Contacts of the strand formed by residues 434 - 442 (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 HIS 434 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A LYS* 4.9 18.4 + - + +
108C ASN* 5.1 2.3 + - - -
113C CYS* 3.4 15.0 - - + -
196C GLN* 4.1 0.4 - - - +
424C THR 3.6 1.0 - - - +
425C HIS* 3.4 3.8 - - - -
426C GLN* 3.1 43.4 + - - +
432C SER 3.9 1.2 + - - -
433C GLY* 1.3 75.3 - - - +
435C TYR* 1.3 82.9 + - - +
436C VAL* 3.7 18.8 - - + +
450C ASP* 2.8 28.4 + - - -
451C ASP* 3.0 28.3 - - - -
472C HIS* 4.4 8.7 - + - -
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Residues in contact with TYR 435 (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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113C CYS* 3.3 11.6 - - - +
114C TYR* 3.6 21.5 - - + +
117C ALA* 3.8 19.1 - - + +
196C GLN* 3.7 18.2 - - - -
197C GLN 2.9 20.8 + - - -
198C ASP* 3.5 5.9 - - - -
199C ALA* 3.0 29.8 - - + -
330C PHE* 4.5 0.5 - - - -
423C LEU* 3.6 9.9 - - + -
424C THR 3.5 1.3 - - - -
425C HIS* 3.3 39.2 - + + -
430C SER* 2.6 30.2 + - - -
434C HIS* 1.3 92.2 - - - +
436C VAL* 1.3 63.8 + - - +
451C ASP* 4.4 2.6 + - - +
475C TYR* 3.7 17.0 - + - -
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Residues in contact with VAL 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ALA* 4.1 3.1 - - - +
424C THR 2.8 28.6 + - - +
434C HIS* 3.7 15.5 - - + +
435C TYR* 1.3 82.8 - - - +
437C SER* 1.3 71.9 + - - +
438C TRP* 3.0 37.2 + - + +
448C LYS* 4.5 5.8 - - + -
449C PHE 3.7 21.8 - - - +
450C ASP* 4.0 8.7 - - + +
472C HIS* 3.4 33.7 - - + +
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Residues in contact with SER 437 (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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116C ASN 4.8 0.2 - - - -
117C ALA* 3.6 33.8 + - - +
120C GLN* 3.1 26.5 - - - +
121C CYS* 3.9 11.0 - - - -
422C VAL 3.6 5.8 - - - -
423C LEU* 4.5 0.4 - - - +
436C VAL* 1.3 81.2 - - - +
438C TRP* 1.3 60.6 + - - +
439C VAL* 4.8 1.6 - - - -
449C PHE* 3.1 43.7 + - - +
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Residues in contact with TRP 438 (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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421C ALA* 3.1 6.9 - - - +
422C VAL* 2.9 58.5 + - + +
424C THR* 3.2 19.7 + - - -
436C VAL* 3.0 30.4 + - + +
437C SER* 1.3 74.0 - - - +
439C VAL* 1.3 63.7 + - - +
446C TRP* 4.0 13.2 - + + -
447C ILE 3.5 7.9 - - - +
448C LYS* 3.5 50.0 - - + -
457C VAL* 4.5 21.5 - - + -
461C ASP* 5.6 6.5 - - + -
462C ILE* 5.4 3.8 - - + -
465C LEU* 3.9 37.0 - - + -
471C TRP* 5.3 7.2 - + - -
472C HIS* 4.1 17.7 - + - -
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Residues in contact with VAL 439 (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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120C GLN* 4.3 16.8 - - + +
124C SER* 3.7 26.9 - - - -
420C GLN 4.1 2.2 - - - +
421C ALA* 4.0 11.9 - - + -
437C SER* 4.8 2.0 - - - -
438C TRP* 1.3 83.1 - - - +
440C LYS* 1.3 75.7 + - - +
441C ARG* 5.5 1.8 - - + -
446C TRP* 3.8 3.7 - - - -
447C ILE* 2.6 46.3 + - + +
449C PHE* 3.5 30.5 - - + -
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Residues in contact with LYS 440 (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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418C ASP* 5.8 12.7 + - - +
419C LEU 4.2 7.9 - - - +
420C GLN* 3.2 26.1 + - - +
439C VAL* 1.3 86.8 - - - +
441C ARG* 1.3 65.6 + - - +
442C LYS 4.2 4.2 - - - +
443C GLN* 4.5 25.7 - - - +
444C ASP 4.7 4.0 - - - +
445C GLU 3.6 12.6 - - - +
446C TRP* 3.5 38.2 - - + +
459C PRO* 6.2 0.7 - - - -
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Residues in contact with ARG 441 (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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101C GLU* 4.6 25.3 + - - +
102C LEU* 5.2 2.4 - - - +
103C PRO* 4.1 23.4 - - - +
439C VAL* 3.8 2.2 + - + +
440C LYS* 1.3 80.3 + - - +
442C LYS* 1.3 70.1 + - + +
445C GLU* 3.2 28.6 + - - +
447C ILE* 4.3 24.2 - - + +
456C ILE* 6.3 0.4 - - - +
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Residues in contact with LYS 442 (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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440C LYS* 4.2 6.3 - - - +
441C ARG* 1.3 85.8 - - + +
443C GLN* 1.3 64.6 + - + +
444C ASP 3.2 0.5 + - - -
445C GLU* 2.6 61.6 + - + +
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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