Contacts of the strand formed by residues 416 - 426 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351B MET* 3.4 24.5 - - + -
352B LEU 3.0 13.0 - - - +
353B ASP* 3.6 28.0 - - + +
370B ARG* 3.3 59.5 + - + +
371B SER* 5.1 1.7 + - - -
374B LYS* 4.7 20.4 - - + +
413B ASN* 3.4 18.7 + - - -
414B CYS 4.2 1.0 + - - -
415B GLY* 1.3 73.9 - - - -
417B TYR* 1.3 73.6 + - - +
482B ARG* 4.3 45.0 + - + +
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Residues in contact with TYR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B LEU* 3.2 32.8 - - + +
320B PRO* 2.5 34.4 + - - +
321B ALA 3.5 19.1 - - - -
323B LEU* 3.8 20.4 - - + -
351B MET* 3.5 13.9 - - - +
352B LEU* 3.2 29.8 + - + -
354B MET* 3.6 31.9 - - + -
413B ASN* 3.8 14.1 + - - -
415B GLY 4.8 1.1 - - - -
416B TYR* 1.3 82.5 - - - +
418B ASP* 1.3 64.2 + - - +
419B LEU 4.2 0.2 - - - -
479B TYR* 3.4 32.5 - - + -
480B GLY 3.1 8.3 - - - +
481B PRO 4.4 1.8 - - - -
482B ARG* 4.4 3.5 - - - +
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Residues in contact with ASP 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 2.7 26.0 - - - +
351B MET* 4.1 6.4 - - - +
417B TYR* 1.3 72.2 - - - +
419B LEU* 1.3 66.9 + - - +
420B GLN* 2.9 10.9 + - - +
440B LYS* 5.6 13.4 + - - +
480B GLY 2.3 31.5 + - - +
481B PRO 3.2 17.2 - - - +
482B ARG* 3.7 25.6 - - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B PHE* 3.9 28.0 - - + -
349B PRO 4.0 9.6 - - - +
350B LEU* 3.2 18.6 + - + +
418B ASP* 1.3 67.9 - - - +
420B GLN* 1.3 62.6 + - - +
421B ALA 3.8 11.2 - - - +
422B VAL* 4.0 11.2 - - + -
440B LYS* 4.0 8.7 - - - +
446B TRP* 3.4 23.0 - - + -
462B ILE* 4.1 11.4 - - + -
477B LEU* 3.9 10.3 - - + -
478B LEU 3.6 23.6 - - - +
479B TYR* 3.1 39.2 - - + -
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Residues in contact with GLN 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B SER* 3.4 34.2 + - - +
125B VAL* 3.8 4.3 - - - +
126B PRO* 4.6 4.4 - - - +
322B TYR* 3.4 39.7 + - - -
418B ASP 2.9 14.1 + - - +
419B LEU* 1.3 69.1 - - - +
421B ALA* 1.3 60.5 + - - +
439B VAL* 4.7 1.1 - - - -
440B LYS* 3.1 34.2 + - - +
446B TRP* 3.1 12.4 - - - -
478B LEU* 2.7 16.5 + - + +
480B GLY* 3.9 11.4 - - - +
481B PRO* 4.7 2.6 + - - +
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B CYS* 3.9 20.4 - - - -
124B SER* 4.1 15.0 - - - +
419B LEU* 3.8 1.2 - - - +
420B GLN* 1.3 79.4 - - - +
422B VAL* 1.3 75.7 + - - +
438B TRP 3.1 12.8 - - - +
439B VAL* 4.0 17.5 - - + -
478B LEU* 3.1 31.9 + - + +
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B CYS* 4.1 2.5 - - - -
348B PHE* 5.2 0.4 - - + -
419B LEU* 4.0 17.7 - - + -
421B ALA* 1.3 88.1 - - - +
423B LEU* 1.3 66.1 + - - +
424B THR* 3.4 19.3 - - - +
438B TRP* 2.9 47.3 + - + +
446B TRP* 4.6 3.1 - - + -
462B ILE* 4.5 9.9 - - + -
465B LEU* 4.3 10.5 - - + -
474B ALA* 3.7 20.4 - - + -
476B VAL 3.3 6.1 - - - +
477B LEU* 3.6 19.3 - - + -
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA* 3.3 27.4 - - + +
118B THR* 3.3 44.0 - - - +
121B CYS* 3.9 12.8 - - - -
199B ALA* 4.1 9.2 - - + -
203B TRP* 4.3 7.4 - - + -
422B VAL* 1.3 74.0 - - - +
424B THR* 1.3 73.4 + - - +
435B TYR* 3.7 25.6 - - + -
436B VAL 3.9 1.6 - - - +
437B SER* 4.5 0.7 - - - +
475B TYR* 2.9 24.5 + - + -
476B VAL* 2.9 38.1 + - + +
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Residues in contact with THR 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B VAL* 3.4 15.8 - - - +
423B LEU* 1.3 80.7 + - - +
425B HIS* 1.3 61.8 + - - +
434B HIS 3.6 1.9 - - - +
435B TYR* 3.2 3.5 - - - -
436B VAL* 2.7 34.6 + - + +
438B TRP* 3.1 27.8 + - - +
465B LEU* 4.2 4.7 - - + +
472B HIS* 3.2 41.7 - - + +
473B ILE 3.6 11.0 - - - +
474B ALA* 3.7 6.6 + - - -
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Residues in contact with HIS 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B PHE* 3.5 21.0 - + + -
341B LYS* 2.9 29.1 + - - +
424B THR* 1.3 75.0 - - - +
426B GLN* 1.3 60.8 + - - +
427B GLY* 3.1 31.2 - - - -
429B SER 3.1 14.4 + - - -
432B SER 2.8 28.6 + - - -
433B GLY* 3.9 2.0 - - - -
434B HIS 3.5 8.3 - - - -
435B TYR* 3.3 49.4 - + + -
473B ILE 3.2 23.6 + - - +
475B TYR* 4.2 9.8 - - + +
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Residues in contact with GLN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B LYS* 3.8 1.8 - - - +
425B HIS* 1.3 77.3 + - - +
427B GLY* 1.3 60.5 + - - +
433B GLY* 3.5 2.4 - - - -
434B HIS* 3.0 36.7 + - - +
470B ASP* 3.9 20.6 - - - +
471B TRP* 4.1 11.4 - - - +
472B HIS* 3.3 56.4 + - + +
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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