Contacts of the strand formed by residues 462 - 470 (chain A) in PDB entry 3DAN
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 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A ASN* 3.5 10.1 - - - +
453A GLU 3.8 0.5 - - - +
454A LEU* 3.4 8.5 - - - +
455A GLY* 2.9 51.7 + - - +
456A GLU 5.0 0.4 - - - -
457A SER* 3.1 20.5 + - - -
461A ALA* 1.3 69.8 - - - +
463A VAL* 1.3 60.6 + - - +
464A THR* 5.1 2.0 + - - +
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Residues in contact with VAL 463 (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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163A ALA* 3.8 1.0 - - - +
164A PHE* 2.9 29.3 + - + +
165A ASN* 3.0 13.0 + - - +
286A PRO* 3.5 27.8 - - + +
289A LEU* 3.7 29.8 - - + -
290A LYS* 4.2 5.6 - - + -
452A ILE* 4.0 27.4 - - + -
453A GLU 3.8 2.5 - - - +
454A LEU* 3.8 15.5 - - + -
461A ALA* 4.0 11.2 - - + +
462A ALA* 1.3 76.6 - - - +
464A THR* 1.3 67.1 + - - +
465A LEU 4.9 0.2 - - - +
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Residues in contact with THR 464 (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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161A LYS* 3.9 9.2 - - + -
162A ALA 3.6 22.9 - - - +
163A ALA* 3.9 11.4 - - + +
452A ILE* 3.1 6.2 - - - -
453A GLU* 2.8 66.5 + - + +
462A ALA* 5.1 2.3 + - - +
463A VAL* 1.3 76.2 + - - +
465A LEU* 1.3 73.8 + - - +
466A THR 3.6 0.2 + - - -
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Residues in contact with LEU 465 (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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149A PHE* 6.2 1.1 - - + -
152A LEU* 3.9 33.4 - - + -
156A LEU* 3.6 5.2 - - + +
161A LYS* 3.5 5.9 - - - -
162A ALA* 2.9 42.2 + - + +
164A PHE* 5.0 7.6 - - + -
289A LEU* 4.4 16.4 - - + -
443A LEU* 6.3 2.5 - - + -
450A PHE* 3.9 14.6 - - + -
451A GLU 3.5 5.8 - - - +
452A ILE* 3.6 22.7 - - + -
464A THR* 1.3 73.6 - - - +
466A THR* 1.3 60.5 + - - +
467A PHE 4.7 2.5 - - - +
468A LEU* 4.1 35.2 - - + -
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Residues in contact with THR 466 (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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156A LEU* 3.9 14.3 - - - +
160A GLY 4.1 8.4 - - - +
161A LYS* 4.5 11.2 - - + +
451A GLU* 2.8 33.5 + - - +
452A ILE 3.6 3.4 + - - -
453A GLU* 3.9 41.3 - - + +
464A THR 4.0 1.3 - - - +
465A LEU* 1.3 78.2 - - - +
467A PHE* 1.3 69.4 + - - +
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Residues in contact with PHE 467 (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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156A LEU* 3.7 7.5 - - + +
450A PHE* 3.2 8.7 - - - +
451A GLU* 2.9 49.3 + - + +
465A LEU* 3.6 1.6 - - - +
466A THR* 1.3 86.9 + - - +
468A LEU* 1.3 86.4 + - - +
469A LYS* 3.5 31.9 - - + -
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Residues in contact with LEU 468 (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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149A PHE* 6.2 0.4 - - + -
152A LEU* 4.6 3.4 - - + -
153A GLU* 3.9 25.7 - - + +
156A LEU* 3.8 21.8 - - + +
443A LEU* 5.4 3.1 - - + -
447A TYR* 3.8 46.7 - - + +
449A SER 3.9 1.8 - - - -
450A PHE* 3.7 17.9 - - + -
465A LEU* 4.1 30.7 - - + -
467A PHE* 1.3 93.4 - - - +
469A LYS* 1.3 61.3 + - - +
470A ARG* 3.5 8.4 + - - +
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Residues in contact with LYS 469 (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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297A GLU* 3.9 19.3 + - - +
447A TYR* 3.2 6.7 - - - +
448A ASP* 2.8 41.1 + - + +
449A SER* 3.0 38.5 + - - +
467A PHE* 3.5 27.1 - - + -
468A LEU* 1.3 69.9 - - - +
470A ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 470 (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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153A GLU* 3.2 31.6 + - + +
446A ARG* 3.8 24.7 + - - +
447A TYR* 4.0 12.3 - - + -
448A ASP* 3.6 9.1 - - - +
468A LEU 3.5 6.3 + - - +
469A LYS* 1.3 73.9 - - - +
471A ALA* 1.3 62.8 + - - +
472A SER* 3.1 23.5 + - - +
473A ILE* 3.2 31.7 + - - +
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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