Contacts of the helix formed by residues 2203 - 2216 (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 GLY2203 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2199H MET 3.1 8.5 + - - -
2200H ARG 3.3 8.9 + - - -
2201H ALA 3.2 3.7 - - - -
2202H LEU* 1.3 77.9 - - - +
2204H MET* 1.3 64.1 + - - +
2205H HIS* 3.3 4.9 - - - -
2206H GLU* 3.2 30.8 + - - +
2207H THR* 3.2 17.4 + - - +
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Residues in contact with MET2204 (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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2156H LEU* 4.8 18.8 - - + -
2160H LEU* 5.3 8.5 - - + -
2164H ARG* 6.0 0.2 - - - +
2186H ILE* 6.4 0.2 - - - -
2192H PHE* 3.6 31.9 - - + -
2199H MET* 3.7 34.2 + - + +
2202H LEU* 3.5 23.7 - - + -
2203H GLY* 1.3 74.1 - - - +
2205H HIS* 1.3 62.9 + - - +
2207H THR* 2.5 31.7 + - - +
2208H VAL* 2.9 16.8 + - + +
2236H PHE* 4.4 16.8 - - + -
2240H PHE* 4.3 10.3 - - + -
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Residues in contact with HIS2205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2199H MET 4.2 1.4 + - - -
2200H ARG* 3.9 35.0 - - + -
2203H GLY* 3.9 3.8 - - - -
2204H MET* 1.3 83.3 + - - +
2206H GLU* 1.3 95.3 + - + +
2208H VAL* 3.4 7.2 + - - +
2209H MET* 2.9 30.9 + - - +
2236H PHE* 5.5 2.7 - - - -
2237H LEU* 5.2 8.7 - - + +
2240H PHE* 3.7 37.1 - + + -
2250H SER* 4.4 25.1 + - - -
2251H MET* 5.1 13.4 - - - +
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Residues in contact with GLU2206 (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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2200H ARG 5.0 0.2 - - - +
2203H GLY* 3.2 18.5 - - - +
2204H MET 3.2 0.4 - - - -
2205H HIS* 1.3 120.8 + - + +
2207H THR* 1.3 57.4 + - + +
2209H MET* 3.3 7.1 + - - +
2210H GLU* 2.9 29.1 + - - +
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Residues in contact with THR2207 (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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2163H ILE* 5.1 11.6 - - - +
2164H ARG* 4.1 34.8 - - + +
2203H GLY 3.2 17.7 - - - +
2204H MET* 2.5 24.2 + - - +
2206H GLU* 1.3 76.2 - - + +
2208H VAL* 1.3 62.0 + - - +
2210H GLU* 3.3 7.2 + - - +
2211H VAL* 2.9 34.2 + - - +
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Residues in contact with VAL2208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2163H ILE* 6.3 1.6 - - + -
2179H MET* 5.7 4.3 - - + -
2183H ILE* 5.3 11.0 - - + -
2186H ILE* 6.0 0.4 - - + -
2204H MET* 2.9 17.8 + - + +
2205H HIS* 4.0 4.0 - - - +
2207H THR* 1.3 84.7 + - - +
2209H MET* 1.3 58.0 + - - +
2211H VAL* 3.3 9.2 + - + +
2212H MET* 2.9 28.2 + - + +
2233H CYS* 3.9 31.6 - - + +
2236H PHE* 3.5 37.2 - - + -
2237H LEU* 4.4 16.4 - - + -
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Residues in contact with MET2209 (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 2.9 18.8 + - - +
2206H GLU* 3.6 7.6 - - - +
2208H VAL* 1.3 76.9 - - - +
2210H GLU* 1.3 56.7 + - - +
2212H MET* 3.3 31.6 + - + +
2213H VAL* 2.9 30.2 + - + +
2237H LEU* 5.3 3.7 - - + +
2251H MET* 4.0 25.1 - - + -
2254H HIS* 3.8 27.6 - - + -
2257H TYR* 4.2 19.5 - - - -
2258H LEU* 4.9 3.1 - - + -
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Residues in contact with GLU2210 (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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2206H GLU 2.9 17.8 + - - +
2207H THR* 3.6 7.2 - - - +
2209H MET* 1.3 74.1 - - - +
2211H VAL* 1.3 58.9 + - + +
2213H VAL* 3.1 13.3 - - + +
2214H ASN* 2.9 32.7 + - - +
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Residues in contact with VAL2211 (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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2163H ILE* 5.0 3.6 - - + -
2167H LEU* 3.7 30.7 - - + -
2179H MET* 3.8 24.2 - - + -
2207H THR* 2.9 23.0 + - - +
2208H VAL* 3.3 7.8 + - - +
2210H GLU* 1.3 75.6 - - + +
2212H MET* 1.3 59.0 + - - +
2214H ASN* 3.3 5.8 + - - +
2215H VAL* 2.9 30.2 + - + +
2229H MET* 3.7 31.9 - - + -
2233H CYS* 5.5 9.0 - - + -
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Residues in contact with MET2212 (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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2208H VAL* 2.9 16.1 + - + +
2209H MET* 3.6 34.1 - - + +
2211H VAL* 1.3 79.8 - - - +
2213H VAL* 1.3 56.6 + - - +
2215H VAL* 3.8 6.7 - - - -
2216H LEU* 2.9 60.4 + - + +
2230H VAL* 5.6 1.1 - - + -
2233H CYS* 4.8 19.1 - - + -
2234H CYS* 4.9 10.8 - - - -
2237H LEU* 4.4 19.1 - - + -
2257H TYR* 4.7 9.9 - - + -
2258H LEU* 3.9 24.7 - - + -
2261H ASN* 5.5 3.4 - - + +
2273H PRO* 5.1 7.9 - - + -
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Residues in contact with VAL2213 (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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2209H MET* 2.9 18.9 + - + +
2210H GLU* 3.1 22.0 - - + +
2212H MET* 1.3 77.6 - - - +
2214H ASN* 1.3 61.0 + - + +
2216H LEU* 4.2 11.2 + - - +
2257H TYR* 3.2 37.0 + - + +
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Residues in contact with ASN2214 (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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2167H LEU 4.4 15.8 + - - -
2210H GLU* 2.9 18.6 + - - +
2211H VAL* 3.7 6.3 - - - +
2212H MET 3.2 0.2 - - - -
2213H VAL* 1.3 81.5 - - + +
2215H VAL* 1.3 61.2 + - - +
2216H LEU 4.6 2.1 - - - -
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Residues in contact with VAL2215 (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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2171H MET* 5.4 4.5 - - + -
2211H VAL* 2.9 24.9 + - + +
2212H MET* 3.5 11.0 - - + +
2214H ASN* 1.3 75.9 - - - +
2216H LEU* 1.3 78.4 + - + +
2225H ARG* 4.8 11.3 - - + +
2226H PHE* 3.7 37.0 - - + +
2229H MET* 4.3 23.6 - - + -
2230H VAL* 5.7 3.6 - - + +
2233H CYS* 5.6 4.3 - - - -
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Residues in contact with LEU2216 (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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2212H MET* 2.9 43.1 + - + +
2213H VAL* 4.2 13.2 - - - +
2214H ASN 4.6 2.0 - - - -
2215H VAL* 1.3 96.1 - - + +
2230H VAL* 4.4 20.6 - - + -
2257H TYR* 5.2 1.3 - - - +
2261H ASN* 3.5 39.3 - - + +
2273H PRO* 5.5 7.2 - - + -
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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