Contacts of the strand formed by residues 424 - 433 (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 LEU 424 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372T GLU* 5.8 6.3 - - + -
373T ILE 3.4 9.2 - - - +
374T SER* 5.5 0.2 - - - -
375T TYR* 4.6 2.2 - - - +
419T ALA 4.2 0.3 - - - +
420T VAL* 3.3 3.0 - - - -
421T LYS* 2.9 37.8 + - + +
423T ASP* 1.3 80.2 - - + +
425T GLY* 1.3 59.8 + - - +
426T LYS 4.2 0.4 + - - -
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Residues in contact with GLY 425 (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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371T LEU 3.6 0.7 - - - +
372T GLU* 3.4 2.1 - - - -
373T ILE* 2.9 36.8 + - - +
375T TYR* 4.2 13.6 - - - +
419T ALA 3.5 7.4 - - - -
420T VAL* 4.2 7.6 - - - -
424T LEU* 1.3 72.2 - - - +
426T LYS* 1.3 59.7 + - - -
427T ILE* 3.5 5.9 + - - +
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Residues in contact with LYS 426 (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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370T GLU* 5.9 4.7 - - + -
371T LEU 3.5 7.6 - - - +
372T GLU* 3.8 17.0 - - + +
417T VAL* 5.0 0.7 - - - -
418T SER* 3.2 27.8 + - - -
419T ALA* 2.9 26.7 + - + +
424T LEU 4.2 0.8 + - - -
425T GLY* 1.3 69.4 - - - -
427T ILE* 1.3 62.0 + - - +
428T VAL* 5.2 0.2 - - - +
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Residues in contact with ILE 427 (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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370T GLU* 3.5 1.8 - - - -
371T LEU* 2.9 37.9 + - + +
404T LEU* 6.3 2.0 - - + -
415T GLY* 4.9 10.3 - - - +
416T ARG 3.3 14.4 - - - +
417T VAL* 4.5 3.6 - - + +
425T GLY 3.5 3.6 + - - +
426T LYS* 1.3 72.6 - - - +
428T VAL* 1.3 61.8 + - - +
429T LEU* 3.6 3.1 + - - +
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Residues in contact with VAL 428 (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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369T THR 3.6 8.3 - - - +
370T GLU* 4.1 10.1 - - + +
415T GLY* 3.3 0.4 - - - -
416T ARG* 2.9 38.1 + - + +
418T SER* 4.7 13.7 - - - -
426T LYS 3.7 2.2 + - - -
427T ILE* 1.3 70.1 - - - +
429T LEU* 1.3 65.7 + - - +
430T THR 3.8 0.3 + - - -
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Residues in contact with LEU 429 (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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368T PHE 4.8 3.6 - - - +
369T THR* 2.9 23.8 + - - +
371T LEU 6.2 0.2 - - - +
413T THR* 5.0 8.3 - - - -
414T GLY 3.6 11.7 - - - +
415T GLY* 3.8 3.8 - - - -
427T ILE* 3.6 4.9 + - + +
428T VAL* 1.3 77.2 - - - +
430T THR* 1.3 65.2 + - - +
431T ASN 3.4 19.4 - - - +
433T VAL* 5.6 4.9 - - + -
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Residues in contact with THR 430 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASP* 6.1 0.4 - - - -
136A ARG* 4.9 12.8 - - - -
264A PHE* 4.0 26.5 - - - -
414T GLY 2.9 16.5 + - - -
415T GLY* 4.4 0.8 - - - -
428T VAL 3.8 1.0 + - - -
429T LEU* 1.3 75.5 - - - +
431T ASN* 1.3 60.4 + - - +
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Residues in contact with ASN 431 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A PHE* 5.6 7.1 - - + -
368T PHE 4.3 0.3 - - - +
369T THR* 5.5 1.0 - - - -
413T THR* 4.9 12.4 - - - -
414T GLY 4.6 1.2 + - - +
429T LEU* 3.4 23.8 - - - +
430T THR* 1.3 78.7 - - - +
432T PRO* 1.3 67.7 - - - +
433T VAL* 3.5 2.1 + - - +
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Residues in contact with PRO 432 (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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298T PRO* 4.3 21.8 - - + +
301T VAL* 5.4 8.1 - - + -
311T CYS* 4.9 10.3 - - + -
355T GLY 4.4 6.6 - - - +
367T ILE* 3.8 26.0 - - + -
368T PHE 3.7 10.3 - - - +
369T THR* 5.5 2.2 - - - -
430T THR 4.4 0.2 - - - -
431T ASN* 1.3 75.6 - - - +
433T VAL* 1.3 59.5 + - - +
434T CYS 4.4 0.2 + - - -
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Residues in contact with VAL 433 (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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355T GLY 5.4 3.6 - - - -
366T GLU 3.4 0.9 - - - +
367T ILE* 4.4 0.4 - - - -
368T PHE* 2.9 42.3 + - + +
408T ILE* 5.9 5.4 - - + -
411T LEU* 5.3 11.9 - - + -
413T THR* 4.9 15.7 - - - -
429T LEU* 5.6 3.8 - - + -
431T ASN 3.5 4.4 + - - +
432T PRO* 1.3 74.1 - - - +
434T CYS* 1.3 60.3 + - - +
435T THR* 4.1 2.9 - - - +
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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