Contacts of the strand formed by residues 438 - 443 (chain A) in PDB entry 3SV1
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 ARG 438 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A PHE* 3.8 30.6 - - + +
434A ILE 4.0 0.2 - - - -
435A SER* 2.9 29.9 + - - +
437A GLN* 1.3 97.8 + - - +
439A ILE* 1.3 77.6 + - - +
440A LYS* 4.2 10.9 - - + +
452A ASP* 3.3 32.6 + - - +
453A HIS 3.0 16.8 - - - +
454A ALA* 3.8 12.7 - - - +
455A LEU* 3.3 4.3 - - - +
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Residues in contact with ILE 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU* 5.6 8.7 - - + -
433A PHE 3.2 9.9 - - - +
434A ILE* 4.2 18.6 - - + -
435A SER 4.5 0.2 - - - +
438A ARG* 1.3 86.9 - - - +
440A LYS* 1.3 60.7 + - - +
441A VAL* 5.5 3.3 - - + +
451A MET* 6.0 0.2 - - - +
453A HIS* 3.0 26.3 + - - +
455A LEU* 3.4 16.8 - - + -
458A ILE* 3.3 28.3 - - + -
470A LEU* 3.9 21.6 - - + +
517A ILE* 3.8 40.6 - - + -
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Residues in contact with LYS 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ASP 3.9 0.3 - - - +
432A LEU* 4.1 2.1 - - - -
433A PHE* 3.1 55.2 + - + -
438A ARG* 4.2 10.1 - - + +
439A ILE* 1.3 74.6 - - - +
441A VAL* 1.3 60.3 + - - +
442A LEU* 3.3 34.5 - - + +
449A THR* 4.3 11.4 + - + -
451A MET 3.2 17.3 - - - +
452A ASP* 3.6 28.5 - - + +
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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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430A VAL* 3.3 39.7 - - + -
431A ASP 3.6 4.5 - - - +
432A LEU* 3.5 12.8 - - + -
439A ILE* 5.5 3.4 - - + +
440A LYS* 1.3 71.4 - - - +
442A LEU* 1.3 72.9 + - - +
450A MET* 2.8 32.3 + - + -
451A MET* 3.0 31.0 + - + +
470A LEU* 6.6 0.2 - - + -
503A HIS* 5.7 1.3 - - + -
505A PHE* 3.3 33.2 - - + -
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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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430A VAL* 3.2 10.6 - - - +
431A ASP* 3.1 32.0 + - + +
433A PHE* 5.2 2.9 - - + +
440A LYS* 3.3 48.2 - - + +
441A VAL* 1.3 97.9 - - - +
443A ASN* 1.3 62.7 + - - +
447A GLN* 3.6 43.7 - - + +
448A GLU 3.4 4.7 - - - +
449A THR* 3.6 18.8 - - - +
450A MET* 3.8 6.7 - - - +
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Residues in contact with ASN 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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428A THR* 5.4 3.1 + - - -
429A GLU 4.3 2.3 - - - +
431A ASP* 5.2 0.4 - - - -
442A LEU* 1.3 69.6 - - - +
444A ALA* 1.3 56.4 + - - +
445A ASP* 2.7 20.1 + - - +
446A THR* 2.8 42.6 + - - +
447A GLN* 2.7 33.0 + - - +
448A GLU* 2.9 21.9 + - - +
450A MET* 3.9 19.6 - - - +
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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