Contacts of the helix formed by residues 254 - 259 (chain G) in PDB entry 3TMP
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 ASN 254 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250G TYR* 3.0 48.0 + - - +
251G LEU 3.2 4.3 - - - -
253G LYS* 1.3 107.2 + - - +
255G ALA* 1.3 61.5 + - - +
256G ASP* 3.2 3.8 - - - -
257G TYR* 3.1 10.1 + - + +
258G PHE* 3.1 38.4 + - + -
290G GLU* 5.2 0.6 - - - +
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Residues in contact with ALA 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251G LEU 2.9 6.3 + - - -
252G MET* 3.5 18.0 + - + +
253G LYS 3.5 1.6 + - - -
254G ASN* 1.3 78.3 - - - +
256G ASP* 1.3 64.2 + - - +
258G PHE 3.8 0.2 - - - -
259G SER* 2.8 34.2 + - - -
266G PHE* 3.7 30.7 - - + -
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Residues in contact with ASP 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G ASN* 3.2 2.1 - - - -
255G ALA* 1.3 78.5 - - - +
257G TYR* 1.3 56.9 + - - +
259G SER* 4.2 4.3 + - - -
260G ASN* 3.4 21.1 + - - -
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Residues in contact with TYR 257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254G ASN* 3.1 11.6 + - + +
255G ALA 3.1 0.2 - - - -
256G ASP* 1.3 79.9 - - - +
258G PHE* 1.3 91.5 + + + +
259G SER 3.3 1.1 + - - -
260G ASN* 3.4 14.1 + - - +
261G TYR* 3.5 43.9 + + - -
286G GLN* 5.3 0.4 - - + -
290G GLU* 4.7 7.9 - - - -
7H THR 4.4 2.6 + - - -
8H LEU* 3.9 35.8 + - + +
10H GLY* 5.3 3.6 - - - -
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Residues in contact with PHE 258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G TYR* 4.1 7.4 - + - -
251G LEU* 3.3 32.3 - - + -
254G ASN* 3.1 43.0 + - + +
257G TYR* 1.3 97.5 - + - +
259G SER* 1.3 59.8 + - - +
260G ASN 3.1 0.2 - - - -
261G TYR* 2.9 27.0 + - - +
262G VAL* 3.6 8.7 + - - +
266G PHE* 4.0 12.3 - - + -
283G ILE* 4.2 14.8 - - + +
286G GLN* 3.8 25.1 - - + -
287G ALA* 4.0 13.5 - - - -
290G GLU* 3.7 31.9 - - - -
8H LEU* 4.1 10.5 - - + -
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Residues in contact with SER 259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255G ALA* 2.8 24.4 + - - -
256G ASP* 4.2 5.9 + - - -
258G PHE* 1.3 77.5 - - - +
260G ASN* 1.3 63.3 + - - +
261G TYR 3.1 0.9 - - - -
262G VAL* 3.1 24.7 - - - +
266G PHE* 3.7 35.6 - - - -
47H GLY* 5.5 1.6 - - - -
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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