Contacts of the helix formed by residues 2226 - 2242 (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 PHE2226 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2171F MET* 3.7 38.1 - - + -
2172F GLY* 4.5 14.6 - - - -
2173F PRO* 5.2 4.7 - - + -
2176F GLU* 5.0 9.0 - - + -
2215F VAL* 3.7 24.6 - - + +
2225F ARG* 1.3 82.7 - - + +
2227F PRO* 1.3 74.5 - - - +
2228F LYS 3.4 2.2 - - - -
2229F MET* 3.4 26.1 + - + +
2230F VAL* 3.2 18.7 + - - +
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Residues in contact with PRO2227 (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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2225F ARG* 3.6 3.8 - - - +
2226F PHE* 1.3 86.3 - - - +
2228F LYS* 1.3 66.6 + - + +
2230F VAL* 3.1 11.9 - - + +
2231F THR* 2.9 32.7 + - + +
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Residues in contact with LYS2228 (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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2180F ILE* 3.6 24.0 - - + +
2226F PHE 3.4 0.4 - - - -
2227F PRO* 1.3 79.7 - - + +
2229F MET* 1.3 58.4 + - - +
2231F THR* 2.7 21.6 + - - -
2232F SER* 2.8 19.2 + - - -
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Residues in contact with MET2229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2171F MET* 4.8 11.9 - - + -
2175F GLU 6.2 0.4 - - - -
2176F GLU* 4.5 22.9 - - + -
2179F MET* 3.6 33.2 - - + -
2180F ILE* 4.4 6.8 - - + +
2211F VAL* 3.7 26.7 - - + -
2215F VAL* 4.3 26.7 - - + -
2226F PHE* 3.4 29.4 + - + +
2227F PRO 3.2 0.2 - - - -
2228F LYS* 1.3 77.7 - - - +
2230F VAL* 1.3 58.3 + - - +
2232F SER* 2.5 21.0 + - - +
2233F CYS* 3.0 20.3 + - + +
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Residues in contact with VAL2230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2212F MET* 5.6 1.8 - - + -
2215F VAL* 5.7 3.4 - - + -
2216F LEU* 4.4 23.3 - - + -
2225F ARG 5.0 4.0 - - - +
2226F PHE 3.2 11.7 + - - +
2227F PRO* 3.1 21.5 - - + +
2229F MET* 1.3 76.8 - - - +
2231F THR* 1.3 70.1 + - + +
2233F CYS* 3.1 11.1 - - - -
2234F CYS* 2.9 45.8 + - - -
2271F SER 5.1 6.7 - - - +
2273F PRO* 5.3 6.5 - - + -
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Residues in contact with THR2231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2227F PRO* 2.9 22.0 + - + +
2228F LYS* 2.7 26.0 + - - -
2230F VAL* 1.3 82.2 - - + +
2232F SER* 1.3 54.5 + - - +
2234F CYS 3.5 0.2 + - - -
2235F ARG* 2.9 41.5 + - - +
2271F SER* 3.7 31.9 - - - +
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Residues in contact with SER2232 (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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2179F MET* 5.8 1.7 - - - +
2180F ILE* 4.0 20.6 - - - +
2183F ILE* 3.8 24.8 - - - +
2228F LYS 2.8 15.1 + - - -
2229F MET* 2.5 27.4 + - - +
2231F THR* 1.3 76.6 + - - +
2233F CYS* 1.3 55.7 + - - +
2235F ARG* 3.3 15.8 + - - +
2236F PHE* 2.9 28.2 + - - +
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Residues in contact with CYS2233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2179F MET* 5.9 4.5 - - + -
2183F ILE* 5.2 5.4 - - + +
2208F VAL* 3.9 22.7 - - + +
2211F VAL* 5.5 7.4 - - + -
2212F MET* 4.8 20.4 - - - -
2215F VAL* 5.6 3.6 - - - -
2229F MET* 3.0 21.6 + - + +
2230F VAL* 3.1 34.5 - - - -
2232F SER* 1.3 76.9 + - - +
2234F CYS* 1.3 61.3 + - - +
2236F PHE* 3.3 7.1 + - - +
2237F LEU* 2.9 34.1 + - + +
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Residues in contact with CYS2234 (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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2212F MET* 4.9 9.4 - - - -
2230F VAL* 2.9 42.6 + - - +
2233F CYS* 1.3 78.2 - - - +
2235F ARG* 1.3 58.8 + - - +
2237F LEU* 3.6 8.5 - - - +
2238F CYS* 2.9 34.0 + - - +
2271F SER* 3.7 23.3 - - - -
2272F THR 4.4 2.7 - - - +
2273F PRO* 4.0 26.5 - - - -
2276F VAL* 3.9 10.8 - - + +
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Residues in contact with ARG2235 (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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2183F ILE* 5.8 2.0 - - - +
2187F MET* 4.1 30.4 - - - +
2231F THR* 2.9 26.8 + - - +
2232F SER* 3.6 11.4 + - - +
2234F CYS* 1.3 76.9 - - - +
2236F PHE* 1.3 57.3 + - - +
2238F CYS* 3.3 5.9 + - - +
2239F TYR* 2.9 52.1 + - + -
2271F SER* 4.5 10.3 - - - -
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Residues in contact with PHE2236 (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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2183F ILE* 3.8 16.2 - - + -
2186F ILE* 3.5 36.6 - - + -
2187F MET* 4.0 23.6 - - + -
2192F PHE* 4.3 21.8 - + - -
2204F MET* 4.4 29.6 - - + -
2205F HIS* 5.4 1.6 - - - -
2208F VAL* 3.5 37.9 - - + -
2232F SER 2.9 17.1 + - - +
2233F CYS* 3.7 5.2 - - - +
2235F ARG* 1.3 74.8 - - - +
2237F LEU* 1.3 62.2 + - + +
2239F TYR* 3.3 7.1 + - + +
2240F PHE* 2.9 35.8 + + + +
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Residues in contact with LEU2237 (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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2205F HIS* 5.2 11.7 - - + +
2208F VAL* 4.4 25.8 - - + +
2209F MET* 5.3 4.3 - - + +
2212F MET* 4.4 27.4 - - + -
2233F CYS 2.9 20.7 + - - +
2234F CYS* 3.6 8.3 - - + +
2236F PHE* 1.3 81.3 - - + +
2238F CYS* 1.3 58.3 + - - +
2240F PHE* 2.9 10.1 + - + +
2241F CYS* 2.9 35.7 + - - -
2251F MET* 3.7 33.0 - - + -
2258F LEU* 5.3 2.0 - - + -
2276F VAL* 4.0 21.5 - - + -
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Residues in contact with CYS2238 (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* 2.9 21.6 + - - +
2235F ARG* 3.7 7.6 - - - +
2237F LEU* 1.3 75.9 - - - +
2239F TYR* 1.3 64.1 + - + +
2240F PHE 3.4 0.3 + - - -
2241F CYS* 3.6 12.6 + - - +
2242F ARG* 3.6 26.2 + - - +
2275F ASP* 4.4 13.5 - - - -
2276F VAL* 3.7 30.1 - - - -
2279F ALA* 4.9 9.3 - - + +
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Residues in contact with TYR2239 (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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2187F MET* 3.7 35.6 - - + +
2192F PHE* 5.2 6.5 - - + -
2193F TYR* 3.9 23.1 - + - -
2235F ARG* 2.9 45.6 + - + +
2236F PHE* 3.7 8.7 - - + +
2237F LEU 3.2 0.2 - - - -
2238F CYS* 1.3 79.4 - - + +
2240F PHE* 1.3 60.1 + - - +
2242F ARG* 3.8 31.3 + - - +
2243F ILE* 3.3 22.3 + - - +
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Residues in contact with PHE2240 (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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2192F PHE* 3.5 33.6 - + + -
2199F MET* 4.2 15.0 - - + -
2200F ARG* 4.9 1.8 - - + -
2204F MET* 4.3 8.1 - - + -
2205F HIS* 3.7 42.8 - + + -
2236F PHE* 2.9 29.1 + + + +
2237F LEU* 2.9 11.2 + - + +
2239F TYR* 1.3 76.8 - - - +
2241F CYS* 1.3 66.8 + - - +
2243F ILE* 3.3 16.2 + - - +
2247F ASN* 3.3 57.5 + - + +
2250F SER* 5.6 2.0 - - - -
2251F MET* 5.3 10.5 - - + -
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Residues in contact with CYS2241 (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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2237F LEU* 2.9 31.1 + - - +
2238F CYS* 3.6 6.0 + - - +
2239F TYR 3.5 0.4 - - - -
2240F PHE* 1.3 80.7 - - - +
2242F ARG* 1.3 58.7 + - + +
2243F ILE 3.2 4.3 + - - -
2244F SER 3.8 13.5 - - - +
2247F ASN* 4.9 6.7 - - - -
2248F GLN* 4.0 29.4 + - - +
2251F MET* 3.7 30.3 - - + -
2276F VAL* 4.1 19.5 - - - -
2279F ALA* 4.9 13.0 - - + +
2280F SER* 5.2 2.0 - - - -
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Residues in contact with ARG2242 (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* 3.6 20.3 + - - +
2239F TYR* 3.8 38.6 + - - +
2240F PHE 3.3 0.8 - - - -
2241F CYS* 1.3 78.7 - - + +
2243F ILE* 1.3 66.5 + - - +
2244F SER 3.8 0.2 - - - -
2279F ALA* 5.3 12.3 - - + +
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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
------------------------------------------------------------
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