Contacts of the strand formed by residues 437 - 443 (chain A) in PDB entry 3DDN
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 SER 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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430A THR 3.7 0.3 - - - +
431A LEU* 3.4 16.9 - - - -
432A TYR* 3.2 22.2 + - - -
433A GLY* 5.4 0.2 - - - -
435A GLN* 3.3 9.8 - - - +
436A LEU* 1.3 79.7 + - - +
438A GLN* 1.3 63.1 + - - +
439A LYS* 3.6 24.2 + - - +
451A ARG* 6.2 1.6 - - - -
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Residues in contact with GLN 438 (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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326A PRO 4.4 4.3 - - - +
329A ASP* 3.2 22.3 + - - +
330A LEU* 4.1 18.5 + - + +
333A LYS* 2.6 45.0 - - - +
430A THR 3.8 4.9 - - - -
431A LEU* 3.5 21.3 - - + -
436A LEU 4.3 4.0 - - - +
437A SER* 1.3 71.8 - - - +
439A LYS* 1.3 67.5 + - - +
451A ARG* 3.6 2.3 - - - +
452A ALA* 3.0 31.2 + - + +
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Residues in contact with LYS 439 (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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330A LEU* 4.0 3.9 - - - +
429A GLY* 2.9 24.9 - - - -
430A THR 2.9 18.5 + - - +
432A TYR* 2.9 35.5 + - + -
437A SER* 3.9 21.1 - - - +
438A GLN* 1.3 83.5 - - - +
440A ILE* 1.3 63.8 + - - +
441A VAL* 4.0 14.4 - - + -
449A ASP* 2.4 40.4 + - - +
450A LEU 3.4 1.3 - - - +
451A ARG* 3.8 31.1 - - - +
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Residues in contact with ILE 440 (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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330A LEU* 5.1 0.2 - - + -
333A LYS* 5.8 0.4 - - + -
334A LEU* 4.5 10.5 - - + -
337A LEU* 3.4 28.7 - - + -
427A VAL* 4.2 17.3 - - + -
428A SER 3.5 10.3 - - - +
439A LYS* 1.3 74.1 - - - +
441A VAL* 1.3 61.7 + - - +
442A GLN 4.3 1.1 - - - +
443A ILE* 4.5 4.5 - - + -
448A PHE* 3.5 31.2 - - + -
449A ASP* 3.6 2.1 - - - -
450A LEU* 2.7 36.6 + - + +
451A ARG 4.2 4.7 - - - +
452A ALA* 3.7 23.3 - - + +
456A ASN* 5.8 1.3 - - - +
499A LEU* 5.6 6.3 - - + -
528A LEU* 3.4 21.5 - - + -
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Residues in contact with VAL 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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409A HIS* 3.6 31.2 - - + +
412A VAL* 3.9 13.0 - - + -
428A SER* 2.8 31.6 + - - +
429A GLY* 3.9 7.2 - - - -
430A THR* 3.3 19.7 - - - +
432A TYR* 5.5 0.2 - - + -
439A LYS* 4.0 14.4 - - + +
440A ILE* 1.3 78.1 - - - +
442A GLN* 1.3 63.7 + - + +
447A HIS* 3.3 9.9 - - + +
448A PHE* 3.0 37.7 + - - +
449A ASP* 4.5 5.4 - - - +
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Residues in contact with GLN 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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354A ARG* 5.1 6.3 - - - +
414A ASP* 4.5 4.9 + - - -
426A THR* 3.8 17.0 - - - +
427A VAL* 3.4 2.4 - - - +
428A SER* 2.9 51.0 + - - +
440A ILE* 3.8 1.3 - - - +
441A VAL* 1.3 83.0 - - + +
443A ILE* 1.3 73.3 + - - +
444A ASN 3.8 4.3 + - - -
445A GLY* 2.8 30.5 + - - +
446A ARG 3.1 14.4 - - - +
447A HIS* 3.9 23.7 + - + -
448A PHE* 4.0 3.5 - - - -
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Residues in contact with ILE 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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337A LEU* 5.2 4.0 - - + -
341A LEU* 3.6 37.0 - - + -
426A THR 3.4 4.7 - - - +
427A VAL* 3.9 14.8 - - + -
440A ILE* 4.5 4.7 - - + -
442A GLN* 1.3 79.1 - - - +
444A ASN* 1.3 84.8 + - + +
445A GLY 3.3 1.3 - - - -
446A ARG* 2.9 25.0 + - + +
448A PHE* 3.6 24.3 - - + -
458A ILE* 5.7 1.8 - - + -
460A HIS* 6.0 2.2 - - + +
486A GLN* 5.4 1.3 - - - +
499A LEU* 3.7 25.6 - - + -
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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