Contacts of the helix formed by residues 2254 - 2263 (chain B) 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 HIS2254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2209B MET* 3.8 31.6 - - + -
2251B MET* 3.3 13.1 + - + +
2252B PHE 3.2 0.8 - - - -
2253B ASP* 1.3 77.2 - - + +
2255B LEU* 1.3 58.5 + - - +
2256B SER* 3.3 3.4 - - - -
2257B TYR* 3.4 11.2 + - + +
2258B LEU* 2.9 33.5 + - + +
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Residues in contact with LEU2255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2251B MET 4.3 0.4 + - - -
2252B PHE* 3.2 45.1 + - + +
2253B ASP 3.3 1.6 - - - -
2254B HIS* 1.3 77.4 - - - +
2256B SER* 1.3 59.5 + - - +
2258B LEU* 3.3 7.5 + - + +
2259B LEU* 2.9 29.7 + - + +
2277B ALA* 3.9 26.7 - - + -
2280B SER* 4.1 14.4 - - - +
2281B VAL* 4.2 14.4 - - + -
2291B LEU* 3.7 23.3 - - + -
2295B ASP* 4.7 14.6 - - + -
2335B PHE* 4.6 7.9 - - + -
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Residues in contact with SER2256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2253B ASP 4.3 9.8 + - - -
2254B HIS* 4.7 0.5 - - - -
2255B LEU* 1.3 78.9 - - - +
2257B TYR* 1.3 58.0 + - - +
2259B LEU* 3.3 5.5 + - - +
2260B GLU* 2.9 29.0 + - - +
2295B ASP* 5.5 6.3 - - - -
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Residues in contact with TYR2257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2209B MET* 4.2 25.4 - - + -
2212B MET* 4.7 9.9 - - + -
2213B VAL* 3.2 38.6 + - + +
2216B LEU* 5.2 1.7 - - - +
2254B HIS* 3.4 14.1 + - + +
2255B LEU 3.3 0.2 - - - -
2256B SER* 1.3 82.8 + - - +
2258B LEU* 1.3 61.3 + - + +
2260B GLU* 3.3 6.9 + - + +
2261B ASN* 2.9 69.1 + - - +
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Residues in contact with LEU2258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2209B MET* 4.9 4.7 - - + -
2212B MET* 3.9 25.4 - - + -
2237B LEU* 5.3 2.0 - - + -
2251B MET* 4.0 18.2 - - + +
2254B HIS* 2.9 26.8 + - + +
2255B LEU* 3.7 8.7 - - - +
2257B TYR* 1.3 80.2 - - + +
2259B LEU* 1.3 56.5 + - - +
2261B ASN* 3.4 4.5 + - + +
2262B SER* 2.9 30.5 + - - -
2273B PRO* 3.8 32.8 - - + +
2276B VAL* 3.8 29.8 - - + -
2277B ALA* 4.4 15.9 - - + +
2280B SER* 5.2 2.9 - - - +
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Residues in contact with LEU2259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2255B LEU* 2.9 20.5 + - + +
2256B SER* 3.8 4.7 - - - +
2258B LEU* 1.3 77.2 - - - +
2260B GLU* 1.3 61.4 + - - +
2262B SER* 2.7 20.2 + - - -
2277B ALA* 5.4 0.6 - - - +
2295B ASP* 4.5 25.4 - - + +
2298B LYS* 5.5 6.5 - - + -
2299B VAL* 6.1 3.4 - - + -
2302B TYR* 3.7 18.6 - - + -
2335B PHE* 5.8 6.3 - - + -
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Residues in contact with GLU2260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2256B SER 2.9 17.4 + - - +
2257B TYR* 3.7 10.8 - - + +
2259B LEU* 1.3 78.7 - - - +
2261B ASN* 1.3 63.6 + - - +
2263B GLY* 3.8 8.3 + - - -
2302B TYR* 4.4 12.8 + - - +
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Residues in contact with ASN2261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2212B MET* 5.5 4.1 - - + +
2216B LEU* 3.5 35.5 - - + +
2257B TYR* 2.9 67.5 + - + +
2258B LEU* 4.0 5.8 - - + +
2260B GLU* 1.3 77.5 - - - +
2262B SER* 1.3 66.0 + - - +
2263B GLY* 3.3 0.6 - - - -
2273B PRO* 4.7 11.2 - - + +
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Residues in contact with SER2262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2258B LEU 2.9 15.4 + - - -
2259B LEU* 2.7 27.4 + - - -
2261B ASN* 1.3 78.9 - - - +
2263B GLY* 1.3 65.7 + - - +
2272B THR* 5.2 5.6 - - - +
2273B PRO* 4.4 8.3 - - - +
2274B LEU* 3.9 41.4 - - - +
2302B TYR* 5.2 0.5 - - - -
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Residues in contact with GLY2263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2259B LEU 3.7 4.8 + - - -
2260B GLU 3.8 5.3 + - - -
2261B ASN 3.3 2.9 - - - -
2262B SER* 1.3 89.6 + - - +
2274B LEU* 5.6 2.4 - - - +
2299B VAL* 6.1 0.5 - - - +
2302B TYR* 3.3 51.1 - - - +
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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