Contacts of the helix formed by residues 2195 - 2207 (chain C) in PDB entry 1PXX
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 ASN2195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2193C GLY 3.1 1.2 + - - -
2194C SER* 1.3 76.2 - - - +
2196C MET* 1.3 60.9 + - - +
2197C MET 3.8 1.8 - - - -
2198C PHE* 3.1 16.8 + - - +
2199C ALA 3.2 18.4 + - - -
2426C PHE 3.4 7.6 - - - +
2427C THR* 3.0 35.3 + - - +
2429C GLN 3.1 17.7 - - - +
2431C ALA* 3.6 11.5 - - - +
2579C SER 3.0 21.8 + - - +
2580C PHE* 3.1 16.0 + - - +
2581C ASN 3.7 10.7 - - - +
2582C VAL* 3.9 9.0 - - + -
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Residues in contact with MET2196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2195C ASN* 1.3 73.8 - - - +
2197C MET* 1.3 64.9 + - - +
2198C PHE 3.0 1.6 - - - -
2199C ALA* 3.7 11.0 - - + +
2200C PHE* 3.0 55.3 + - + +
2391C LEU* 4.5 6.3 - - + -
2392C PRO* 3.2 37.7 - - + -
2395C PHE* 3.7 8.3 - - + -
2426C PHE* 3.0 34.8 + - + +
2429C GLN* 3.1 30.6 + - + -
2430C ILE 4.4 1.1 - - - +
2431C ALA* 3.9 24.9 - - - -
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Residues in contact with MET2197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2195C ASN* 3.3 8.6 + - - +
2196C MET* 1.3 77.3 - - - +
2198C PHE* 1.3 56.2 + - - +
2201C PHE* 3.0 16.8 + - - +
2300C MET* 3.5 36.3 - - + +
2301C TYR* 2.6 43.9 + - + +
2423C VAL* 4.0 9.0 - - + -
2426C PHE* 3.3 15.5 + - - -
2427C THR* 3.3 31.0 - - - +
2564C ILE* 5.2 1.8 - - + -
2568C ILE* 3.8 23.8 - - + -
2578C THR* 3.5 17.7 - - + +
2579C SER 3.7 10.5 - - - +
2580C PHE* 3.4 5.6 - - + -
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Residues in contact with PHE2198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2194C SER* 3.9 19.1 - - - -
2195C ASN* 3.1 11.1 + - - +
2196C MET 3.0 0.6 - - - -
2197C MET* 1.3 77.1 - - - +
2199C ALA* 1.3 69.8 + - - +
2201C PHE* 3.2 2.1 + - - +
2202C ALA* 3.0 23.7 + - + +
2348C TYR* 3.8 30.0 - + - -
2351C HIS* 3.6 18.4 - + - -
2352C LEU* 2.8 43.7 - - + -
2387C TRP* 4.2 12.3 - + - -
2390C LEU* 4.0 26.5 - - + -
2517C ILE* 5.1 2.9 - - + -
2518C PHE* 5.8 0.2 - + - -
2580C PHE* 3.3 39.0 - + + +
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Residues in contact with ALA2199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2195C ASN 3.2 13.4 + - - +
2196C MET* 3.4 24.9 + - + +
2198C PHE* 1.3 86.7 - - - +
2200C PHE* 1.3 57.7 + - + +
2202C ALA* 3.6 3.1 + - - +
2203C GLN 3.2 19.6 + - - -
2390C LEU* 4.0 29.2 - - + -
2391C LEU* 5.4 0.7 - - + +
2431C ALA* 4.4 3.6 - - + -
2601C HEM 3.5 19.6 - - + +
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Residues in contact with PHE2200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2196C MET* 3.0 46.5 + - + +
2199C ALA* 1.3 75.3 - - + +
2201C PHE* 1.3 60.4 + - - +
2202C ALA 3.4 0.2 - - - -
2203C GLN* 3.2 18.1 - - - +
2204C HIS* 2.8 31.7 + - - +
2295C VAL* 3.6 9.4 - - + -
2297C GLY* 3.8 18.4 - - - +
2298C LEU* 4.0 1.7 - - - +
2300C MET* 6.1 0.4 - - - -
2301C TYR* 3.7 16.3 - - + -
2391C LEU* 5.1 2.5 - - + -
2395C PHE* 3.9 22.4 - + - -
2407C PHE* 3.9 13.5 - + - -
2426C PHE* 3.7 35.2 - + + -
2601C HEM 3.5 26.7 - - + -
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Residues in contact with PHE2201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2197C MET 3.0 21.7 + - - +
2198C PHE 3.2 5.5 + - - +
2200C PHE* 1.3 77.6 - - - +
2202C ALA* 1.3 54.8 + - - +
2204C HIS* 3.6 3.6 - - + +
2205C PHE* 2.8 51.0 + + + +
2301C TYR* 3.4 31.6 - + - +
2305C TRP* 4.6 22.7 - + - -
2340C THR* 5.5 2.5 - - + -
2343C ILE* 3.8 20.2 - - + -
2344C VAL* 4.1 22.0 - - + -
2348C TYR* 3.3 31.4 - + + -
2564C ILE* 4.0 17.5 - - + -
2580C PHE* 3.7 14.6 - + + -
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Residues in contact with ALA2202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2198C PHE* 3.0 13.2 + - + +
2199C ALA* 3.7 6.5 - - - +
2201C PHE* 1.3 80.5 - - - +
2203C GLN* 1.3 50.6 + - - +
2205C PHE* 4.6 1.3 - - - -
2206C THR* 2.7 42.3 + - - +
2348C TYR* 2.6 39.6 - - + +
2387C TRP* 4.3 11.0 - - + -
2390C LEU* 5.2 0.4 - - + -
2601C HEM 3.6 12.8 - - + -
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Residues in contact with GLN2203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2199C ALA 3.2 17.4 + - - +
2200C PHE* 3.2 25.6 - - - +
2201C PHE 3.2 0.2 - - - -
2202C ALA* 1.3 73.9 - - - +
2204C HIS* 1.3 65.4 + - - +
2206C THR* 3.9 0.2 - - - -
2207C HIS* 2.7 45.2 + - + +
2295C VAL* 4.4 2.3 - - - +
2298C LEU* 3.0 38.7 - - + +
2601C HEM 3.4 68.4 + - + +
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Residues in contact with HIS2204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2200C PHE 2.8 21.9 + - - +
2201C PHE* 3.6 4.4 - - - +
2203C GLN* 1.3 74.4 - - - +
2205C PHE* 1.3 62.4 + - - +
2207C HIS* 3.4 5.7 + - - +
2232C HIS* 3.1 46.4 + + - -
2233C ILE* 4.8 3.4 - - + +
2292C PHE* 3.3 37.4 - + - -
2298C LEU* 3.5 33.7 - - + +
2301C TYR* 3.6 19.1 - - + +
2302C ALA* 3.6 16.3 + - - -
2305C TRP* 3.5 33.3 + + + -
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Residues in contact with PHE2205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2201C PHE* 2.8 31.9 + + + +
2202C ALA 4.1 0.7 - - - +
2204C HIS* 1.3 75.2 - - - +
2206C THR* 1.3 81.6 + - + +
2207C HIS 2.9 6.1 + - - -
2208C GLN* 3.1 51.4 + - - +
2209C PHE* 3.9 24.2 - + - -
2228C VAL* 4.2 11.9 - - + -
2232C HIS* 4.6 1.3 - - - -
2340C THR* 3.9 15.7 - - + -
2344C VAL* 3.6 45.3 - - + -
2348C TYR* 4.8 10.8 - + - -
2385C TYR* 4.6 0.9 - - - -
2534C LEU* 4.1 12.6 - - + -
2701C DIF 4.4 12.8 - - - -
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Residues in contact with THR2206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2202C ALA 2.7 34.4 + - - +
2203C GLN 3.5 0.2 + - - -
2205C PHE* 1.3 79.0 - - + +
2207C HIS* 1.3 73.1 + - - +
2208C GLN 3.2 2.0 + - - -
2209C PHE* 3.5 15.2 + - + -
2210C PHE* 3.1 46.5 + - + +
2348C TYR* 4.3 0.2 - - - +
2385C TYR* 3.1 43.5 - - + +
2601C HEM 3.6 10.0 - - - +
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Residues in contact with HIS2207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2203C GLN* 2.7 42.9 + - + +
2204C HIS 4.2 2.0 - - - -
2205C PHE 2.9 2.6 + - - -
2206C THR* 1.3 84.8 + - - +
2208C GLN* 1.3 61.0 + - - +
2210C PHE* 4.0 13.1 + - - +
2211C LYS* 3.5 3.3 - - - +
2289C GLN* 2.6 33.4 + - - +
2291C VAL* 4.8 11.7 - - + -
2292C PHE* 3.6 28.3 - + + -
2298C LEU* 4.9 2.9 - - + -
2601C HEM 3.6 59.5 + + + +
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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