Contacts of the helix formed by residues 429 - 433 (chain X) in PDB entry 3F6E
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 GLY 429 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427X GLY 3.1 0.6 - - - -
428X ASP* 1.3 82.9 + - - +
430X SER* 1.3 65.3 + - - +
432X ASN* 3.1 22.1 + - - +
433X TYR* 3.6 16.4 - - - -
457X THR 5.0 1.4 + - - -
458X TYR* 3.6 30.1 + - - -
478X VAL* 4.4 6.3 - - - +
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Residues in contact with SER 430 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375X GLU* 3.2 50.3 + - - +
377X THR* 4.8 4.3 + - - +
403X LEU* 3.4 26.9 - - - +
404X GLY* 4.3 1.2 + - - -
407X LEU* 5.9 1.2 - - - +
426X ILE* 3.9 3.8 - - - +
427X GLY* 3.3 6.1 + - - -
429X GLY* 1.3 73.8 - - - +
431X ALA* 1.3 64.5 + - - +
432X ASN 3.0 1.4 + - - -
433X TYR* 3.2 27.5 + - - +
434X SER 4.5 1.2 + - - -
458X TYR* 5.3 0.4 - - - -
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Residues in contact with ALA 431 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407X LEU* 3.7 12.4 - - + +
426X ILE* 3.6 16.4 - - + +
427X GLY 2.9 17.9 + - - +
428X ASP 4.0 0.7 - - - +
429X GLY 3.1 0.8 - - - -
430X SER* 1.3 77.9 - - - +
432X ASN* 1.3 60.4 + - - +
433X TYR 3.6 0.2 + - - -
434X SER 4.0 1.0 + - - -
435X ILE* 3.5 27.7 + - + +
452X ILE* 4.2 16.4 - - + -
483X PHE* 3.7 27.1 - - + -
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Residues in contact with ASN 432 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428X ASP 2.8 26.8 + - - -
429X GLY* 3.1 13.6 + - - +
430X SER 3.0 1.2 + - - -
431X ALA* 1.3 78.3 - - - +
433X TYR* 1.3 67.5 + - + +
434X SER 3.2 0.7 + - - -
435X ILE* 3.4 21.1 + - + +
458X TYR* 5.7 1.2 + - - -
478X VAL* 5.4 3.6 - - - +
481X ILE* 3.6 30.5 - - - +
483X PHE* 4.0 10.9 - - - -
486X LEU* 4.4 6.9 - - - +
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Residues in contact with TYR 433 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X GLN* 5.3 4.9 - - - +
48X ALA* 5.4 2.6 - - - +
403X LEU* 3.7 43.1 - - + +
404X GLY* 3.6 19.7 - - - -
429X GLY 3.6 17.9 - - - -
430X SER* 3.2 17.1 + - - +
432X ASN* 1.3 77.0 - - + +
434X SER* 1.4 62.2 + - - +
435X ILE 4.1 0.2 + - - -
458X TYR* 3.8 22.7 + + - -
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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