Contacts of the helix formed by residues 2226 - 2242 (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 PHE2226 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2171H MET* 3.7 37.7 - - + -
2172H GLY* 4.5 15.3 - - - -
2173H PRO* 5.2 5.4 - - + -
2176H GLU* 5.0 9.4 - - + -
2215H VAL* 3.7 25.6 - - + +
2225H ARG* 1.3 85.2 - - + +
2227H PRO* 1.3 75.1 - - - +
2228H LYS 3.4 2.2 - - - +
2229H MET* 3.4 23.3 + - + +
2230H VAL* 3.2 18.9 + - - +
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Residues in contact with PRO2227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2225H ARG* 3.6 4.5 - - - +
2226H PHE* 1.3 85.6 - - - +
2228H LYS* 1.3 67.6 + - + +
2230H VAL* 3.1 12.5 - - + +
2231H THR* 2.9 30.7 + - + +
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Residues in contact with LYS2228 (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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2180H ILE* 3.6 22.7 - - + +
2226H PHE 3.4 0.8 - - - -
2227H PRO* 1.3 81.0 - - - +
2229H MET* 1.3 57.0 + - - +
2231H THR* 2.7 21.6 + - - -
2232H SER* 2.8 19.6 + - - -
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Residues in contact with MET2229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2171H MET* 4.8 13.0 - - + -
2176H GLU* 4.5 23.7 - - + +
2179H MET* 3.6 32.5 - - + -
2180H ILE* 4.4 6.3 - - + +
2211H VAL* 3.7 26.5 - - + -
2215H VAL* 4.3 25.8 - - + -
2226H PHE* 3.4 29.0 + - + +
2227H PRO 3.2 0.4 - - - -
2228H LYS* 1.3 79.2 - - - +
2230H VAL* 1.3 57.7 + - - +
2232H SER* 2.5 21.2 + - - +
2233H CYS* 3.0 19.9 + - + +
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Residues in contact with VAL2230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2212H MET* 5.6 1.3 - - + -
2215H VAL* 5.7 3.4 - - + -
2216H LEU* 4.4 24.9 - - + -
2225H ARG 5.0 3.6 - - - +
2226H PHE 3.2 12.4 + - - +
2227H PRO* 3.1 20.6 - - + +
2229H MET* 1.3 75.7 - - - +
2231H THR* 1.3 70.9 + - + +
2233H CYS* 3.1 11.5 - - - -
2234H CYS* 2.9 46.1 + - - -
2271H SER 5.1 5.2 - - - +
2273H PRO* 5.3 5.8 - - + -
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Residues in contact with THR2231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2227H PRO* 2.9 22.7 + - + +
2228H LYS* 2.7 26.4 + - - -
2230H VAL* 1.3 81.7 - - + +
2232H SER* 1.3 55.7 + - - +
2235H ARG* 2.9 40.6 + - - +
2271H SER* 3.7 33.0 - - - +
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Residues in contact with SER2232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2179H MET* 5.8 1.7 - - - +
2180H ILE* 4.0 20.7 - - - +
2183H ILE* 3.8 24.0 - - - +
2228H LYS 2.8 15.5 + - - -
2229H MET* 2.5 27.4 + - - +
2231H THR* 1.3 76.6 + - - +
2233H CYS* 1.3 54.8 + - - +
2235H ARG* 3.3 14.0 + - - +
2236H PHE* 2.9 28.8 + - - +
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Residues in contact with CYS2233 (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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2179H MET* 5.9 3.8 - - + -
2183H ILE* 5.2 5.8 - - + +
2208H VAL* 3.9 23.4 - - + +
2211H VAL* 5.5 8.5 - - + -
2212H MET* 4.8 20.6 - - + -
2215H VAL* 5.6 3.4 - - - -
2229H MET* 3.0 21.8 + - + +
2230H VAL* 3.1 34.3 - - - -
2232H SER* 1.3 76.3 + - - +
2234H CYS* 1.3 61.1 + - - +
2236H PHE* 3.3 7.6 + - - +
2237H LEU* 2.9 33.8 + - + +
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Residues in contact with CYS2234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2212H MET* 4.9 9.2 - - - -
2230H VAL* 2.9 43.0 + - - +
2233H CYS* 1.3 78.6 - - - +
2235H ARG* 1.3 59.4 + - - +
2237H LEU* 3.3 8.8 + - - +
2238H CYS* 2.9 34.7 + - - +
2271H SER* 3.7 23.1 - - - -
2272H THR 4.4 2.7 - - - +
2273H PRO* 4.0 25.8 - - - -
2276H VAL* 3.9 10.4 - - + +
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Residues in contact with ARG2235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2183H ILE* 5.8 1.2 - - - +
2187H MET* 4.1 30.5 - - - +
2231H THR* 2.9 26.6 + - - +
2232H SER* 3.3 12.0 + - - +
2234H CYS* 1.3 77.4 - - - +
2236H PHE* 1.3 57.9 + - - +
2238H CYS* 3.3 5.9 + - - +
2239H TYR* 2.9 51.4 + - + -
2271H SER* 4.5 10.3 - - - -
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Residues in contact with PHE2236 (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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2183H ILE* 3.8 15.9 - - + -
2186H ILE* 3.5 36.8 - - + -
2187H MET* 4.0 22.4 - - + -
2192H PHE* 4.3 22.0 - + - -
2204H MET* 4.4 29.6 - - + -
2205H HIS* 5.4 1.6 - - - -
2208H VAL* 3.5 37.2 - - + -
2232H SER 2.9 16.5 + - - +
2233H CYS* 3.3 5.4 + - - +
2235H ARG* 1.3 75.6 - - - +
2237H LEU* 1.3 62.9 + - + +
2239H TYR* 3.3 6.6 + - + +
2240H PHE* 2.9 35.7 + + + +
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Residues in contact with LEU2237 (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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2205H HIS* 5.2 12.1 - - + +
2208H VAL* 4.4 25.8 - - + +
2209H MET* 5.3 3.6 - - + +
2212H MET* 4.4 28.7 - - + -
2233H CYS* 2.9 21.0 + - + +
2234H CYS* 3.6 8.3 - - + +
2236H PHE* 1.3 80.8 - - + +
2238H CYS* 1.3 57.7 + - - +
2240H PHE* 2.9 9.8 + - + +
2241H CYS* 2.9 34.9 + - - -
2251H MET* 3.7 33.7 - - + -
2258H LEU* 5.3 1.6 - - + -
2273H PRO* 6.5 0.2 - - + -
2276H VAL* 4.0 21.8 - - + -
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Residues in contact with CYS2238 (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* 2.9 21.6 + - - +
2235H ARG* 3.7 7.2 - - - +
2237H LEU* 1.3 76.9 - - - +
2239H TYR* 1.3 64.9 + - + +
2240H PHE 3.4 0.3 + - - -
2241H CYS* 3.6 12.3 + - - +
2242H ARG* 3.6 26.1 + - - +
2275H ASP* 4.4 13.0 - - - -
2276H VAL* 3.7 29.8 - - - -
2279H ALA* 4.9 9.0 - - + +
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Residues in contact with TYR2239 (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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2187H MET* 3.7 35.6 - - + +
2192H PHE* 5.2 5.8 - - + -
2193H TYR* 3.9 22.7 - + - -
2235H ARG* 2.9 43.8 + - + +
2236H PHE* 3.7 8.7 - - + +
2238H CYS* 1.3 79.8 - - + +
2240H PHE* 1.3 61.6 + - - +
2242H ARG* 3.8 32.3 + - - +
2243H ILE* 3.3 22.6 + - + +
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Residues in contact with PHE2240 (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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2192H PHE* 3.5 33.0 - + + -
2199H MET* 4.2 15.9 - - + -
2200H ARG* 4.9 1.8 - - + -
2204H MET* 4.3 8.1 - - + -
2205H HIS* 3.7 42.8 - + + -
2236H PHE* 2.9 29.0 + + + +
2237H LEU* 2.9 10.7 + - + +
2239H TYR* 1.3 77.0 - - - +
2241H CYS* 1.3 67.3 + - - +
2243H ILE* 3.3 16.8 + - - +
2247H ASN* 3.3 56.7 + - + +
2250H SER* 5.6 1.6 - - - -
2251H MET* 5.3 11.4 - - + -
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Residues in contact with CYS2241 (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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2237H LEU* 2.9 30.5 + - - +
2238H CYS* 3.6 6.0 + - - +
2239H TYR 3.5 0.2 - - - -
2240H PHE* 1.3 80.1 - - - +
2242H ARG* 1.3 58.4 + - + +
2243H ILE 3.2 4.1 + - - -
2244H SER 3.8 14.0 - - - +
2247H ASN* 4.9 6.7 - - - -
2248H GLN* 4.0 28.1 + - - +
2251H MET* 3.7 30.5 - - + -
2276H VAL* 4.1 20.0 - - - -
2279H ALA* 4.9 13.0 - - + +
2280H SER* 5.2 2.0 - - - -
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Residues in contact with ARG2242 (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* 3.6 20.1 + - - +
2239H TYR* 4.1 39.4 - - - +
2240H PHE 3.3 1.4 - - - -
2241H CYS* 1.3 78.7 - - + +
2243H ILE* 1.3 66.6 + - - +
2279H ALA* 5.3 11.9 - - + +
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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
------------------------------------------------------------
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