Contacts of the strand formed by residues 416 - 426 (chain C) in PDB entry 2AYN
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 TYR 416 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351C MET* 3.4 25.1 - - + -
352C LEU 2.9 12.3 - - - +
353C ASP* 3.8 27.1 - - + +
370C ARG* 3.2 61.3 + - + +
371C SER* 5.0 0.7 + - - -
374C LYS* 4.6 21.8 - - + +
413C ASN* 3.6 17.5 + - - -
414C CYS 4.2 1.0 + - - -
415C GLY* 1.3 77.1 - - - -
417C TYR* 1.3 73.4 + - - +
482C ARG* 4.1 48.9 + - + +
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Residues in contact with TYR 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C LEU* 3.5 14.5 - - + +
320C PRO* 2.5 50.4 + - - +
321C ALA 3.1 18.6 - - - -
323C LEU* 3.8 20.4 - - + -
351C MET* 3.4 13.2 - - - +
352C LEU* 3.0 32.3 + - + -
354C MET* 3.5 36.6 - - + -
413C ASN* 3.7 14.5 + - - -
415C GLY 5.1 0.9 - - - -
416C TYR* 1.3 82.5 - - - +
418C ASP* 1.3 62.0 + - - +
419C LEU 4.2 0.2 - - - -
479C TYR* 3.4 29.8 - - + -
480C GLY 3.2 11.7 - - - -
481C PRO 4.4 2.9 - - - -
482C ARG* 4.6 1.1 - - - -
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Residues in contact with ASP 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C LEU* 2.6 28.5 - - - +
351C MET* 3.9 8.1 - - - +
417C TYR* 1.3 70.9 - - - +
419C LEU* 1.3 67.3 + - - +
420C GLN* 2.9 10.6 + - - +
440C LYS* 5.8 12.4 + - - +
480C GLY* 2.4 30.6 + - - +
481C PRO 3.2 16.7 - - - +
482C ARG* 3.9 24.8 - - - +
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Residues in contact with LEU 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C PHE* 3.5 35.7 - - + -
349C PRO 3.9 6.7 - - - +
350C LEU* 3.3 18.2 + - + +
418C ASP* 1.3 66.0 - - - +
420C GLN* 1.3 67.0 + - - +
421C ALA 3.9 4.7 - - - +
422C VAL* 3.9 10.3 - - + -
440C LYS* 4.2 7.4 - - - +
446C TRP* 3.3 18.2 - - + -
462C ILE* 4.0 16.8 - - + -
477C LEU* 3.9 8.1 - - + -
478C LEU 3.4 26.7 - - - +
479C TYR* 3.1 42.6 - - + -
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Residues in contact with GLN 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C SER* 3.2 35.8 + - - +
125C VAL* 3.8 4.7 - - - +
126C PRO* 4.4 4.4 - - - +
322C TYR* 3.2 41.2 + - - -
418C ASP 2.9 14.9 + - - +
419C LEU* 1.3 76.6 - - - +
421C ALA* 1.3 60.7 + - - +
439C VAL* 4.8 1.1 - - - -
440C LYS* 3.2 33.1 + - - +
446C TRP* 3.2 7.3 - - - -
478C LEU* 2.7 16.2 + - + +
479C TYR 4.8 0.2 - - - -
480C GLY* 3.9 11.8 - - - +
481C PRO* 4.7 3.2 - - - +
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Residues in contact with ALA 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C CYS* 3.8 23.8 - - + -
124C SER* 4.0 16.2 - - - +
419C LEU* 3.9 0.7 - - - +
420C GLN* 1.3 80.0 - - - +
422C VAL* 1.3 74.6 + - - +
438C TRP 3.1 14.6 - - - +
439C VAL* 4.0 13.0 - - + -
446C TRP* 4.5 0.2 - - - -
478C LEU* 3.2 30.3 + - + +
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Residues in contact with VAL 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C CYS* 3.8 3.6 - - - -
348C PHE* 5.1 0.4 - - + -
419C LEU* 3.9 20.2 - - + -
421C ALA* 1.3 87.1 - - - +
423C LEU* 1.3 64.8 + - - +
424C THR* 3.2 22.7 - - - +
438C TRP* 2.9 53.6 + - + -
446C TRP* 4.5 7.2 - - + -
462C ILE* 4.7 5.2 - - + -
465C LEU* 4.3 11.4 - - + -
474C ALA* 3.6 19.5 - - + -
476C VAL 3.4 4.3 - - - +
477C LEU* 3.7 20.6 - - + -
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Residues in contact with LEU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ALA* 3.3 27.1 - - + +
118C THR* 3.2 41.3 - - - +
121C CYS* 3.5 15.2 - - - -
199C ALA* 3.9 8.7 - - + -
203C TRP* 4.3 8.1 - - + -
422C VAL* 1.3 74.2 - - - +
424C THR* 1.3 72.2 + - - +
425C HIS 4.9 0.2 - - - +
435C TYR* 3.6 27.1 - - + -
436C VAL 3.9 2.9 - - - +
475C TYR* 2.9 24.8 + - + -
476C VAL* 2.9 40.1 + - + +
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Residues in contact with THR 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C VAL* 3.2 26.0 - - - +
423C LEU* 1.3 74.5 + - - +
425C HIS* 1.3 60.4 + - - +
426C GLN 4.0 0.2 + - - -
434C HIS 3.6 1.4 - - - +
435C TYR* 3.5 2.3 - - - -
436C VAL* 2.8 32.7 + - + +
438C TRP* 3.2 21.5 + - - +
465C LEU* 4.2 4.6 - - + +
472C HIS* 3.2 39.0 - - + +
473C ILE 3.2 17.3 - - - +
474C ALA* 3.5 6.8 + - - -
475C TYR 4.1 0.7 - - - +
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Residues in contact with HIS 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330C PHE* 3.4 19.1 - + + -
341C LYS* 2.9 41.7 + - - +
424C THR* 1.3 74.6 - - - +
426C GLN* 1.3 59.7 + - - +
427C GLY* 3.3 27.7 - - - -
429C SER 2.9 19.3 + - - -
432C SER 2.8 29.0 + - - -
434C HIS 3.4 11.0 - - - -
435C TYR* 3.3 45.7 - + + -
473C ILE 3.3 21.5 + - - +
475C TYR* 4.1 9.9 - - + +
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Residues in contact with GLN 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PRO* 5.3 15.4 + - - +
186A ALA 6.3 0.4 - - - -
187A GLU* 5.7 7.2 - - + +
341C LYS* 4.2 1.3 - - - +
425C HIS* 1.3 76.0 - - - +
427C GLY* 1.3 60.6 + - - +
433C GLY* 3.6 2.6 - - - -
434C HIS* 3.1 35.9 + - - +
470C ASP* 3.9 19.9 - - - +
471C TRP* 4.2 13.2 - - - +
472C HIS* 3.2 57.1 + - + +
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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