Contacts of the strand formed by residues 407 - 414 (chain A) in PDB entry 3DL2
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 LYS 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A GLN* 3.6 9.5 - - - +
396A ASP* 2.7 36.7 + - - +
400A SER* 3.6 17.3 - - - +
405A LYS* 3.1 21.0 - - + +
406A LYS* 1.3 77.7 - - - +
408A VAL* 1.3 71.5 + - - +
409A HIS* 3.4 25.1 - - - +
431A CYS 3.5 0.2 - - - +
432A ILE* 4.3 0.7 - - - -
433A LEU* 3.1 23.7 + - - -
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Residues in contact with VAL 408 (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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324A GLN* 5.6 0.7 + - - -
342A GLU* 5.4 4.0 - - - +
344A TRP* 3.4 43.7 - - + -
406A LYS 5.1 1.6 - - - +
407A LYS* 1.3 84.5 - - - +
409A HIS* 1.3 68.2 + - - +
430A PRO* 3.8 23.8 - - + -
431A CYS 3.2 11.7 - - - +
432A ILE* 4.0 20.4 - - + -
442A ILE* 4.2 15.7 - - + -
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Residues in contact with HIS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ASN* 2.9 24.7 + - - +
324A GLN* 3.8 7.5 + - - -
344A TRP* 4.4 1.6 - - - -
396A ASP* 3.2 29.4 - - - -
397A MET* 3.6 15.0 - - + +
400A SER* 2.7 28.2 + - - -
407A LYS* 3.4 27.6 - - - +
408A VAL* 1.3 75.2 + - - +
410A SER* 1.3 56.6 + - - +
411A VAL* 3.3 21.2 + - + +
430A PRO* 4.2 1.8 - - - -
431A CYS* 2.7 41.4 + - - +
433A LEU* 3.7 22.4 - - + -
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Residues in contact with SER 410 (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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319A CYS 4.1 1.8 - - - -
320A ASN* 2.9 32.7 + - - +
323A SER* 3.4 26.2 - - - -
344A TRP* 4.2 15.8 - - - -
345A VAL 2.7 19.9 + - - -
346A ILE* 3.9 3.6 - - - +
409A HIS* 1.3 68.9 - - - +
411A VAL* 1.3 58.3 + - - +
428A SER* 2.7 26.3 + - - -
429A LEU 3.4 9.5 + - - -
430A PRO* 4.0 2.0 - - - -
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Residues in contact with VAL 411 (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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315A ILE* 4.1 31.4 - - + -
316A GLY 3.2 12.1 - - - +
317A ILE 4.6 1.6 - - - -
320A ASN* 4.6 0.2 - - + -
397A MET* 3.7 30.5 - - - -
409A HIS* 3.8 22.2 - - + +
410A SER* 1.3 77.4 - - - +
412A SER* 1.3 66.4 + - - +
413A ALA* 3.1 3.1 + - - +
428A SER* 3.5 6.7 - - - -
429A LEU 2.9 24.0 + - - +
431A CYS* 4.0 21.5 - - + -
433A LEU* 4.2 8.1 - - + -
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Residues in contact with SER 412 (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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296A VAL* 3.8 15.0 - - - +
297A GLU* 4.6 5.5 + - - +
300A THR* 3.9 9.6 - - - -
315A ILE* 3.3 12.5 - - - +
316A GLY* 2.8 39.8 + - - -
318A GLY* 3.1 25.2 + - - -
411A VAL* 1.3 67.6 - - - +
413A ALA* 1.3 58.5 + - - +
426A PHE* 4.0 18.4 - - - -
427A LEU 3.5 11.0 - - - -
428A SER* 4.0 1.4 + - - +
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Residues in contact with ALA 413 (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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311A ALA 5.9 0.9 - - - +
314A VAL 5.0 2.0 - - - -
315A ILE* 4.9 0.7 - - + -
411A VAL* 3.1 10.3 + - + +
412A SER* 1.3 74.6 - - - +
414A LEU* 1.3 70.2 + - - +
415A ALA* 3.0 5.4 + - - -
426A PHE* 3.4 9.4 - - - -
427A LEU 2.9 28.1 + - - +
429A LEU* 4.4 8.4 - - + +
431A CYS* 3.9 23.1 - - - -
438A VAL* 4.9 9.0 - - + -
441A VAL* 5.3 2.9 - - + -
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Residues in contact with LEU 414 (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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304A TRP* 4.1 17.5 - - + -
311A ALA* 3.8 29.8 + - + -
413A ALA* 1.3 71.1 - - - +
415A ALA* 1.3 60.9 + - - +
416A LYS* 3.8 15.3 + - + +
418A TYR* 4.0 15.1 - - - -
424A GLU* 4.0 29.2 - - + +
425A VAL 3.7 11.4 - - - +
426A PHE* 3.4 34.0 - - + -
429A LEU* 4.3 3.0 - - - +
441A VAL* 5.7 0.9 - - - +
169B GLY* 4.3 15.6 + - - +
171B SER* 4.7 8.1 - - - -
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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