Contacts of the helix formed by residues 2203 - 2216 (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 GLY2203 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2199F MET 3.1 7.5 + - - -
2200F ARG 3.3 9.4 + - - -
2201F ALA 3.2 4.3 - - - -
2202F LEU* 1.3 79.3 - - - +
2204F MET* 1.3 65.3 + - - +
2205F HIS* 3.3 4.5 - - - -
2206F GLU* 3.2 31.0 + - - +
2207F THR* 3.2 17.4 + - - +
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Residues in contact with MET2204 (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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2156F LEU* 4.8 18.6 - - + -
2160F LEU* 5.3 8.7 - - + -
2164F ARG* 6.0 0.2 - - - +
2186F ILE* 6.4 0.2 - - - -
2192F PHE* 3.6 31.6 - - + -
2199F MET* 3.7 33.8 + - + +
2202F LEU* 3.5 23.1 - - + -
2203F GLY* 1.3 74.9 - - - +
2205F HIS* 1.3 63.0 + - - +
2207F THR* 2.5 31.5 + - - +
2208F VAL* 2.9 17.4 + - + +
2236F PHE* 4.4 16.4 - - + -
2240F PHE* 4.3 10.8 - - + -
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Residues in contact with HIS2205 (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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2199F MET 4.2 1.0 + - - -
2200F ARG* 3.9 34.1 - - + -
2203F GLY* 3.9 3.4 - - - -
2204F MET* 1.3 83.6 + - - +
2206F GLU* 1.3 96.2 + - + +
2208F VAL* 3.4 7.2 + - - +
2209F MET* 2.9 30.4 + - - +
2236F PHE* 5.5 2.5 - - - -
2237F LEU* 5.2 7.7 - - + +
2240F PHE* 3.7 37.9 - + + -
2250F SER* 4.4 25.5 + - - -
2251F MET* 5.1 14.9 - - - +
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Residues in contact with GLU2206 (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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2203F GLY* 3.2 18.3 - - - +
2204F MET 3.2 0.4 - - - -
2205F HIS* 1.3 120.4 + - - +
2207F THR* 1.3 57.1 + - + +
2209F MET* 3.3 7.1 + - - +
2210F GLU* 2.9 30.1 + - - +
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Residues in contact with THR2207 (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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2163F ILE* 5.1 11.6 - - - +
2164F ARG* 4.1 35.9 - - + +
2203F GLY 3.2 17.5 - - - +
2204F MET* 2.5 24.9 + - - +
2206F GLU* 1.3 76.9 - - + +
2208F VAL* 1.3 60.4 + - - +
2210F GLU* 3.3 7.3 + - - +
2211F VAL* 2.9 34.1 + - - +
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Residues in contact with VAL2208 (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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2163F ILE* 6.3 1.6 - - + -
2179F MET* 5.7 4.5 - - + -
2183F ILE* 5.3 9.9 - - + -
2186F ILE* 6.0 0.4 - - + -
2204F MET* 2.9 17.6 + - + +
2205F HIS* 3.4 4.2 + - - +
2207F THR* 1.3 86.0 + - - +
2209F MET* 1.3 57.3 + - - +
2211F VAL* 3.3 9.3 + - + +
2212F MET* 2.9 28.2 + - + +
2233F CYS* 3.9 31.9 - - + +
2236F PHE* 3.5 37.5 - - + -
2237F LEU* 4.4 15.0 - - + -
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Residues in contact with MET2209 (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 2.9 18.1 + - - +
2206F GLU* 3.6 7.4 - - - +
2208F VAL* 1.3 77.1 - - - +
2210F GLU* 1.3 57.4 + - - +
2212F MET* 3.3 31.3 + - + +
2213F VAL* 2.9 31.3 + - + +
2237F LEU* 5.3 3.3 - - + +
2251F MET* 4.0 25.4 - - + -
2254F HIS* 3.8 27.6 - - + -
2257F TYR* 4.2 20.0 - - - -
2258F LEU* 4.9 2.9 - - + -
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Residues in contact with GLU2210 (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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2206F GLU 2.9 17.9 + - - +
2207F THR* 3.6 7.0 - - - +
2209F MET* 1.3 75.0 - - - +
2211F VAL* 1.3 60.9 + - + +
2213F VAL* 3.1 13.7 - - + +
2214F ASN* 2.9 32.4 + - - +
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Residues in contact with VAL2211 (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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2163F ILE* 5.0 4.3 - - + -
2167F LEU* 3.7 29.8 - - + -
2179F MET* 3.8 24.5 - - + -
2207F THR* 2.9 22.5 + - - +
2208F VAL* 3.6 9.0 - - + +
2210F GLU* 1.3 74.6 - - + +
2212F MET* 1.3 59.5 + - - +
2214F ASN* 3.3 6.0 + - - +
2215F VAL* 2.9 29.7 + - + +
2229F MET* 3.7 31.0 - - + -
2233F CYS* 5.5 8.7 - - + -
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Residues in contact with MET2212 (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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2208F VAL* 2.9 16.5 + - + +
2209F MET* 3.6 33.0 - - + +
2210F GLU 3.2 0.4 - - - -
2211F VAL* 1.3 78.2 - - - +
2213F VAL* 1.3 57.2 + - - +
2215F VAL* 3.8 6.1 - - - -
2216F LEU* 2.9 59.3 + - + +
2230F VAL* 5.6 1.3 - - - -
2233F CYS* 4.8 19.5 - - - -
2234F CYS* 4.9 10.3 - - - -
2237F LEU* 4.4 20.0 - - + -
2257F TYR* 4.7 9.9 - - + -
2258F LEU* 3.9 24.7 - - + -
2261F ASN* 5.5 2.9 - - + +
2273F PRO* 5.1 7.4 - - - -
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Residues in contact with VAL2213 (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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2209F MET* 2.9 18.3 + - + +
2210F GLU* 3.1 22.9 - - + +
2212F MET* 1.3 77.3 - - - +
2214F ASN* 1.3 61.2 + - + +
2216F LEU* 4.2 11.0 + - - +
2257F TYR* 3.2 38.3 + - + +
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Residues in contact with ASN2214 (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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2167F LEU* 4.4 15.4 + - - +
2210F GLU* 2.9 18.0 + - - +
2211F VAL* 3.7 6.3 - - - +
2212F MET 3.2 0.2 - - - -
2213F VAL* 1.3 81.5 - - + +
2215F VAL* 1.3 61.4 + - - +
2216F LEU* 4.6 2.3 - - - -
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Residues in contact with VAL2215 (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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2171F MET* 5.4 4.5 - - + -
2211F VAL* 2.9 25.1 + - + +
2212F MET* 3.5 10.8 - - + +
2214F ASN* 1.3 75.8 - - - +
2216F LEU* 1.3 78.7 + - + +
2225F ARG* 4.8 9.9 - - + +
2226F PHE* 3.7 37.0 - - + +
2229F MET* 4.3 22.2 - - + -
2230F VAL* 5.7 3.8 - - + -
2233F CYS* 5.6 5.2 - - - -
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Residues in contact with LEU2216 (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* 2.9 43.7 + - + +
2213F VAL* 4.2 12.6 - - - +
2214F ASN 3.5 2.4 - - - -
2215F VAL* 1.3 95.6 - - + +
2230F VAL* 4.4 21.5 - - + -
2257F TYR* 5.3 1.1 - - - +
2261F ASN* 3.5 38.6 - - + +
2273F PRO* 5.5 6.7 - - + -
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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