Contacts of the helix formed by residues 2254 - 2263 (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 HIS2254 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2209F MET* 3.8 31.6 - - + -
2250F SER 5.0 0.4 + - - -
2251F MET* 3.3 12.9 + - + +
2252F PHE 3.2 1.2 - - - -
2253F ASP* 1.3 75.2 - - + +
2255F LEU* 1.3 57.9 + - - +
2256F SER* 3.3 3.4 - - - -
2257F TYR* 3.4 11.4 + - + +
2258F LEU* 2.9 33.6 + - + +
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Residues in contact with LEU2255 (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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2251F MET 4.3 1.1 + - - -
2252F PHE* 3.2 45.7 + - + +
2253F ASP 3.3 1.6 + - - -
2254F HIS* 1.3 78.5 - - - +
2256F SER* 1.3 58.3 + - - +
2258F LEU* 3.3 7.0 + - + +
2259F LEU* 2.9 29.6 + - + +
2277F ALA* 3.9 27.4 - - + -
2280F SER* 4.1 14.1 - - - +
2281F VAL* 4.2 13.7 - - + -
2291F LEU* 3.7 23.3 - - + -
2295F ASP* 4.7 15.0 - - + -
2335F PHE* 4.6 8.3 - - + -
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Residues in contact with SER2256 (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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2253F ASP 4.3 9.4 + - - -
2254F HIS* 4.7 0.5 - - - -
2255F LEU* 1.3 77.9 - - - +
2257F TYR* 1.3 58.4 + - - +
2259F LEU* 3.3 6.8 + - - +
2260F GLU* 2.9 29.0 + - - +
2295F ASP* 5.5 5.8 - - - -
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Residues in contact with TYR2257 (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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2209F MET* 4.2 25.8 - - - -
2212F MET* 4.7 10.1 - - + -
2213F VAL* 3.2 38.4 - - + +
2216F LEU* 5.3 1.9 - - - +
2254F HIS* 3.4 14.2 + - + +
2255F LEU 3.3 0.6 - - - -
2256F SER* 1.3 80.7 + - - +
2258F LEU* 1.3 60.6 + - + +
2260F GLU* 3.3 6.6 + - + +
2261F ASN* 2.9 68.9 + - - +
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Residues in contact with LEU2258 (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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2209F MET* 4.9 3.8 - - + -
2212F MET* 3.9 25.6 - - + -
2237F LEU* 5.3 1.3 - - + -
2251F MET* 4.0 18.6 - - + +
2254F HIS* 2.9 27.7 + - + +
2255F LEU* 3.7 8.1 - - - +
2256F SER 3.3 0.2 - - - -
2257F TYR* 1.3 79.3 - - + +
2259F LEU* 1.3 57.0 + - - +
2261F ASN* 3.4 3.9 + - + +
2262F SER* 2.9 30.5 + - - -
2273F PRO* 3.8 32.7 - - + +
2276F VAL* 3.8 29.6 - - + -
2277F ALA* 4.4 16.6 - - + +
2280F SER* 5.2 2.7 - - - +
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Residues in contact with LEU2259 (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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2255F LEU* 2.9 20.6 + - + +
2256F SER* 3.8 4.0 - - - +
2258F LEU* 1.3 76.5 - - - +
2260F GLU* 1.3 61.7 + - - +
2262F SER* 2.7 20.2 + - - -
2277F ALA* 5.4 0.6 - - - +
2295F ASP* 4.5 25.1 - - + +
2298F LYS* 5.5 6.5 - - + -
2299F VAL* 6.1 3.4 - - + -
2302F TYR* 3.7 18.6 - - + -
2335F PHE* 5.8 6.7 - - + -
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Residues in contact with GLU2260 (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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2256F SER 2.9 17.4 + - - +
2257F TYR* 3.7 10.1 - - + +
2258F LEU 3.3 0.2 - - - -
2259F LEU* 1.3 78.5 - - - +
2261F ASN* 1.3 65.8 + - - +
2263F GLY* 3.8 8.5 + - - -
2302F TYR* 4.4 12.9 + - - +
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Residues in contact with ASN2261 (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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2212F MET* 5.5 3.3 - - + +
2216F LEU* 3.5 35.8 - - + +
2257F TYR* 2.9 68.4 + - + +
2258F LEU* 4.0 5.8 - - + +
2260F GLU* 1.3 78.7 - - - +
2262F SER* 1.3 64.8 + - - +
2263F GLY* 4.5 0.3 - - - -
2273F PRO* 4.7 10.7 - - + +
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Residues in contact with SER2262 (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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2258F LEU 2.9 15.2 + - - -
2259F LEU* 2.7 27.9 + - - -
2261F ASN* 1.3 77.3 - - - +
2263F GLY* 1.3 66.0 + - - +
2272F THR* 5.2 5.4 - - - +
2273F PRO* 4.4 8.9 - - - +
2274F LEU* 3.9 41.7 - - - +
2302F TYR* 5.2 0.7 - - - -
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Residues in contact with GLY2263 (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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2259F LEU 3.7 5.3 + - - -
2260F GLU 3.8 4.8 + - - -
2261F ASN 3.3 2.8 - - - -
2262F SER* 1.3 89.5 + - - +
2274F LEU* 5.6 2.6 - - - +
2299F VAL* 6.1 0.3 - - - +
2302F TYR* 3.3 51.7 - - - +
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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