Contacts of the strand formed by residues 424 - 433 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372S GLU* 5.8 6.7 - - + -
373S ILE 3.4 9.2 - - - +
374S SER* 4.7 0.2 - - - +
375S TYR* 4.6 2.4 - - - +
419S ALA 4.2 0.3 - - - +
420S VAL* 3.3 2.8 - - - -
421S LYS* 2.9 37.6 + - + +
422S ALA 4.2 0.4 - - - +
423S ASP* 1.3 79.6 - - + +
425S GLY* 1.3 58.8 + - - +
426S LYS 4.2 0.2 + - - -
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Residues in contact with GLY 425 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371S LEU 3.6 0.5 - - - +
372S GLU* 3.4 2.0 - - - -
373S ILE* 2.9 37.5 + - - +
375S TYR* 4.2 12.3 - - - +
419S ALA 3.5 7.4 - - - -
420S VAL* 4.2 7.2 - - - -
424S LEU* 1.3 73.0 - - - +
426S LYS* 1.3 60.1 + - - -
427S ILE* 3.5 6.2 + - - +
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Residues in contact with LYS 426 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370S GLU* 5.9 4.7 - - + -
371S LEU 3.5 7.4 - - - +
372S GLU* 3.8 16.6 - - + +
417S VAL* 5.0 0.9 - - - -
418S SER* 3.2 28.4 + - - -
419S ALA* 2.9 27.5 + - + +
424S LEU 4.2 1.2 + - - -
425S GLY* 1.3 69.8 - - - -
427S ILE* 1.3 61.6 + - - +
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Residues in contact with ILE 427 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370S GLU* 3.5 1.8 - - - -
371S LEU* 2.9 36.8 + - + +
404S LEU* 6.3 2.2 - - + -
415S GLY* 4.9 10.1 - - - +
416S ARG 3.3 14.1 - - - +
417S VAL* 4.5 4.0 - - + +
425S GLY 3.5 3.4 + - - +
426S LYS* 1.3 72.4 - - - +
428S VAL* 1.3 60.2 + - - +
429S LEU* 3.6 3.0 + - - +
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Residues in contact with VAL 428 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369S THR 3.6 9.2 - - - +
370S GLU* 4.1 10.3 - - + +
415S GLY* 3.3 0.8 - - - -
416S ARG* 2.9 38.4 + - + +
418S SER* 4.7 13.2 - - - -
426S LYS 3.7 1.8 + - - -
427S ILE* 1.3 69.4 - - - +
429S LEU* 1.3 65.4 + - - +
430S THR 3.8 0.2 + - - -
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Residues in contact with LEU 429 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368S PHE 4.8 3.6 - - - +
369S THR* 2.9 25.2 + - - +
371S LEU 6.2 0.4 - - - +
413S THR* 5.0 8.5 - - - -
414S GLY 3.6 11.4 - - - +
415S GLY* 3.8 3.4 - - - -
427S ILE* 3.6 4.7 + - + +
428S VAL* 1.3 75.7 - - - +
430S THR* 1.3 65.6 + - - +
431S ASN 3.4 18.6 - - - +
433S VAL* 5.6 4.5 - - + -
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Residues in contact with THR 430 (chain S).
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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133B ASP* 5.9 0.7 - - - -
136B ARG* 4.6 15.0 - - - -
264B PHE* 3.7 33.0 - - - -
414S GLY 2.9 14.1 + - - -
415S GLY* 4.4 0.4 - - - -
428S VAL 3.8 1.2 + - - -
429S LEU* 1.3 75.4 - - - +
431S ASN* 1.3 59.9 + - - +
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Residues in contact with ASN 431 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B PHE* 5.2 8.5 - - + -
368S PHE 4.3 0.2 - - - +
369S THR* 5.5 1.2 - - - -
413S THR* 4.9 13.6 - - - -
414S GLY 4.6 1.2 + - - -
429S LEU* 3.4 22.6 - - - +
430S THR* 1.3 79.3 - - - +
432S PRO* 1.3 66.8 - - - +
433S VAL* 3.5 2.1 + - - +
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Residues in contact with PRO 432 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298S PRO* 4.3 22.1 - - + +
301S VAL* 5.4 9.0 - - + -
311S CYS* 4.9 10.5 - - + -
355S GLY 4.4 6.6 - - - +
367S ILE* 3.8 25.8 - - + -
368S PHE 3.7 9.9 - - - +
369S THR* 5.5 1.8 - - - -
431S ASN* 1.3 76.7 - - - +
433S VAL* 1.3 58.6 + - - +
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Residues in contact with VAL 433 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355S GLY 5.4 3.1 - - - -
366S GLU 3.4 1.2 - - - +
367S ILE* 4.4 0.4 - - - -
368S PHE* 2.9 41.2 + - + +
408S ILE* 5.9 5.4 - - + -
411S LEU* 5.3 11.7 - - + -
413S THR* 4.9 15.5 - - - -
429S LEU* 5.6 3.8 - - + -
431S ASN 3.5 4.2 + - - +
432S PRO* 1.3 73.5 - - - +
434S CYS* 1.3 61.3 + - - +
435S THR* 4.1 2.5 - - - +
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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