Contacts of the strand formed by residues 440 - 447 (chain A) in PDB entry 5SUY
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 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A GLU* 3.6 19.9 + - + +
439A VAL* 1.3 78.2 - - - +
441A ASP* 1.3 60.3 + - - +
442A ARG* 3.8 18.8 - - + +
449B ILE 3.6 0.7 - - - +
451B ASN 3.4 4.6 + - - -
452B ALA* 3.0 36.0 + - + +
453B PHE* 4.7 2.0 - - - +
454B LEU* 4.3 16.7 - - - +
457B ASP* 3.1 40.0 + - - -
502B TYR* 4.1 25.8 + - + -
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Residues in contact with ASP 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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440A ARG* 1.3 73.2 - - - +
442A ARG* 1.3 58.9 + - - +
448B THR* 3.5 19.0 + - - +
449B ILE 3.1 27.6 + - - -
450B PRO* 3.7 23.4 - - + +
451B ASN 4.4 1.1 - - - +
438D GLU* 2.8 27.1 + - - +
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Residues in contact with ARG 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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440A ARG* 3.5 19.0 - - + +
441A ASP* 1.3 80.3 + - - +
443A MET* 1.3 62.3 + - - +
444A TRP* 3.7 23.2 - - + +
446B LYS* 3.3 43.8 - - + +
447B ILE 3.4 5.2 - - - +
448B THR* 5.4 1.3 - - - +
449B ILE 5.2 1.3 - - - -
452B ALA* 5.4 1.8 - - - +
502B TYR* 3.8 9.7 + - - -
457C ASP* 3.4 15.0 + - - -
438D GLU* 2.8 31.2 + - - +
439D VAL 3.2 35.2 + - - +
440D ARG* 3.4 40.3 - - - +
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Residues in contact with MET 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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442A ARG* 1.3 74.7 - - - +
444A TRP* 1.3 77.0 + - - +
445A LEU* 3.6 36.6 - - + -
445B LEU 3.7 0.3 - - - +
446B LYS* 3.4 4.9 - - - +
447B ILE* 2.7 51.8 + - + +
449B ILE* 3.3 39.9 - - + +
452B ALA* 4.9 4.3 - - + -
491B THR* 3.5 24.5 - - - +
492B VAL* 5.4 1.8 - - + -
502B TYR* 3.5 37.0 - - + -
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Residues in contact with TRP 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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442A ARG* 3.7 23.5 - - + +
443A MET* 1.3 85.3 - - - +
445A LEU* 1.3 59.5 + - - +
502A TYR* 6.3 0.4 - + - -
444B TRP* 4.1 44.1 - + + -
445B LEU 3.4 19.5 - - - -
446B LYS* 3.6 44.9 - - + -
502B TYR* 3.7 35.6 - - + +
440D ARG* 3.6 32.2 - - - +
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Residues in contact with LEU 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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443A MET* 3.6 14.3 - - + +
444A TRP* 1.3 74.1 - - - +
446A LYS* 1.3 68.8 + - - +
447A ILE* 3.6 24.9 + - + -
443B MET 3.7 0.5 - - - +
444B TRP* 3.4 6.7 - - - -
445B LEU* 2.9 43.4 + - + +
447B ILE* 4.2 18.2 - - + -
492B VAL* 3.7 37.5 - - + -
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Residues in contact with LYS 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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445A LEU* 1.3 82.3 - - - +
447A ILE* 1.3 69.8 - - - +
448A THR* 4.3 5.5 + - - +
442B ARG* 4.1 31.8 - - + +
443B MET 3.4 10.1 - - - +
444B TRP* 3.3 48.7 - - + +
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Residues in contact with ILE 447 (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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445A LEU* 3.6 32.5 - - + +
446A LYS* 1.3 83.3 - - - +
448A THR* 1.3 66.3 + - - +
449A ILE* 3.3 22.5 + - + +
442B ARG* 3.4 2.1 - - - +
443B MET* 2.9 55.9 + - + +
445B LEU* 5.0 6.5 - - + -
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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