Contacts of the helix formed by residues 2268 - 2284 (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 ASN2268 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2203L LEU* 5.8 0.2 - - - +
2206L THR* 5.2 8.9 - - - +
2228L VAL* 3.2 40.9 - - + +
2231L MET* 4.1 21.2 - - - +
2266L LEU 5.3 0.2 + - - -
2267L MET* 1.3 82.3 - - - +
2269L SER* 1.3 60.6 + - - +
2270L LEU* 3.4 7.4 - - + +
2271L VAL* 3.9 15.1 - - + +
2272L SER* 3.1 27.4 + - - -
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Residues in contact with SER2269 (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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2267L MET 3.8 1.0 + - - -
2268L ASN* 1.3 74.3 - - - +
2270L LEU* 1.3 71.6 + - - +
2272L SER* 3.0 9.1 + - - -
2273L GLN* 2.9 41.5 + - - +
353P LYS* 6.3 1.1 - - - -
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Residues in contact with LEU2270 (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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2228L VAL* 5.6 5.6 - - + -
2232L ARG* 4.4 34.1 - - + +
2236L ARG* 5.3 5.4 - - - +
2268L ASN* 3.4 5.6 - - + +
2269L SER* 1.3 90.5 - - - +
2271L VAL* 1.3 67.3 + - + +
2273L GLN* 3.1 19.2 + - - +
2274L VAL* 3.0 29.3 + - + +
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Residues in contact with VAL2271 (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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2199L LEU* 4.2 5.8 - - + -
2228L VAL* 4.1 8.5 - - + +
2231L MET* 3.8 40.4 - - + +
2232L ARG* 3.9 18.6 - - + +
2235L ALA* 4.2 5.4 - - + -
2267L MET* 3.6 35.2 - - + -
2268L ASN* 3.8 21.5 + - + +
2269L SER 3.6 0.2 - - - -
2270L LEU* 1.3 74.2 - - + +
2272L SER* 1.3 57.5 + - - +
2274L VAL* 3.2 6.0 + - - +
2275L ILE* 2.9 32.9 + - + +
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Residues in contact with SER2272 (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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2261L ILE* 6.1 0.2 - - - -
2262L SER* 4.5 12.8 - - - +
2264L SER 5.9 0.2 - - - -
2267L MET* 4.1 13.8 - - - +
2268L ASN 3.1 18.5 + - - -
2269L SER* 3.0 15.1 + - - -
2271L VAL* 1.3 74.3 - - - +
2273L GLN* 1.3 64.4 + - - +
2275L ILE* 3.7 7.3 - - - -
2276L CYS* 2.8 39.9 + - - -
335P GLU* 5.1 4.0 - - - +
355P SER* 4.1 18.5 + - - -
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Residues in contact with GLN2273 (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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2269L SER* 2.9 37.3 + - - +
2270L LEU* 3.1 21.2 + - - +
2272L SER* 1.3 77.7 + - - +
2274L VAL* 1.3 59.8 + - + +
2276L CYS* 3.3 1.7 + - - +
2277L ASP* 2.9 35.7 + - - +
335P GLU* 3.5 40.6 + - + +
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Residues in contact with VAL2274 (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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2232L ARG* 5.0 4.0 - - + +
2235L ALA* 3.1 44.9 - - + +
2236L ARG* 3.7 24.2 - - + +
2239L LEU* 3.6 22.0 - - + -
2270L LEU* 3.0 16.8 + - + +
2271L VAL* 3.6 6.3 - - - +
2273L GLN* 1.3 77.3 - - + +
2275L ILE* 1.3 57.6 + - - +
2277L ASP* 3.1 10.6 + - - +
2278L VAL* 2.9 26.5 + - - +
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Residues in contact with ILE2275 (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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2199L LEU* 3.9 19.3 - - + -
2235L ALA* 3.8 24.2 - - + +
2238L LEU* 4.5 2.7 - - + -
2258L LEU* 3.6 30.3 - - + +
2261L ILE* 3.8 20.6 - - + -
2262L SER* 3.6 22.7 - - - -
2271L VAL* 2.9 24.6 + - + +
2272L SER* 3.2 7.8 + - - +
2274L VAL* 1.3 75.9 - - - +
2276L CYS* 1.3 56.8 + - - +
2278L VAL* 3.0 15.0 - - + +
2279L LEU* 2.9 28.0 + - + +
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Residues in contact with CYS2276 (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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2262L SER* 4.0 13.7 - - - -
2272L SER* 2.8 31.0 + - - +
2273L GLN 3.8 2.0 - - - +
2275L ILE* 1.3 76.1 - - - +
2277L ASP* 1.3 60.2 + - - +
2279L LEU* 3.7 7.4 - - - -
2280L PHE* 2.9 24.6 + - - +
329P GLN* 3.2 10.0 + - - -
334P ARG* 3.4 21.5 - - - +
335P GLU* 3.6 21.3 - - - +
354P PHE* 3.4 30.1 - - + -
355P SER* 5.9 1.1 - - - -
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Residues in contact with ASP2277 (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* 3.9 25.6 - - + +
2273L GLN* 2.9 17.7 + - - +
2274L VAL* 3.1 13.2 + - - +
2276L CYS* 1.3 75.8 - - - +
2278L VAL* 1.3 58.2 + - - +
2280L PHE* 3.2 4.5 + - - +
2281L LEU* 3.0 30.0 + - - +
334P ARG* 3.1 43.8 + - - +
335P GLU* 4.8 3.1 - - - +
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Residues in contact with VAL2278 (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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2235L ALA 5.4 0.4 - - - +
2238L LEU* 3.7 18.4 - - + +
2239L LEU* 4.1 14.6 - - + +
2242L ALA* 3.4 26.5 - - + -
2251L PHE* 4.5 5.2 - - + -
2258L LEU* 4.2 19.5 - - + -
2274L VAL 2.9 14.9 + - - +
2275L ILE* 3.0 34.5 - - + +
2277L ASP* 1.3 73.2 - - - +
2279L LEU* 1.3 60.5 + - - +
2281L LEU* 3.3 4.0 + - - +
2282L ILE* 2.9 47.8 + - + +
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Residues in contact with LEU2279 (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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2255L GLU* 4.0 11.9 - - + +
2258L LEU* 3.8 35.2 - - + +
2259L LEU* 3.9 16.8 - - + +
2262L SER* 3.2 35.4 - - - +
2275L ILE 2.9 18.4 + - - +
2276L CYS* 3.8 7.6 - - - +
2278L VAL* 1.3 76.4 - - - +
2280L PHE* 1.3 57.0 + - - +
2282L ILE* 3.8 5.3 - - + +
2283L GLY* 2.9 22.9 + - - -
320P TRP* 3.5 41.2 - - + +
354P PHE* 4.6 11.2 - - + -
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Residues in contact with PHE2280 (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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2276L CYS 2.9 14.5 + - - +
2277L ASP 3.2 8.5 - - - +
2278L VAL 3.1 0.2 - - - -
2279L LEU* 1.3 74.5 - - - +
2281L LEU* 1.3 68.0 + - + +
2282L ILE 3.0 0.3 + - - -
2283L GLY 3.1 0.2 + - - -
2284L GLN* 2.6 68.3 + - + +
329P GLN* 3.7 39.4 + - + +
331P PRO* 4.1 29.6 - - + -
334P ARG* 3.9 42.8 - - + -
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Residues in contact with LEU2281 (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* 3.5 32.8 - - + -
2242L ALA* 4.0 22.7 - - + +
2243L LYS* 3.6 31.0 - - + +
2245L ASP* 5.8 2.5 - - - +
2248L HIS* 3.4 20.9 + - + -
2277L ASP 3.0 14.4 + - - +
2278L VAL* 3.3 6.3 + - - +
2280L PHE* 1.3 84.5 - - + +
2282L ILE* 1.3 60.5 + - - +
2284L GLN* 3.7 24.6 + - - +
2285L SER* 3.7 7.1 + - - -
334P ARG* 5.4 6.5 - - - +
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Residues in contact with ILE2282 (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* 4.3 7.2 - - + -
2248L HIS* 4.9 15.1 - - + +
2251L PHE* 3.5 53.4 - - + -
2252L THR* 5.7 1.6 - - + +
2255L GLU* 3.6 30.3 - - + +
2258L LEU* 3.5 21.5 - - + -
2278L VAL* 2.9 27.9 + - + +
2279L LEU* 4.0 5.4 - - + +
2281L LEU* 1.3 79.4 - - - +
2283L GLY* 1.3 61.4 + - - +
2285L SER* 3.8 13.9 + - - -
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Residues in contact with GLY2283 (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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2279L LEU 2.9 17.7 + - - -
2280L PHE* 5.1 0.2 - - - -
2282L ILE* 1.3 75.9 - - - +
2284L GLN* 1.3 62.2 + - - +
2285L SER 2.9 15.0 + - - +
320P TRP* 4.3 3.4 - - - -
324P LYS* 3.5 45.4 - - - +
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Residues in contact with GLN2284 (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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2245L ASP* 5.3 6.5 + - - -
2248L HIS* 5.6 0.4 + - - -
2280L PHE* 2.6 59.4 + - + +
2281L LEU* 3.7 27.9 + - - +
2283L GLY* 1.3 70.7 - - - +
2285L SER* 1.3 68.9 + - - +
327P LYS* 6.1 5.9 - - - +
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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