Contacts of the strand formed by residues 486 - 490 (chain A) in PDB entry 4A3K
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 GLU 486 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A ARG* 2.6 60.7 + - + +
351A THR* 3.2 22.6 + - - +
352A VAL* 3.9 16.7 - - + +
353A ILE* 4.6 0.2 - - - -
446A ARG* 4.1 10.4 - - - +
447A GLN 5.6 0.5 + - - -
484A GLY 3.7 5.6 + - - +
485A ASP* 1.4 73.5 - - - +
487A MET* 1.3 69.1 + - - +
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Residues in contact with MET 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ARG* 3.3 23.7 - - - +
351A THR 2.9 8.3 + - - -
353A ILE* 3.4 43.0 - - + +
444A PHE* 3.5 26.7 - - + -
445A ASN 3.4 12.6 - - - +
446A ARG* 3.6 25.1 - - + +
468A PHE* 3.3 10.9 - - + -
470A LEU* 3.4 24.2 - - + -
478A TYR* 4.3 10.5 - - + -
480A ALA* 3.6 16.6 - - + -
486A GLU* 1.3 80.4 - - - +
488A ASN* 1.3 66.1 + - - +
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Residues in contact with ASN 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A SER* 6.5 0.2 - - - -
349A ALA 3.5 3.1 - - - +
350A ARG* 3.1 42.4 + - - +
443A LEU 3.6 0.7 - - - +
444A PHE* 3.3 8.2 - - - -
445A ASN* 2.8 55.7 + - - +
447A GLN* 3.2 34.9 + - - +
487A MET* 1.3 72.2 - - - +
489A LEU* 1.3 61.0 + - - +
490A HIS* 4.3 17.3 + - + +
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Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A SER* 3.2 7.1 - - - -
349A ALA* 2.8 32.4 + - + +
364A VAL* 4.5 3.8 - - + -
366A VAL* 4.1 16.4 - - + -
370A ILE* 5.5 0.2 - - + -
374A LEU* 3.8 26.0 - - + -
436A ILE* 5.9 2.0 - - + -
442A VAL* 3.9 31.6 - - + -
443A LEU 3.2 7.4 - - - +
444A PHE* 4.2 13.5 - - + -
468A PHE* 3.7 36.8 - - + -
488A ASN* 1.3 75.7 - - - +
490A HIS* 1.3 66.1 + - - +
491A VAL* 3.8 13.7 - - + -
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Residues in contact with HIS 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A VAL* 3.7 31.2 - - + +
346A ASP 5.2 0.2 + - - -
347A PHE 3.4 5.8 + - - +
348A SER* 3.8 17.2 - - - -
442A VAL* 3.7 3.8 - - - -
443A LEU* 2.8 53.7 + - + +
445A ASN* 4.9 2.3 + - + -
455A MET* 4.5 23.4 - - + +
488A ASN* 4.3 21.2 + - + +
489A LEU* 1.3 78.8 - - - +
491A VAL* 1.3 62.4 + - - +
492A PRO* 3.7 2.1 - - - +
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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