Contacts of the strand formed by residues 444 - 449 (chain A) in PDB entry 1X6N
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 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A TYR* 3.2 21.7 - + - +
391A ASP* 2.7 29.0 + - - -
404A GLN* 2.9 32.3 + - - -
442A ALA* 3.1 25.0 + - + +
443A MET* 1.3 87.8 - - - +
445A GLY* 1.3 66.5 + - - +
446A ARG* 4.0 6.7 - - + -
476A ILE* 4.1 11.9 - - + -
477A VAL 3.2 14.8 - - - +
478A ASP* 4.6 3.6 - - - +
479A TYR* 3.9 2.7 - - - +
482A ILE* 4.7 0.9 - - - -
515A PHE* 3.9 10.4 - - - +
539A TRP* 3.7 37.7 - + + -
540A GLU* 5.7 1.8 - - + -
543A ALA* 5.1 3.4 - - + -
601A AMI 3.2 9.6 - - - -
1B NAA 3.8 19.5 - - + +
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Residues in contact with GLY 445 (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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404A GLN* 3.5 2.0 - - - -
444A TYR* 1.3 77.1 - - - +
446A ARG* 1.3 63.4 + - - -
476A ILE* 3.4 6.4 - - - +
477A VAL* 2.8 39.4 + - - +
482A ILE* 3.9 9.1 - - - +
513A ILE* 4.3 1.1 - - - -
514A THR 3.1 13.7 - - - -
515A PHE* 3.5 10.1 - - - -
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Residues in contact with ARG 446 (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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391A ASP* 2.6 38.8 + - - +
393A TYR 3.2 28.0 - - - +
394A GLY* 4.0 12.8 - - - -
395A ALA* 5.2 2.4 - - - +
396A PHE* 4.2 20.2 - - - -
404A GLN* 3.5 22.1 - - + +
444A TYR* 4.0 6.2 - - + -
445A GLY* 1.3 77.0 - - - +
447A GLY* 1.3 59.0 + - - +
448A TRP* 5.2 0.9 - - - -
468A VAL* 5.0 0.2 - - - -
474A ASN 5.7 0.2 + - - -
475A GLY 3.2 10.7 + - - +
476A ILE* 3.6 32.4 - - + +
477A VAL* 5.6 0.2 - - - -
513A ILE* 3.5 2.6 - - - -
514A THR* 2.9 37.8 + - + +
601A AMI 3.6 10.9 + - - -
1B NAA 4.3 5.1 + - - +
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Residues in contact with GLY 447 (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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395A ALA* 3.8 7.5 - - - +
446A ARG* 1.3 76.6 - - - +
448A TRP* 1.3 69.3 + - - -
467A PRO* 3.7 3.5 - - - +
468A VAL* 2.9 30.7 + - - +
475A GLY* 3.1 19.0 + - - -
512A LEU 2.8 13.7 - - - -
513A ILE* 4.1 2.0 - - - -
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Residues in contact with TRP 448 (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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393A TYR* 4.0 5.8 - - + -
394A GLY* 2.8 45.3 + - - -
395A ALA* 3.8 16.6 - - - -
397A ASP 3.2 7.2 + - - -
398A LEU* 3.9 8.5 - - + -
401A LEU* 3.3 25.1 - - + +
402A GLY 3.3 27.8 - - - -
446A ARG 4.5 0.7 - - - -
447A GLY* 1.3 74.8 - - - -
449A THR* 1.3 61.2 + - - +
451A VAL* 3.8 7.4 - - + -
460A PHE* 3.9 8.1 - + - -
464A ALA* 3.4 24.0 - - + -
466A GLY 3.4 4.9 - - - -
468A VAL* 3.5 9.9 - - - +
510A GLY 4.3 0.4 - - - -
511A ASP* 3.3 3.5 - - - -
512A LEU* 2.8 69.0 + - + +
514A THR* 3.8 19.1 - - + -
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Residues in contact with THR 449 (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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448A TRP* 1.3 73.2 - - - +
450A GLY* 1.3 70.6 + - - +
451A VAL 3.0 5.1 + - - -
464A ALA* 3.5 2.6 - - - +
465A THR* 3.0 32.1 + - - +
466A GLY* 2.8 27.8 + - - +
467A PRO 3.7 12.3 - - - +
468A VAL* 4.3 1.3 - - - -
469A LYS 5.6 0.2 - - - -
509A THR* 3.8 5.0 + - - -
510A GLY 3.8 2.0 - - - -
511A ASP* 2.8 24.5 + - - -
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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