Contacts of the helix formed by residues 2272 - 2282 (chain H) in PDB entry 6X34
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 THR2272 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2234H CYS* 4.4 4.4 - - - +
2262H SER* 5.2 7.6 - - - +
2271H SER* 1.3 79.3 + - - +
2273H PRO* 1.3 77.0 - - + +
2274H LEU* 3.6 35.4 - - + +
2275H ASP* 2.8 32.0 + - - +
2276H VAL* 3.6 3.8 + - - +
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Residues in contact with PRO2273 (chain H).
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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2212H MET* 5.1 9.2 - - - -
2216H LEU* 5.5 6.3 - - + -
2230H VAL* 5.3 6.1 - - + -
2234H CYS* 4.0 18.2 - - - -
2258H LEU* 3.8 34.9 - - + +
2261H ASN* 4.7 10.5 - - + +
2262H SER* 4.4 17.9 - - - +
2271H SER 4.7 0.2 - - - +
2272H THR* 1.3 92.0 - - + +
2274H LEU* 1.3 56.4 + - - +
2275H ASP 3.2 0.2 - - - -
2276H VAL* 3.2 15.1 + - + +
2277H ALA* 2.9 26.5 + - - +
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Residues in contact with LEU2274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2258H LEU 5.5 0.2 - - - -
2262H SER* 3.9 25.5 - - - +
2263H GLY 5.6 1.8 - - - +
2272H THR* 3.0 29.3 + - + +
2273H PRO* 1.3 78.8 - - - +
2275H ASP* 1.3 65.6 + - + +
2277H ALA* 3.3 8.7 + - - +
2278H ALA* 2.9 29.8 + - + +
2331H ARG* 3.5 42.2 - - + +
2332H TYR* 5.7 1.8 - - - -
2334H ASP* 6.0 2.2 - - + -
2335H PHE* 4.4 11.8 - - + +
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Residues in contact with ASP2275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2238H CYS* 4.4 13.1 - - - -
2271H SER* 5.8 2.0 - - - -
2272H THR* 2.8 19.2 + - - +
2274H LEU* 1.3 86.1 - - + +
2276H VAL* 1.3 59.2 + - - +
2278H ALA* 3.3 7.0 + - - +
2279H ALA* 2.9 29.5 + - - +
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Residues in contact with VAL2276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2234H CYS* 3.9 19.3 - - + +
2237H LEU* 4.0 15.3 - - + -
2238H CYS* 3.7 23.8 - - - -
2241H CYS* 4.1 17.0 - - - -
2251H MET* 3.9 19.5 - - + -
2258H LEU* 3.8 19.7 - - + -
2272H THR 3.6 2.9 + - - +
2273H PRO* 3.2 20.9 + - + +
2275H ASP* 1.3 76.5 - - - +
2277H ALA* 1.3 57.4 + - - +
2279H ALA* 3.3 4.8 + - - +
2280H SER* 2.9 27.5 + - - -
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Residues in contact with ALA2277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2255H LEU* 3.9 14.1 - - + -
2258H LEU* 4.4 13.8 - - + +
2259H LEU* 5.4 5.4 - - + +
2273H PRO 2.9 13.1 + - - +
2274H LEU* 3.5 11.7 - - - +
2275H ASP 3.3 0.2 - - - -
2276H VAL* 1.3 76.8 - - - +
2278H ALA* 1.3 56.6 + - - +
2280H SER* 2.5 23.1 + - - -
2281H VAL* 2.9 19.9 + - - +
2335H PHE* 3.7 20.9 - - + -
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Residues in contact with ALA2278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2274H LEU* 2.9 17.8 + - + +
2275H ASP* 3.8 7.2 - - - +
2277H ALA* 1.3 75.8 - - - +
2279H ALA* 1.3 57.6 + - - +
2281H VAL* 3.5 3.9 + - - +
2282H ILE* 3.0 31.6 + - - +
2334H ASP* 5.2 0.7 - - + -
2335H PHE* 4.0 22.2 - - + +
2338H PHE* 3.6 35.0 - - + +
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Residues in contact with ALA2279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2238H CYS* 4.9 11.4 - - + -
2241H CYS* 4.9 13.7 - - + +
2242H ARG* 5.3 12.7 - - + +
2248H GLN* 3.4 10.9 + - - -
2275H ASP 2.9 17.8 + - - +
2276H VAL* 3.7 8.1 - - - +
2278H ALA* 1.3 76.2 - - - +
2280H SER* 1.3 59.8 + - - +
2282H ILE* 3.3 24.3 - - + +
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Residues in contact with SER2280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2241H CYS* 5.1 2.7 - - - +
2248H GLN* 2.9 39.3 + - - +
2251H MET* 5.1 12.8 - - - -
2252H PHE* 5.0 13.9 - - - -
2255H LEU* 4.1 10.6 - - - +
2258H LEU* 5.2 2.8 - - - +
2276H VAL* 2.9 14.5 + - - -
2277H ALA* 2.5 27.7 + - - -
2279H ALA* 1.3 77.3 - - - +
2281H VAL* 1.3 58.7 + - - +
2282H ILE 3.7 2.1 + - - +
2287H LEU* 3.6 11.9 - - - +
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Residues in contact with VAL2281 (chain H).
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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2252H PHE* 5.6 1.1 - - + -
2255H LEU* 4.2 16.4 - - + -
2277H ALA 2.9 17.1 + - - +
2278H ALA* 4.1 4.3 - - - +
2280H SER* 1.3 76.9 - - - +
2282H ILE* 1.3 64.3 + - - +
2283H ASP 3.9 0.3 + - - -
2284H ASN 4.0 10.2 + - - +
2287H LEU* 3.8 25.4 - - + +
2288H ALA* 5.2 7.2 - - + +
2291H LEU* 4.3 16.6 - - + -
2335H PHE* 4.1 22.2 - - + +
2338H PHE 4.9 2.7 - - - +
2339H ALA* 4.0 33.0 - - + +
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Residues in contact with ILE2282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2248H GLN* 4.3 3.8 + - - -
2278H ALA 3.0 16.8 + - - +
2279H ALA* 3.3 27.9 - - - +
2280H SER 3.8 4.2 - - - +
2281H VAL* 1.3 79.0 - - - +
2283H ASP* 1.3 85.8 + - + +
2284H ASN* 3.4 1.2 + - - +
2337H ARG* 6.2 0.4 - - - +
2338H PHE* 3.2 41.5 + - + +
2341H PHE* 3.7 18.2 - - + +
2342H VAL* 5.6 0.7 - - - -
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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