Contacts of the strand formed by residues 403 - 408 (chain T) in PDB entry 6O81
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 VAL 403 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A PHE* 4.2 26.7 - - + +
265A ASP* 4.2 16.8 - - + +
267A GLN* 6.1 2.2 - - - +
401T ASN 4.4 0.4 + - - -
402T GLU* 1.3 75.6 - - - +
404T LEU* 1.3 60.1 + - - +
415T GLY 3.5 9.6 - - - +
416T ARG* 4.5 2.2 - - + +
444T SER 4.6 1.7 - - - +
445T ARG* 5.0 10.0 + - - +
451T TRP* 4.8 9.9 - - + -
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Residues in contact with LEU 404 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402T GLU 4.7 2.5 - - - +
403T VAL* 1.3 77.1 - - - +
405T MET* 1.3 61.6 + - - +
406T VAL* 3.4 6.9 + - + +
414T GLY* 3.4 2.6 - - - -
415T GLY* 2.9 34.3 + - - +
417T VAL* 6.5 0.7 - - + -
443T LEU* 5.0 9.2 - - + -
444T SER 3.5 18.2 - - - +
445T ARG* 5.9 0.2 - - + -
451T TRP* 4.7 3.4 - - - -
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Residues in contact with MET 405 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ASP 4.8 4.0 - - - +
264A PHE* 3.6 27.8 - - + -
79T ILE* 6.6 0.7 - - - -
404T LEU* 1.3 69.9 - - - +
406T VAL* 1.3 64.0 + - - +
407T ASN* 3.3 7.6 + - + +
412T SER* 3.9 27.6 - - - +
413T THR 3.7 20.4 - - - -
414T GLY* 3.8 3.6 - - - -
442T ALA* 5.5 0.2 - - - +
443T LEU* 4.0 1.1 + - - -
444T SER* 3.2 35.4 + - - -
451T TRP* 3.7 55.2 - - + +
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Residues in contact with VAL 406 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404T LEU* 3.4 5.7 + - + +
405T MET* 1.3 70.1 - - - +
407T ASN* 1.3 60.3 + - - +
408T ILE* 3.6 3.4 + - + +
411T LEU 3.2 4.2 - - - +
412T SER* 4.4 0.4 - - - -
413T THR* 2.9 40.1 + - - +
415T GLY* 5.9 1.3 - - - +
441T ILE* 5.3 7.4 - - + -
442T ALA 3.4 16.8 - - - +
443T LEU* 4.6 2.0 - - + +
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Residues in contact with ASN 407 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143T ALA* 4.2 29.2 - - + +
144T THR* 5.1 1.1 - - - +
147T ASN* 3.5 14.9 - - - +
405T MET* 3.3 8.2 + - + +
406T VAL* 1.3 70.8 - - - +
408T ILE* 1.3 60.0 + - - +
409T GLY 3.2 12.2 + - - +
410T SER 6.2 0.2 - - - -
411T LEU 3.4 7.0 - - - -
412T SER* 4.1 13.5 - - - +
442T ALA* 3.7 20.6 + - + +
444T SER* 6.4 0.4 - - - -
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Residues in contact with ILE 408 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406T VAL* 3.6 4.9 + - + +
407T ASN* 1.3 68.1 - - - +
409T GLY* 1.3 59.4 + - - +
410T SER 3.1 0.9 + - - -
411T LEU* 2.9 37.7 + - + +
433T VAL* 5.9 5.6 - - + -
435T THR* 4.2 26.0 - - - -
439T GLU* 6.0 3.6 - - + -
440T LYS 4.7 2.5 - - - +
441T ILE* 4.7 19.7 - - + +
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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