Contacts of the strand formed by residues 440 - 446 (chain A) in PDB entry 3D8F
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 ALA 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A VAL* 4.1 1.3 - - - -
435A GLU* 3.1 21.9 + - + -
438A SER* 3.1 16.8 - - - +
439A GLN* 1.3 75.9 - - - +
441A LEU* 1.3 67.0 + - - +
442A LEU* 3.0 9.9 + - - +
387C PRO* 4.0 14.4 - - + -
388C GLY* 3.5 34.8 - - - +
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Residues in contact with LEU 441 (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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432A LYS* 3.8 38.6 - - + +
433A LEU 4.0 3.8 - - - +
434A VAL* 4.5 6.7 - - + +
439A GLN 3.8 4.0 + - - -
440A ALA* 1.3 69.4 - - - +
442A LEU* 1.3 63.4 + - - +
443A HIS 3.2 30.5 - - - +
444A ALA* 4.0 13.0 - - + -
387C PRO* 5.1 6.5 - - - +
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Residues in contact with LEU 442 (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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422A LEU* 3.6 31.2 - - + -
433A LEU* 2.8 22.6 + - + +
435A GLU* 3.9 25.6 - - + +
440A ALA 3.0 18.8 + - - +
441A LEU* 1.3 76.3 - - - +
443A HIS* 1.3 59.9 + - + +
437B GLN* 5.6 13.7 - - + -
387C PRO 5.4 0.7 - - - +
388C GLY* 4.0 21.8 - - - +
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Residues in contact with HIS 443 (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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431A LEU* 5.0 1.8 - - + -
432A LYS* 3.5 0.6 - - - -
433A LEU* 3.0 49.1 + - + -
441A LEU* 3.2 12.7 - - - +
442A LEU* 1.3 78.2 + - + +
444A ALA* 1.3 84.6 + - - +
445A GLN* 4.0 16.5 + - + -
467A TYR* 4.0 22.5 + - - -
471A ASP* 6.1 0.9 - - - -
480A HIS* 5.7 8.3 + + - -
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Residues in contact with ALA 444 (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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430A THR* 4.0 14.8 - - + -
431A LEU 3.5 5.2 - - - -
432A LYS* 4.6 1.1 - - - +
441A LEU* 4.0 20.9 - - + -
443A HIS* 1.3 89.7 + - - +
445A GLN* 1.3 59.8 + - - +
446A PRO* 3.3 11.8 - - - +
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Residues in contact with GLN 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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430A THR* 3.5 3.1 - - - +
431A LEU* 2.7 50.1 + - + +
443A HIS* 4.0 11.8 + - - +
444A ALA* 1.3 70.2 - - - +
446A PRO* 1.3 97.6 + - - +
447A ILE 2.9 0.7 + - - -
449A SER* 3.5 5.1 + - - -
450A ILE* 3.7 24.5 - - + -
467A TYR* 4.0 22.8 - - + +
469A ALA* 3.0 28.8 - - - +
470A ARG 4.6 2.3 - - - +
472A LYS* 3.5 21.4 + - - +
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Residues in contact with PRO 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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429A GLU 4.0 6.7 - - - +
430A THR* 4.5 5.6 - - + +
444A ALA 3.3 11.0 - - - +
445A GLN* 1.3 98.8 + - - +
447A ILE* 1.3 66.0 + - - +
448A ILE* 3.2 6.7 - - + +
449A SER* 3.0 26.4 + - - +
450A ILE 3.7 1.2 + - - -
472A LYS* 4.4 15.5 - - - -
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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