Contacts of the strand formed by residues 455 - 460 (chain B) in PDB entry 4L28
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 ILE 455 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B PRO* 5.0 0.2 - - + -
448B VAL 3.7 7.0 - - - +
449B VAL* 4.1 17.7 - - + +
453B GLY 3.6 0.2 + - - -
454B VAL* 1.3 78.7 - - - +
456B LEU* 1.3 66.1 + - - +
457B GLY 3.9 10.5 - - - +
487B PHE* 3.4 30.9 - - + -
489B GLN* 3.9 23.2 - - - +
510B LEU* 3.7 28.9 - - + -
512B VAL* 3.9 19.3 - - + -
527B ARG 4.0 20.0 - - - +
530B VAL* 4.0 8.5 - - + -
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Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B PRO* 3.7 36.6 - - + -
448B VAL* 2.6 21.5 + - + +
450B ASP* 4.3 13.9 - - + +
454B VAL* 3.8 27.1 - - + +
455B ILE* 1.3 81.3 - - - +
457B GLY* 1.3 55.9 + - - +
483B ILE* 4.0 11.0 - - + +
485B LYS* 3.8 21.4 - - + +
487B PHE* 3.9 3.8 - - - -
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Residues in contact with GLY 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B PRO* 3.3 2.6 - - - +
448B VAL* 2.9 27.9 + - - +
455B ILE* 3.6 5.8 - - - +
456B LEU* 1.3 81.8 - - - +
458B MET* 1.3 75.0 + - - +
483B ILE* 3.9 4.0 - - - -
484B TYR 3.4 11.9 - - - -
487B PHE* 3.9 13.5 - - - -
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Residues in contact with MET 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B GLN* 4.9 3.6 - - - -
446B ALA 3.7 9.4 - - - +
447B PRO* 3.8 24.0 - - + -
448B VAL* 4.2 0.9 - - - +
457B GLY* 1.3 86.0 - - - +
459B VAL* 1.3 73.7 + - - +
460B THR* 4.6 1.6 - - + -
483B ILE* 3.4 3.7 - - - +
484B TYR* 2.6 44.9 + - + +
487B PHE* 5.4 3.1 - - + -
508B PHE* 3.6 49.8 - - + -
510B LEU* 3.5 37.0 - - + -
533B VAL* 4.2 12.1 - - - -
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Residues in contact with VAL 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B VAL* 4.4 7.2 - - + -
434B THR* 5.5 8.5 - - - +
438B LEU* 4.9 5.7 - - + +
445B GLN* 3.3 3.6 - - - +
446B ALA* 2.9 49.9 + - + +
448B VAL* 4.0 12.8 - - + -
458B MET* 1.3 81.7 - - - +
460B THR* 1.3 66.0 + - - +
464B MET* 5.1 6.5 - - + -
479B VAL* 3.5 29.6 - - + -
482B VAL* 4.3 13.2 - - + +
483B ILE* 3.8 16.2 - - - +
484B TYR* 4.9 2.0 - - - -
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Residues in contact with THR 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B LEU* 4.7 2.9 - - - -
444B ASN 3.6 7.9 - - - -
445B GLN* 3.8 20.6 - - + +
458B MET* 4.6 0.4 - - + -
459B VAL* 1.3 79.2 - - - +
461B LEU* 1.3 65.2 + - - +
462B GLY 4.3 1.8 - - - -
463B ASN* 3.2 16.5 + - - +
464B MET* 3.3 23.9 + - - +
484B TYR* 3.4 16.0 + - + -
508B PHE* 4.1 8.1 - - + -
201D GLU* 2.8 44.0 + - + +
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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