Contacts of the strand formed by residues 446 - 451 (chain A) in PDB entry 3SJE
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 GLY 446 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A TYR* 3.8 11.7 - - - -
373A ILE* 5.7 1.8 - - - -
441A LEU 4.0 0.2 + - - -
442A LEU* 2.8 31.3 + - - +
445A ARG* 1.4 70.2 - - - +
447A VAL* 1.3 64.5 + - - +
448A ALA 3.7 1.1 - - - -
530A ILE* 4.0 12.9 - - - +
669A MET* 3.4 4.5 - - - +
673A ARG* 2.8 28.9 + - - +
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Residues in contact with VAL 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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370A ARG* 3.9 29.2 - - + -
371A TYR 2.8 18.4 + - - +
372A VAL* 4.1 12.8 - - + -
414A ARG* 4.2 10.3 - - - -
445A ARG 4.0 0.7 - - - +
446A GLY* 1.3 77.5 - - - +
448A ALA* 1.3 68.8 + - + +
530A ILE* 4.0 2.7 - - - +
531A ALA* 3.8 9.0 + - - +
587A LEU* 4.5 3.4 - - + -
593A LEU* 3.6 35.4 - - + -
595A PHE* 3.5 21.2 - - + -
669A MET* 3.9 21.6 - - + +
673A ARG* 5.4 0.3 + - - -
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Residues in contact with ALA 448 (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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371A TYR 3.6 2.4 + - - +
372A VAL* 3.6 3.4 - - + +
373A ILE* 2.9 29.7 + - - +
446A GLY* 3.7 1.0 - - - -
447A VAL* 1.3 85.1 - - + +
449A TYR* 1.3 62.3 + - - +
450A ILE* 4.2 0.4 - - + -
470A MET* 4.0 9.6 - - + -
530A ILE* 3.7 6.8 - - - +
531A ALA 3.1 12.6 - - - +
587A LEU* 3.8 39.3 - - + -
595A PHE* 4.4 1.6 - - + -
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Residues in contact with TYR 449 (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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373A ILE* 3.4 33.7 - - + -
375A GLY* 3.1 17.7 + - - -
421A TRP* 2.9 25.2 + + - -
448A ALA* 1.3 76.0 - - - +
450A ILE* 1.3 64.0 + - - +
451A ASN* 2.8 38.6 + - - -
520A ASP* 3.7 3.4 - - - +
521A PHE* 3.4 30.3 - - + -
524A PHE* 3.6 40.6 - + + -
530A ILE* 4.4 3.8 - - + -
531A ALA 2.9 7.5 + - - -
532A SER* 3.0 18.7 - - - +
533A GLY 2.9 24.6 + - - -
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Residues in contact with ILE 450 (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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372A VAL* 5.4 1.3 - - + -
373A ILE 2.8 12.8 + - - +
374A LEU* 3.4 19.4 - - + +
375A GLY 3.0 25.3 + - - -
448A ALA* 5.3 0.4 - - + -
449A TYR* 1.3 84.3 - - - +
451A ASN* 1.3 73.0 + - - +
470A MET* 4.0 11.2 - - + -
533A GLY* 3.5 10.3 - - - +
534A ARG* 5.3 2.0 - - - -
580A ARG* 4.3 22.9 - - + +
583A MET* 3.9 32.3 - - + -
584A VAL* 3.9 17.0 - - + -
587A LEU* 3.9 23.8 - - + -
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Residues in contact with ASN 451 (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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375A GLY 3.3 5.2 - - - +
376A GLY* 4.6 1.2 - - - -
449A TYR* 2.8 36.5 + - + -
450A ILE* 1.3 86.9 - - - +
452A ALA* 1.3 67.9 + - - +
453A ASP 3.7 3.2 - - - +
519A ASN* 3.0 30.9 + - - +
520A ASP* 3.6 7.4 - - - +
521A PHE* 3.5 19.6 + - + -
533A GLY 2.9 17.2 + - - +
534A ARG* 4.1 14.2 - - + +
580A ARG* 3.8 10.7 + - - +
1754A CL 3.3 23.4 - - - +
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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