Contacts of the strand formed by residues 440 - 449 (chain A) in PDB entry 3IJE
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 VAL 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PHE* 3.9 14.8 - - + -
2A ASN* 3.9 19.3 - - - +
351A ASP* 4.3 18.4 - - + +
419A TYR* 3.2 20.1 + - + +
439A PRO* 1.3 74.3 - - - +
441A ILE* 1.3 67.3 + - - +
442A THR* 5.3 2.2 - - - +
483A GLY* 3.5 16.5 - - - -
484A LYS 4.1 0.7 + - - -
487A LEU* 4.3 1.0 - - - +
577A ILE* 3.3 21.8 - - + +
579A ASN* 4.0 36.6 - - + +
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Residues in contact with ILE 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 VAL* 1.3 75.1 - - - +
442A THR* 1.3 63.5 + - - +
443A VAL* 4.0 5.4 + - + -
482A ASP* 3.5 19.1 - - - +
483A GLY* 4.2 0.2 - - - -
487A LEU* 3.4 31.0 - - + -
491A LEU* 3.9 30.7 - - + -
493A PHE* 4.9 4.3 - - + -
563A LEU* 4.2 18.2 - - + -
576A PRO* 4.4 12.6 - - + -
577A ILE 3.0 17.4 + - - +
578A LEU* 3.7 25.6 - - + +
579A ASN* 3.1 23.6 + - - +
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Residues in contact with THR 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 VAL* 5.3 2.3 - - - +
441A ILE* 1.3 73.3 - - - +
443A VAL* 1.3 64.4 + - - +
444A ASN* 3.8 19.1 - - - +
480A LYS* 3.9 5.7 + - - +
481A ALA* 3.4 1.7 - - - -
482A ASP* 2.7 36.1 + - - +
483A GLY* 5.8 0.2 - - - -
579A ASN* 4.3 17.6 + - - +
582A THR* 4.9 9.6 - - + +
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Residues in contact with VAL 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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441A ILE* 4.0 4.2 + - + +
442A THR* 1.3 75.4 - - - +
444A ASN* 1.3 70.3 + - - +
445A ALA 4.1 1.4 + - - +
479A LEU* 5.0 6.1 - - + -
480A LYS 3.3 6.5 - - - +
481A ALA* 3.8 9.4 - - + -
493A PHE* 3.7 34.3 - - + -
527A ILE* 5.9 0.2 - - + -
561A TYR* 3.0 42.7 + - + +
578A LEU* 4.6 17.7 - - + -
582A THR* 3.8 23.7 - - + +
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Residues in contact with ASN 444 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A THR* 3.8 15.2 - - - +
443A VAL* 1.3 80.8 - - - +
445A ALA* 1.3 60.8 + - - +
479A LEU* 4.7 1.8 - - - -
480A LYS* 2.6 70.8 + - + +
533A MET* 3.2 14.5 - - + +
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Residues in contact with ALA 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 VAL 4.0 2.8 + - - -
444A ASN* 1.3 73.1 - - - +
446A GLY* 1.3 59.2 - - - +
478A CYS 3.4 4.9 - - - -
479A LEU* 3.8 8.5 - - + -
533A MET* 4.1 1.6 - - - -
559A MET* 3.4 30.7 - - + -
561A TYR* 3.6 22.8 + - + +
586A ILE* 3.9 20.8 - - + +
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Residues in contact with GLY 446 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A ALA* 1.3 72.8 - - - +
447A LEU* 1.3 60.8 - - - +
476A ARG 4.5 0.9 - - - -
477A PHE* 3.4 7.0 - - - +
478A CYS* 2.8 37.0 + - - +
533A MET* 3.6 13.8 - - - +
559A MET* 3.9 4.7 - - - +
586A ILE* 4.8 2.5 - - - -
588A ARG* 5.4 0.4 - - - -
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Residues in contact with LEU 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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446A GLY* 1.3 73.7 - - - +
448A GLU* 1.3 71.0 + - - +
449A VAL* 6.0 0.2 - - + -
475A VAL* 4.3 22.2 - - + -
476A ARG 3.5 13.0 - - - +
477A PHE* 4.3 10.3 - - + -
497A LEU* 5.2 2.0 - - + -
557A ILE* 3.6 33.2 - - + +
559A MET* 4.2 16.6 - - + -
586A ILE* 3.7 28.9 - - + +
587A SER 4.2 0.4 - - - -
588A ARG* 3.2 52.0 + - + +
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Residues in contact with GLU 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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447A LEU* 1.3 82.1 - - - +
449A VAL* 1.3 70.3 + - - +
450A TYR* 3.1 37.4 + - + -
474A ASN 3.9 0.3 - - - +
475A VAL* 3.7 2.8 - - - +
476A ARG* 3.0 57.0 + - - +
588A ARG* 4.7 7.4 - - + -
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Residues in contact with VAL 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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447A LEU* 6.0 0.7 - - + -
448A GLU* 1.3 79.2 - - - +
450A TYR* 1.3 67.1 + - - +
451A PRO 3.2 18.9 - - - +
452A SER* 3.4 16.4 + - - +
473A PHE* 4.1 8.5 - - + -
474A ASN 3.2 13.5 - - - +
475A VAL* 3.8 18.2 - - + -
557A ILE* 3.7 29.4 - - + -
588A ARG* 4.6 16.5 - - + +
589A GLN 4.6 17.0 - - - +
590A ALA* 4.7 4.0 - - + -
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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