Contacts of the strand formed by residues 481 - 488 (chain A) in PDB entry 4LT6
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 LYS 481 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A THR 4.8 0.2 - - - -
378A ALA* 4.6 0.2 - - - -
379A SER* 2.6 48.5 + - - -
389A TRP* 2.8 11.1 + - - -
467A TYR* 3.6 13.1 + - - +
479A GLY 3.6 3.7 + - - +
480A MET* 1.3 74.7 - - - +
482A ILE* 1.3 68.2 + - - +
483A GLU* 3.9 28.5 - - + +
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Residues in contact with ILE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 4.1 9.0 - - + -
377A THR 3.4 12.8 - - - +
378A ALA* 4.4 0.7 - - + -
389A TRP* 3.5 19.3 - - + -
393A VAL* 3.7 34.3 - - + -
462A PHE* 4.0 27.1 - - + -
463A THR* 3.9 18.2 - - + +
466A VAL* 4.3 17.3 - - + -
467A TYR* 2.8 40.8 + - + -
481A LYS* 1.3 78.1 + - - +
483A GLU* 1.3 64.7 + - - +
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Residues in contact with GLU 483 (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 VAL 3.5 1.3 - - - +
376A LEU* 3.5 2.7 - - - +
377A THR* 2.6 54.0 + - + +
463A THR* 4.5 3.1 - - - -
481A LYS* 3.9 27.8 - - + +
482A ILE* 1.3 77.3 - - - +
484A ALA* 1.3 61.1 + - - +
485A THR* 4.0 22.0 - - + +
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Residues in contact with ALA 484 (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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374A ILE* 4.2 12.1 - - + -
375A VAL 3.2 6.1 - - - +
376A LEU* 3.8 20.4 - - + -
400A LEU* 5.9 0.9 - - + -
459A ILE* 3.4 40.8 - - + +
462A PHE* 5.0 3.8 - - + -
463A THR* 4.2 10.9 - - + +
483A GLU* 1.3 78.8 - - - +
485A THR* 1.3 64.4 + - - +
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Residues in contact with THR 485 (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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374A ILE* 4.6 2.9 - - - -
375A VAL* 3.1 33.9 + - - +
459A ILE* 4.7 0.2 - - - -
483A GLU* 4.0 24.2 + - + +
484A ALA* 1.3 76.9 - - - +
486A HIS* 1.3 66.9 + - - +
487A VAL* 3.4 5.4 - - - +
495A TYR* 3.9 27.1 + - - +
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Residues in contact with HIS 486 (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 HIS* 3.3 38.8 + + + +
373A TYR 3.3 16.2 - - - -
374A ILE* 4.6 4.0 - - + +
440A ILE* 5.6 0.4 - - + -
442A PHE* 4.7 6.8 - + - -
454A ASP* 5.5 5.0 - - - -
455A LEU* 3.4 42.6 + - + +
456A THR* 5.8 6.4 - - + +
459A ILE* 4.1 7.7 - - + +
484A ALA 4.1 1.4 + - - -
485A THR* 1.3 74.7 - - - +
487A VAL* 1.3 79.7 + - - +
488A LYS* 4.7 6.7 + - + -
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Residues in contact with VAL 487 (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 HIS* 3.7 1.2 - - - -
373A TYR* 2.9 39.0 + - + +
375A VAL* 3.7 15.9 - - + -
485A THR* 3.4 14.6 - - - +
486A HIS* 1.3 85.0 - - - +
488A LYS* 1.3 76.0 + - - +
491A GLN* 3.6 31.4 - - + +
492A LEU* 3.9 4.7 - - + +
495A TYR* 3.5 33.2 - - + +
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Residues in contact with LYS 488 (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 ARG* 3.8 9.6 - - - +
372A HIS* 4.4 23.6 - - + +
373A TYR* 5.0 0.4 - - - -
486A HIS* 4.6 6.1 - - + +
487A VAL* 1.3 93.0 - - - +
489A LYS* 1.3 65.1 + - - +
490A LYS* 3.3 15.3 - - + +
491A GLN* 3.2 14.1 + - + +
492A LEU* 3.3 3.6 + - - +
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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