Contacts of the helix formed by residues 2254 - 2264 (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 TYR2254 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2190L GLY* 4.6 10.0 - - - -
2192L ILE* 3.7 18.4 - - + -
2193L GLY* 3.5 29.4 + - - -
2196L LEU* 3.5 19.5 - - + -
2250L GLU 3.2 26.9 - - - -
2251L PHE* 2.8 9.7 + - - +
2252L THR 4.0 5.4 - - - -
2253L LEU* 1.3 90.2 - - + +
2255L GLU* 1.3 56.8 + - - +
2256L SER* 3.2 3.1 - - - -
2257L ARG* 3.1 39.3 + - - +
2258L LEU* 2.9 32.6 + - + +
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Residues in contact with GLU2255 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2251L PHE 3.0 11.6 + - - +
2252L THR* 4.8 12.3 - - - +
2253L LEU 3.8 1.0 - - - +
2254L TYR* 1.3 77.4 - - - +
2256L SER* 1.3 58.2 + - - +
2258L LEU* 3.4 12.8 + - - +
2259L LEU* 2.9 26.2 + - - +
2279L LEU* 4.0 6.5 - - + +
2282L ILE* 3.6 27.0 - - + +
925O GLN* 4.2 19.1 + - - +
320P TRP* 2.7 24.7 + - + +
324P LYS* 2.5 39.3 + - - +
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Residues in contact with SER2256 (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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2253L LEU 5.1 5.1 + - - -
2254L TYR 4.7 1.2 - - - +
2255L GLU* 1.3 79.7 - - - +
2257L ARG* 1.3 67.6 + - - +
2259L LEU* 3.3 9.5 - - - +
2260L ASP* 2.9 27.5 + - - +
925O GLN* 6.0 0.4 - - - +
174P ARG* 5.8 2.3 + - - -
317P GLN* 4.0 34.5 + - - -
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Residues in contact with ARG2257 (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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2193L GLY* 3.6 21.4 + - - -
2196L LEU* 3.7 19.5 - - + +
2197L GLY* 3.9 2.6 - - - +
2200L GLU* 3.0 40.3 + - - +
2253L LEU 4.7 10.9 + - - -
2254L TYR* 3.1 38.0 + - - +
2256L SER* 1.3 85.0 + - - +
2258L LEU* 1.3 61.0 + - - +
2260L ASP* 3.3 8.0 + - + +
2261L ILE* 2.9 34.6 + - - +
170P GLU* 3.6 36.2 + - - +
174P ARG* 4.4 24.4 - - - +
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Residues in contact with LEU2258 (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* 6.0 0.2 - - + -
2196L LEU* 3.6 26.2 - - + +
2238L LEU* 4.0 15.9 - - + -
2251L PHE* 4.2 12.8 - - + -
2254L TYR* 2.9 19.0 + - + +
2255L GLU* 3.6 13.9 - - - +
2257L ARG* 1.3 74.3 - - - +
2259L LEU* 1.3 65.6 + - - +
2261L ILE* 3.2 4.9 + - + -
2262L SER* 2.9 22.5 + - - -
2275L ILE* 3.6 17.5 - - + +
2278L VAL* 4.2 18.6 - - + -
2279L LEU* 3.8 16.8 - - + -
2282L ILE* 3.5 31.4 - - + -
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Residues in contact with LEU2259 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2255L GLU 2.9 14.3 + - - +
2256L SER* 3.3 9.4 - - - +
2258L LEU* 1.3 75.9 - - - +
2260L ASP* 1.3 63.5 + - - +
2262L SER* 2.9 11.0 + - - +
2263L VAL* 2.9 32.5 + - + +
2279L LEU* 3.9 12.0 - - + +
316P ILE* 3.7 30.5 - - + +
317P GLN* 3.7 23.6 - - + -
320P TRP* 3.4 48.2 - - + -
354P PHE* 6.0 4.9 - - + -
357P ILE* 5.9 4.9 - - + -
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Residues in contact with ASP2260 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2200L GLU* 5.9 1.3 - - - +
2256L SER 2.9 15.1 + - - +
2257L ARG* 3.3 12.1 + - - +
2259L LEU* 1.3 76.0 - - - +
2261L ILE* 1.3 62.8 + - + +
2263L VAL* 3.3 12.3 - - - +
2264L SER* 3.2 24.3 + - - -
174P ARG* 4.2 19.8 + - - +
313P PRO* 6.0 3.9 - - - +
316P ILE* 6.0 0.7 - - - -
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Residues in contact with ILE2261 (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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2196L LEU* 3.6 30.5 - - + -
2199L LEU* 3.8 17.9 - - + -
2200L GLU* 3.8 30.3 - - + +
2203L LEU* 4.4 16.2 - - + +
2257L ARG 2.9 17.0 + - - +
2258L LEU* 3.6 4.0 - - + +
2260L ASP* 1.3 79.7 - - + +
2262L SER* 1.3 64.6 + - - +
2264L SER* 3.4 13.0 + - - -
2267L MET* 3.6 32.9 - - + +
2275L ILE* 3.8 23.8 - - + -
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Residues in contact with SER2262 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2258L LEU 2.9 7.3 + - - -
2259L LEU* 2.9 15.2 + - - +
2261L ILE* 1.3 80.9 - - - +
2263L VAL* 1.3 69.9 + - - +
2264L SER 3.1 8.3 + - - +
2267L MET* 5.4 0.2 - - - +
2272L SER* 4.5 11.4 - - - -
2275L ILE* 3.6 25.6 - - - -
2276L CYS* 4.0 19.2 - - - -
2279L LEU* 3.2 19.4 - - - +
354P PHE* 4.5 8.3 - - - +
355P SER* 3.9 15.0 + - - -
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Residues in contact with VAL2263 (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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2259L LEU* 2.9 16.4 + - + +
2260L ASP* 3.3 23.3 - - - +
2262L SER* 1.3 78.2 + - - +
2264L SER* 1.3 66.7 + - - +
316P ILE* 4.3 32.3 - - + -
354P PHE* 3.8 17.3 - - + +
355P SER* 3.9 4.2 - - - +
357P ILE* 3.9 16.2 - - + -
358P PRO* 3.3 41.6 - - + +
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Residues in contact with SER2264 (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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2203L LEU* 4.1 13.2 - - - +
2260L ASP* 3.2 15.8 + - - -
2261L ILE 3.5 14.4 - - - -
2262L SER 3.1 9.2 - - - +
2263L VAL* 1.3 80.5 - - - +
2265L PRO* 1.3 72.3 - - - +
2266L LEU* 3.3 25.5 + - - +
2267L MET* 3.9 13.2 + - - +
2272L SER* 5.9 0.2 - - - -
355P SER* 4.5 7.3 + - - -
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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