Contacts of the helix formed by residues 254 - 259 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170C HIS* 5.6 5.7 - - + -
250E TYR* 2.9 58.3 + - - +
251E LEU 3.2 5.2 - - - -
252E MET 3.1 0.2 - - - -
253E LYS* 1.3 92.3 - - - +
255E ALA* 1.3 64.6 + - - +
256E ASP* 3.3 3.1 - - - -
257E TYR* 3.0 18.9 + - + +
258E PHE* 3.1 32.0 + - + -
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Residues in contact with ALA 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ASN* 4.5 0.9 - - - -
45B PHE* 6.0 0.2 - - + -
46B ALA* 3.6 32.5 - - + -
251E LEU 3.0 6.8 + - - -
252E MET 3.3 16.7 + - - +
253E LYS 3.5 1.4 + - - -
254E ASN* 1.3 77.7 - - - +
256E ASP* 1.3 58.7 + - - +
259E SER* 2.8 37.9 + - - -
266E PHE* 3.8 20.9 - - + -
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Residues in contact with ASP 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ASP 4.3 0.5 - - - +
260A ASN* 3.2 37.4 + - - +
46B ALA* 5.6 2.9 + - - -
66B THR* 4.2 14.4 - - - +
68B HIS* 2.6 44.4 + - - -
254E ASN 3.3 1.5 - - - -
255E ALA* 1.3 78.6 - - - +
257E TYR* 1.3 56.6 + - - +
259E SER* 4.4 0.4 - - - -
260E ASN* 3.4 15.4 + - - -
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Residues in contact with TYR 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C HIS* 3.4 61.9 - + + +
254E ASN* 3.0 12.2 + - + +
256E ASP* 1.3 77.9 - - - +
258E PHE* 1.3 91.7 + + + +
259E SER 3.3 1.1 + - - -
260E ASN* 3.4 12.7 + - - +
261E TYR* 3.2 50.3 + + - -
6F LYS* 6.2 2.0 - - + -
8F LEU* 2.7 28.2 + - + -
9F THR 3.5 0.7 - - - -
10F GLY* 3.2 15.7 + - - -
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Residues in contact with PHE 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C HIS* 5.0 0.9 - + - -
250E TYR* 3.9 12.3 - + - -
251E LEU* 3.5 32.5 - - + -
254E ASN* 3.1 44.2 + - + +
257E TYR* 1.3 95.0 - + - +
259E SER* 1.3 60.1 + - - +
260E ASN 3.1 2.5 - - - -
261E TYR* 2.9 27.9 + - - +
262E VAL* 3.7 8.1 + - - +
266E PHE* 3.9 12.1 - - + -
283E ILE* 4.5 9.0 - - + -
286E GLN* 3.9 19.3 - - + -
287E ALA* 4.2 15.5 - - + -
290E GLU* 3.5 27.4 - - - -
8F LEU* 3.9 16.4 - - + -
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Residues in contact with SER 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A SER* 5.3 1.2 + - - -
260A ASN* 3.3 17.3 + - - -
46B ALA 6.2 1.6 - - - -
255E ALA* 2.8 23.4 + - - -
256E ASP 4.4 1.2 + - - -
258E PHE* 1.3 77.0 - - - +
260E ASN* 1.3 63.1 + - - +
261E TYR 3.1 0.8 + - - -
262E VAL* 3.1 25.1 + - - +
266E PHE* 3.6 36.6 - - - -
47F 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