Contacts of the strand formed by residues 483 - 489 (chain B) in PDB entry 3DLX
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 483 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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406B LYS* 3.4 30.5 - - - -
407B TYR* 3.4 12.1 - - - -
477B ASP 3.9 0.7 - - - +
478B VAL* 3.6 2.1 - - - -
479B ASP* 2.9 34.6 + - - +
482B LYS* 1.3 79.5 - - - +
484B LEU* 1.3 61.6 + - - -
485B THR* 4.0 1.2 + - - -
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Residues in contact with LEU 484 (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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405B SER 4.8 2.9 - - - +
406B LYS* 4.0 20.5 + - - +
452B ILE* 3.7 16.6 - - + -
469B ILE* 3.8 11.9 - - + -
476B PHE* 3.7 33.0 - - + -
477B ASP 3.4 1.3 - - - -
478B VAL* 3.7 28.9 - - + -
482B LYS 4.0 3.0 + - - +
483B GLY* 1.3 72.4 - - - -
485B THR* 1.3 60.8 + - - +
502B THR* 4.5 2.9 - - + -
504B CYS* 3.7 29.8 - - - -
505B ASP 4.4 0.9 - - - +
506B PHE* 3.5 17.3 - - + -
507B ALA* 2.9 27.0 + - - +
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Residues in contact with THR 485 (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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476B PHE* 3.1 7.2 - - - -
477B ASP* 2.9 41.3 + - - +
483B GLY 4.0 1.6 + - - -
484B LEU* 1.3 74.7 + - - +
486B LEU* 1.3 66.1 + - - +
487B ILE* 3.4 14.2 + - + +
507B ALA* 3.4 16.3 - - + +
508B VAL 4.1 2.2 - - - -
509B SER* 3.6 29.2 - - - +
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Residues in contact with LEU 486 (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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474B ALA* 3.1 35.9 - - + -
475B VAL 3.7 2.7 - - - +
476B PHE* 3.3 22.5 - - + -
485B THR* 1.3 69.4 - - - +
487B ILE* 1.3 59.0 + - - +
488B GLU 3.6 11.0 - - - +
489B LEU* 4.2 15.9 - - + -
495B VAL* 3.9 23.6 - - + -
498B VAL* 4.6 3.4 - - + -
506B PHE* 3.8 26.9 - - + -
507B ALA 2.7 17.4 + - - +
508B VAL* 4.5 2.5 - - + -
509B SER 2.9 23.4 + - - -
512B LEU* 3.3 18.1 - - + +
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Residues in contact with ILE 487 (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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308B ARG* 4.9 2.5 - - - +
468B ARG* 3.6 29.8 - - - +
475B VAL* 2.9 36.4 + - + +
477B ASP* 2.7 35.0 - - - +
485B THR* 3.9 17.9 - - + +
486B LEU* 1.3 76.2 - - - +
488B GLU* 1.3 73.2 + - + +
509B SER* 3.9 13.4 - - - +
511B LYS 4.7 0.9 - - - +
512B LEU* 3.6 7.8 - - - -
513B MET* 3.4 18.5 + - - +
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Residues in contact with GLU 488 (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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308B ARG* 3.0 32.9 + - - -
474B ALA* 3.3 7.4 - - - +
475B VAL* 2.9 40.2 + - + +
486B LEU* 3.6 3.7 - - - +
487B ILE* 1.3 95.7 - - + +
489B LEU* 1.3 60.8 + - - +
512B LEU* 4.2 3.4 - - - -
513B MET* 3.3 14.2 - - + +
514B PRO 3.9 15.5 - - - +
515B MET* 3.4 5.2 - - - -
516B GLN* 2.9 40.9 + - - +
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Residues in contact with LEU 489 (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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473B LYS 3.7 15.3 - - - +
474B ALA* 4.8 1.1 - - + -
486B LEU* 4.2 13.9 - - + -
488B GLU* 1.3 75.6 - - - +
490B TRP* 1.3 68.9 + - - +
491B GLU* 4.3 0.3 - - - -
493B LEU* 3.2 28.9 - - + +
494B THR* 3.6 31.2 - - - +
495B VAL* 3.7 11.4 - - + +
498B VAL* 4.0 18.4 - - + +
512B LEU* 4.6 11.0 - - + -
513B MET 3.4 5.5 + - - +
514B PRO* 3.1 9.6 - - + +
515B MET* 2.8 26.2 + - - -
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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