Contacts of the helix formed by residues 2195 - 2203 (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 HIS2195 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2143F TYR* 2.9 36.5 + + - +
2144F THR 4.6 1.8 - - - -
2145F ILE* 4.6 16.3 - - + +
2146F SER* 4.7 12.3 + - - -
2191F VAL* 3.1 36.3 + - + +
2192F PHE* 4.5 3.4 - - - +
2194F GLN* 1.3 96.4 + - + +
2196F PRO* 1.3 65.8 - - - +
2197F ASN 3.2 1.1 - - - +
2198F LEU* 3.3 22.9 + - + +
2199F MET* 3.5 9.9 + - - +
3643F HIS* 4.7 15.6 - - + +
3644F ARG* 5.1 10.9 - - + +
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Residues in contact with PRO2196 (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 4.8 5.6 - - - +
2193F TYR 4.9 4.0 - - - +
2194F GLN 3.3 12.6 - - - +
2195F HIS* 1.3 83.5 - - - +
2197F ASN* 1.3 67.4 + - - +
2199F MET* 3.2 9.6 + - + +
2200F ARG* 2.9 33.9 + - - +
2243F ILE* 3.8 30.7 - - + -
2244F SER* 4.5 15.3 - - - -
2246F GLN* 6.2 1.1 - - + -
2247F ASN* 4.1 12.0 - - - +
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Residues in contact with ASN2197 (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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2143F TYR* 3.6 33.5 + - + -
2195F HIS 3.2 1.0 - - - -
2196F PRO* 1.3 81.7 - - - +
2198F LEU* 1.3 57.6 + - - +
2200F ARG* 2.5 41.1 + - - +
2201F ALA* 2.9 30.4 + - - +
2246F GLN* 4.9 5.7 - - - +
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Residues in contact with LEU2198 (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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1735F ILE* 3.8 35.9 - - + -
2141F ARG 5.9 0.9 - - - +
2143F TYR* 3.6 35.9 - - + -
2145F ILE* 4.0 20.2 - - + -
2153F THR* 5.3 5.2 - - + -
2156F LEU* 5.8 7.0 - - + -
2157F LEU* 6.2 0.7 - - + -
2191F VAL* 4.8 15.9 - - + -
2195F HIS* 3.3 19.2 + - + +
2196F PRO 3.2 0.4 - - - -
2197F ASN* 1.3 79.4 - - - +
2199F MET* 1.3 57.3 + - - +
2201F ALA* 3.4 4.3 + - + +
2202F LEU* 2.9 46.3 + - + +
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Residues in contact with MET2199 (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* 4.4 12.8 - - + +
2195F HIS 3.5 8.6 + - - +
2196F PRO* 3.2 12.2 + - + +
2198F LEU* 1.3 79.2 - - - +
2200F ARG* 1.3 63.0 + - - +
2202F LEU* 4.0 0.6 - - - -
2203F GLY* 3.1 16.6 + - - -
2204F MET* 3.7 43.5 + - + +
2205F HIS* 4.2 2.6 + - - -
2240F PHE* 4.2 14.6 - - + -
2247F ASN* 5.4 0.2 - - - +
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Residues in contact with ARG2200 (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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2196F PRO* 2.9 14.6 + - - +
2197F ASN* 2.5 40.0 + - - +
2199F MET* 1.3 75.5 - - - +
2201F ALA* 1.3 64.1 + - - +
2203F GLY* 3.3 11.8 + - - -
2205F HIS* 3.9 18.1 - - + -
2240F PHE* 4.9 1.3 - - + -
2246F GLN* 3.4 35.4 - - - +
2247F ASN* 3.2 26.6 + - - +
2250F SER* 4.0 20.9 + - - +
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Residues in contact with ALA2201 (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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2140F PRO 3.7 22.9 - - - +
2141F ARG* 4.3 17.1 - - - +
2142F ALA 5.6 0.2 - - - +
2143F TYR* 5.6 4.5 - - + -
2197F ASN 2.9 17.2 + - - +
2198F LEU* 3.4 9.4 + - + +
2200F ARG* 1.3 79.0 - - - +
2202F LEU* 1.3 66.1 + - + +
2203F GLY* 3.4 1.0 + - - -
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Residues in contact with LEU2202 (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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1733F GLU* 4.7 12.3 - - + -
1735F ILE* 3.8 26.9 - - + -
2141F ARG 5.9 2.0 - - - +
2156F LEU* 5.2 6.3 - - + -
2157F LEU* 4.3 14.1 - - + -
2160F LEU* 3.7 30.1 - - + -
2164F ARG* 3.3 24.5 + - - +
2198F LEU* 2.9 36.2 + - + +
2199F MET 4.1 3.8 - - - +
2201F ALA* 1.3 79.6 - - + +
2203F GLY* 1.3 62.7 + - - +
2204F MET* 3.5 18.1 - - + +
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Residues in contact with GLY2203 (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 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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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