15.5 - - + +
2301L PRO* 4.7 4.3 - - + -
2345L ILE* 2.7 23.2 + - + +
2346L ALA 3.7 6.4 - - - +
2348L LEU* 1.3 69.7 - - - +
2350L GLY* 1.3 54.3 - - - +
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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