Contacts of the strand formed by residues 448 - 454 (chain A) in PDB entry 1EUT
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 TRP 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444A ALA* 3.8 21.5 - - + -
445A SER* 2.9 38.4 + - - +
446A PRO 3.7 6.6 - - - +
447A ASP* 1.3 85.2 + - - +
449A GLN* 1.3 66.2 + - - +
450A VAL* 3.6 10.4 + - + +
469A ILE* 4.4 11.9 - - + -
470A THR 3.6 6.3 - - - +
471A VAL* 3.9 11.2 - - + +
472A PRO* 3.5 17.6 - - + +
475A THR* 3.7 31.8 + - + +
480A TYR* 3.4 52.3 - + + -
481A ARG* 5.7 0.9 - - - -
482A VAL* 4.3 10.3 - - + -
499A VAL* 4.3 20.2 - - + -
501A VAL* 4.1 10.5 - - + -
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Residues in contact with GLN 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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446A PRO 5.1 1.6 + - - -
447A ASP* 3.8 21.3 + - - +
448A TRP* 1.3 72.1 - - - +
450A VAL* 1.3 61.2 + - - +
451A GLN* 4.0 17.5 - - - +
468A THR 3.4 1.9 - - - +
469A ILE* 3.3 2.9 - - - -
470A THR* 2.7 70.1 + - - +
472A PRO* 5.5 1.6 - - - +
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Residues in contact with VAL 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU* 3.9 37.0 - - + +
444A ALA* 4.2 27.8 - - + +
448A TRP* 3.6 11.9 + - + +
449A GLN* 1.3 73.0 - - - +
451A GLN* 1.3 71.0 + - - +
467A VAL* 5.1 1.1 - - + -
468A THR 3.1 3.1 - - - -
469A ILE* 3.6 36.8 - - + -
482A VAL* 4.8 6.7 - - + -
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Residues in contact with GLN 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU* 3.6 7.4 - - - -
449A GLN* 4.0 16.5 - - - +
450A VAL* 1.3 87.8 + - - +
452A GLY* 1.3 59.5 + - - +
466A GLN* 4.8 0.8 - - - +
467A VAL* 3.1 3.8 - - - +
468A THR* 2.6 53.1 + - - +
470A THR* 5.2 0.9 + - - -
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Residues in contact with GLY 452 (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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440A LEU* 3.8 32.8 + - - +
442A LEU* 3.6 9.0 - - - +
451A GLN* 1.3 77.1 - - - +
453A SER* 1.3 63.0 + - - -
466A GLN* 2.9 14.6 - - - -
467A VAL* 4.1 0.7 - - - -
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Residues in contact with SER 453 (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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425A VAL* 4.6 0.2 - - - +
440A LEU* 4.1 10.2 - - - +
452A GLY* 1.3 77.6 - - - -
454A VAL* 1.3 57.2 + - - +
465A GLY* 2.7 28.9 - - - -
466A GLN* 2.8 38.8 + - - +
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Residues in contact with VAL 454 (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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425A VAL* 5.4 3.1 - - + -
427A VAL* 3.8 28.7 - - + -
438A PRO* 3.5 37.7 + - + +
439A SER 4.5 5.8 - - - +
440A LEU* 5.0 6.7 - - + -
453A SER* 1.3 78.0 - - - +
455A GLU* 1.3 77.0 + - - +
456A PRO* 4.7 0.3 - - - +
457A LEU* 4.9 2.0 - - + -
463A ALA* 4.1 6.7 - - + -
464A LYS 3.2 13.9 - - - +
465A GLY* 3.7 1.3 - - - -
486A LEU* 3.8 19.7 - - + -
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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