Contacts of the helix formed by residues 2272 - 2282 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2234F CYS* 4.4 5.0 - - - +
2262F SER* 5.2 7.9 - - - +
2271F SER* 1.3 79.7 + - - +
2273F PRO* 1.3 75.9 - - + +
2274F LEU* 3.6 35.4 - - + +
2275F ASP* 2.8 31.9 + - - +
2276F VAL* 3.6 4.3 + - - +
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Residues in contact with PRO2273 (chain F).
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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2212F MET* 5.1 10.1 - - - -
2216F LEU* 5.5 7.0 - - + -
2230F VAL* 5.3 5.8 - - + -
2234F CYS* 4.0 16.6 - - - -
2237F LEU* 6.5 0.2 - - + -
2258F LEU* 3.8 33.9 - - + +
2261F ASN* 4.7 9.2 - - + +
2262F SER* 4.4 18.2 - - - +
2271F SER 4.7 0.4 - - - +
2272F THR* 1.3 90.1 - - + +
2274F LEU* 1.3 56.7 + - - +
2275F ASP 3.2 0.4 - - - -
2276F VAL* 3.2 15.9 + - + +
2277F ALA* 2.9 26.5 + - - +
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Residues in contact with LEU2274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2258F LEU 5.5 0.2 - - - -
2262F SER* 3.9 25.7 - - - +
2263F GLY 5.6 2.2 - - - +
2272F THR* 3.0 28.9 + - + +
2273F PRO* 1.3 79.2 - - - +
2275F ASP* 1.3 65.7 + - + +
2277F ALA* 3.3 8.9 + - - +
2278F ALA* 2.9 29.8 + - + +
2331F ARG* 3.5 42.0 - - + +
2332F TYR* 5.5 2.2 - - - +
2334F ASP* 6.0 2.0 - - + -
2335F PHE* 4.4 11.0 - - + +
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Residues in contact with ASP2275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2238F CYS* 4.4 13.3 - - - -
2271F SER* 5.8 1.8 - - - -
2272F THR* 2.8 18.7 + - - +
2274F LEU* 1.3 86.2 - - + +
2276F VAL* 1.3 58.8 + - - +
2278F ALA* 3.3 6.1 + - - +
2279F ALA* 2.9 29.5 + - - +
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Residues in contact with VAL2276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2234F CYS* 3.9 19.7 - - + +
2237F LEU* 4.0 14.8 - - + -
2238F CYS* 3.7 23.3 - - - -
2241F CYS* 4.1 16.7 - - - -
2251F MET* 3.9 19.3 - - + -
2258F LEU* 3.8 20.2 - - + -
2272F THR 3.6 2.9 + - - +
2273F PRO* 3.2 21.4 + - + +
2275F ASP* 1.3 74.8 - - - +
2277F ALA* 1.3 58.0 + - - +
2279F ALA* 3.3 4.4 + - - +
2280F SER* 2.9 28.1 + - - -
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Residues in contact with ALA2277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2255F LEU* 3.9 14.4 - - + -
2258F LEU* 4.4 14.3 - - + +
2259F LEU* 5.4 5.8 - - + +
2273F PRO 2.9 13.1 + - - +
2274F LEU* 3.5 12.1 - - - +
2275F ASP 3.3 0.2 - - - -
2276F VAL* 1.3 76.8 - - - +
2278F ALA* 1.3 56.5 + - - +
2280F SER* 2.5 23.3 + - - -
2281F VAL* 2.9 20.1 + - - +
2335F PHE* 3.7 20.0 - - + -
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Residues in contact with ALA2278 (chain F).
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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2274F LEU* 2.9 18.4 + - + +
2275F ASP* 3.3 7.4 + - - +
2277F ALA* 1.3 75.8 - - - +
2279F ALA* 1.3 58.0 + - - +
2281F VAL* 3.5 3.9 + - - +
2282F ILE* 3.0 30.7 + - - +
2334F ASP* 5.2 0.7 - - + -
2335F PHE* 4.0 20.3 - - + +
2338F PHE* 3.6 36.8 - - + +
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Residues in contact with ALA2279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2238F CYS* 4.9 11.4 - - + -
2241F CYS* 4.9 14.1 - - + +
2242F ARG* 5.3 13.5 - - + +
2248F GLN* 3.4 10.9 + - - -
2275F ASP 2.9 17.4 + - - +
2276F VAL* 3.7 7.2 - - - +
2277F ALA 3.2 0.2 - - - -
2278F ALA* 1.3 76.7 - - - +
2280F SER* 1.3 63.1 + - - +
2282F ILE* 3.3 24.2 - - + +
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Residues in contact with SER2280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2241F CYS* 5.1 3.1 - - - +
2248F GLN* 2.9 39.1 + - - +
2251F MET* 5.1 12.1 - - - -
2252F PHE* 5.0 14.4 - - - -
2255F LEU* 4.1 10.2 - - - +
2258F LEU* 5.2 2.9 - - - +
2276F VAL* 2.9 14.3 + - - -
2277F ALA* 2.5 27.0 + - - -
2279F ALA* 1.3 77.0 - - - +
2281F VAL* 1.3 59.4 + - - -
2282F ILE 3.8 1.7 - - - +
2287F LEU* 3.6 11.9 - - - +
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Residues in contact with VAL2281 (chain F).
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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2252F PHE* 5.6 1.1 - - + -
2255F LEU* 4.2 17.3 - - + -
2277F ALA 2.9 16.2 + - - +
2278F ALA* 4.1 3.8 - - - +
2280F SER* 1.3 77.0 - - - +
2282F ILE* 1.3 63.4 + - - +
2283F ASP 3.9 0.2 + - - -
2284F ASN 4.0 10.4 + - - +
2287F LEU* 3.8 25.9 - - + +
2288F ALA* 5.2 6.8 - - + +
2291F LEU* 4.3 16.8 - - + -
2335F PHE* 4.1 22.0 - - + +
2338F PHE 4.9 2.3 - - - +
2339F ALA* 4.0 33.0 - - + +
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Residues in contact with ILE2282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2248F GLN* 4.3 3.6 + - - -
2278F ALA 3.0 17.7 + - - +
2279F ALA* 3.3 27.9 - - + +
2280F SER 3.8 4.5 - - - +
2281F VAL* 1.3 78.6 - - - +
2283F ASP* 1.3 85.4 + - + +
2284F ASN* 3.4 1.2 + - - +
2337F ARG* 6.1 0.2 - - - +
2338F PHE* 3.2 42.8 + - + +
2341F PHE* 3.7 18.2 - - + +
2342F VAL* 5.6 1.1 - - - -
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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