Contacts of the helix formed by residues 2195 - 2203 (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 HIS2195 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2143H TYR* 2.9 37.2 + + - +
2144H THR 4.6 2.0 - - - -
2145H ILE* 4.6 16.1 - - + +
2146H SER* 4.7 12.1 + - - -
2191H VAL* 3.1 37.2 + - + +
2192H PHE* 4.5 3.5 - - - +
2194H GLN* 1.3 95.7 + - + +
2196H PRO* 1.3 66.5 - - - +
2197H ASN 3.2 2.2 - - - +
2198H LEU* 3.3 23.5 + - + +
2199H MET* 3.5 9.9 + - - +
3643H HIS* 4.7 15.4 - - + +
3644H ARG* 5.1 9.8 - - + +
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Residues in contact with PRO2196 (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 4.6 5.6 - - - +
2193H TYR 4.9 3.4 - - - +
2194H GLN 3.3 13.2 - - - +
2195H HIS* 1.3 84.3 - - - +
2197H ASN* 1.3 66.9 + - - +
2199H MET* 3.2 9.8 + - + +
2200H ARG* 2.9 33.3 + - - +
2243H ILE* 3.8 29.8 - - + -
2244H SER* 4.5 15.7 - - - -
2246H GLN* 6.2 1.3 - - + -
2247H ASN* 4.1 12.2 - - - +
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Residues in contact with ASN2197 (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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2143H TYR* 3.6 33.0 + - + -
2195H HIS 3.2 1.0 - - - -
2196H PRO* 1.3 81.3 - - - +
2198H LEU* 1.3 58.9 + - - +
2200H ARG* 2.5 40.9 + - - +
2201H ALA* 2.9 30.0 + - - +
2246H GLN* 4.9 6.1 - - - +
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Residues in contact with LEU2198 (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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1735H ILE* 3.8 36.3 - - + -
2141H ARG 5.9 0.7 - - - +
2143H TYR* 3.6 36.1 - - + -
2145H ILE* 4.0 20.0 - - + -
2153H THR* 5.3 5.6 - - + -
2156H LEU* 5.8 7.0 - - + -
2157H LEU* 6.2 0.9 - - + -
2191H VAL* 4.8 15.7 - - + -
2195H HIS* 3.3 19.8 + - + +
2196H PRO 3.2 0.6 - - - -
2197H ASN* 1.3 80.8 - - - +
2199H MET* 1.3 55.8 + - - +
2201H ALA* 3.3 4.6 + - + -
2202H LEU* 2.9 46.0 + - + +
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Residues in contact with MET2199 (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* 4.4 11.9 - - + +
2195H HIS 3.5 8.2 + - - +
2196H PRO* 3.2 12.8 + - + +
2198H LEU* 1.3 77.9 - - - +
2200H ARG* 1.3 61.5 + - - +
2202H LEU 4.0 0.2 - - - -
2203H GLY* 3.1 15.9 + - - -
2204H MET* 3.7 44.7 + - + +
2205H HIS* 4.2 2.7 + - - -
2240H PHE* 4.2 14.8 - - + -
2247H ASN* 5.4 0.4 - - - +
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Residues in contact with ARG2200 (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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2196H PRO* 2.9 13.2 + - - +
2197H ASN* 2.5 39.6 + - - +
2199H MET* 1.3 75.3 - - - +
2201H ALA* 1.3 63.6 + - - +
2203H GLY* 3.3 12.0 + - - -
2205H HIS* 3.9 18.1 - - + -
2206H GLU* 5.0 0.2 - - - +
2240H PHE* 4.9 1.1 - - + -
2246H GLN* 3.4 35.4 - - - +
2247H ASN* 3.2 27.7 + - - +
2250H SER* 4.0 21.0 + - - +
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Residues in contact with ALA2201 (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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2140H PRO 3.7 23.1 - - - +
2141H ARG* 4.3 16.4 - - - +
2143H TYR* 5.6 4.9 - - + -
2197H ASN 2.9 17.2 + - - +
2198H LEU* 3.3 8.9 + - + +
2200H ARG* 1.3 78.8 - - - +
2202H LEU* 1.3 65.3 + - + +
2203H GLY* 3.4 0.9 + - - -
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Residues in contact with LEU2202 (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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1733H GLU* 4.7 13.2 - - + -
1735H ILE* 3.8 26.2 - - + -
2141H ARG 5.9 1.6 - - - +
2156H LEU* 5.2 5.8 - - + -
2157H LEU* 4.3 14.4 - - + -
2160H LEU* 3.7 30.1 - - + -
2164H ARG* 3.3 24.2 + - - +
2198H LEU* 2.9 35.4 + - + +
2199H MET 4.1 3.6 - - - +
2201H ALA* 1.3 81.4 - - + +
2203H GLY* 1.3 62.5 + - - +
2204H MET* 3.5 18.5 + - + +
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Residues in contact with GLY2203 (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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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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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