Contacts of the helix formed by residues 2244 - 2252 (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 SER2244 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2196F PRO* 4.5 16.8 - - - -
2241F CYS 3.8 6.4 - - - +
2242F ARG 3.8 0.2 - - - -
2243F ILE* 1.3 88.2 - - - +
2245F ARG* 1.3 73.8 + - - +
2246F GLN* 2.7 24.6 + - - -
2247F ASN* 3.7 6.3 + - - +
2248F GLN* 3.3 19.1 + - - +
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Residues in contact with ARG2245 (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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2244F SER* 1.3 82.3 + - - +
2246F GLN* 1.3 66.0 + - - +
2248F GLN* 3.2 6.8 + - + +
2249F ARG* 2.9 58.9 + - - +
2283F ASP 5.7 0.2 + - - -
2284F ASN* 3.3 30.4 + - - +
2285F ASN* 4.8 2.4 - - - +
2286F GLU* 3.4 32.5 - - - +
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Residues in contact with GLN2246 (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* 6.2 1.6 - - + -
2197F ASN* 5.0 3.6 - - - +
2200F ARG* 3.4 37.6 - - - +
2244F SER* 2.7 30.1 + - - +
2245F ARG* 1.3 77.6 + - - +
2247F ASN* 1.3 60.4 + - - +
2249F ARG* 3.3 14.8 + - - +
2250F SER* 2.9 31.5 + - - -
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Residues in contact with ASN2247 (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* 5.4 0.4 - - - -
2196F PRO* 4.1 14.4 - - - +
2199F MET* 5.4 0.2 - - - +
2200F ARG* 3.2 26.2 + - - +
2240F PHE* 3.3 59.8 + - + +
2241F CYS* 5.0 1.6 - - - -
2243F ILE* 3.4 23.5 - - - +
2244F SER* 3.7 13.0 + - - +
2245F ARG 3.3 0.2 - - - -
2246F GLN* 1.3 76.4 - - - +
2248F GLN* 1.3 56.5 + - - +
2250F SER* 3.3 5.9 + - - -
2251F MET* 2.9 32.6 + - - +
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Residues in contact with GLN2248 (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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2241F CYS* 4.0 22.9 + - - +
2244F SER 3.3 12.2 + - - +
2245F ARG* 3.2 14.0 + - - +
2247F ASN* 1.3 79.6 - - - +
2249F ARG* 1.3 57.9 + - - +
2251F MET* 3.3 3.7 + - - +
2252F PHE* 2.9 24.1 + - - +
2279F ALA 3.4 9.3 + - - -
2280F SER* 2.9 51.5 + - - +
2282F ILE 4.3 4.2 + - - +
2283F ASP* 5.4 2.4 + - - +
2284F ASN* 4.2 15.0 - - + +
2287F LEU* 3.9 18.9 - - + +
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Residues in contact with ARG2249 (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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2245F ARG* 2.9 59.5 + - - +
2246F GLN* 3.8 14.6 - - - +
2248F GLN* 1.3 75.8 - - - +
2250F SER* 1.3 61.6 + - - +
2252F PHE* 3.5 20.7 + - + +
2253F ASP* 4.0 10.6 + - - +
2284F ASN* 5.4 1.8 - - - +
2286F GLU* 4.5 10.5 - - - +
2287F LEU* 5.6 2.7 - - - -
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Residues in contact with SER2250 (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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2200F ARG* 4.0 17.9 + - - +
2205F HIS* 4.4 26.2 + - - -
2240F PHE* 5.6 1.6 - - - -
2246F GLN 2.9 18.8 + - - -
2247F ASN* 3.7 7.2 - - - -
2249F ARG* 1.3 78.9 - - - +
2251F MET* 1.3 60.2 + - - +
2252F PHE 3.6 0.3 + - - -
2253F ASP* 3.6 21.0 + - - +
2254F HIS 5.0 0.3 + - - -
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Residues in contact with MET2251 (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* 5.1 15.9 - - + +
2209F MET* 4.0 18.6 - - + -
2237F LEU* 3.7 36.8 - - + -
2240F PHE* 5.3 8.7 - - + -
2241F CYS* 3.7 25.6 - - - -
2247F ASN 2.9 17.4 + - - +
2248F GLN* 4.0 6.1 - - - +
2250F SER* 1.3 72.9 - - - +
2252F PHE* 1.3 64.8 + - - +
2253F ASP 3.1 4.2 + - - -
2254F HIS* 3.3 15.3 + - + +
2255F LEU* 4.3 2.3 + - - -
2258F LEU* 4.0 17.8 - - + +
2276F VAL* 3.9 21.3 - - + -
2280F SER* 5.1 7.3 - - - -
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Residues in contact with PHE2252 (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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2248F GLN* 2.9 22.7 + - - +
2249F ARG* 3.7 14.6 - - + +
2250F SER 3.3 0.8 - - - -
2251F MET* 1.3 76.2 - - - +
2253F ASP* 1.3 65.0 + - - +
2254F HIS 3.2 1.1 + - - -
2255F LEU* 3.2 46.2 + - + +
2280F SER* 5.0 9.0 - - - -
2281F VAL* 5.6 1.8 - - + -
2287F LEU* 3.8 52.9 - - + -
2290F ALA* 5.0 8.7 - - + -
2291F LEU* 4.6 13.0 - - + -
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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