Contacts of the strand formed by residues 372 - 380 (chain B) 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 HIS 372 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B TYR* 3.5 3.8 - - - +
371B ARG* 1.3 92.8 - - + +
373B TYR* 1.3 74.3 + - - +
440B ILE* 3.2 35.7 + - + +
442B PHE* 3.3 40.2 - + + -
486B HIS* 3.3 28.0 + + + +
487B VAL 3.7 4.0 - - - -
488B LYS* 3.9 35.6 - - + +
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Residues in contact with TYR 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B PHE* 2.3 58.7 + + - -
367B PHE* 3.2 19.3 - + - -
370B TYR* 3.0 47.7 + + + -
371B ARG 4.4 2.9 - - - -
372B HIS* 1.3 89.5 - - - +
374B ILE* 1.3 64.5 + - - +
375B VAL* 5.3 0.2 - - + -
437B PHE* 4.6 8.7 - - + -
438B LEU 3.0 20.9 - - - -
439B GLY* 3.9 1.1 - - - -
440B ILE* 4.5 2.7 - - - -
486B HIS* 3.5 4.5 - - - -
487B VAL* 2.7 41.8 + - + +
489B LYS* 4.6 6.5 - - + -
492B LEU* 4.0 36.3 - - + -
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B TYR* 1.3 75.8 - - - +
375B VAL* 1.3 72.0 + - - +
376B LEU* 5.5 0.4 - - - -
400B LEU* 4.6 14.1 - - + -
404B LEU* 3.9 19.7 - - + -
436B TRP 3.8 0.5 - - - +
437B PHE* 3.5 4.3 - - - +
438B LEU* 2.9 44.7 + - + +
440B ILE* 3.5 20.2 - - + -
455B LEU* 3.6 26.9 - - + -
459B ILE* 4.3 23.6 - - + -
484B ALA* 4.3 7.4 - - + -
485B THR 3.2 15.7 - - - +
486B HIS* 4.1 4.9 - - - -
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B TYR 5.2 0.9 - - - +
374B ILE* 1.3 77.3 - - - +
376B LEU* 1.3 63.7 + - - +
377B THR* 4.0 7.0 + - - +
435B MET* 3.5 33.7 - - + -
436B TRP 3.5 4.7 - - - +
437B PHE* 3.6 26.5 - - + -
484B ALA* 3.2 5.0 - - - +
485B THR* 2.7 46.0 + - - +
487B VAL* 4.3 11.7 - - + -
492B LEU* 4.7 4.3 - - + -
495B TYR* 4.1 30.5 - - + -
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ILE* 5.5 0.9 - - + -
375B VAL* 1.3 75.0 - - - +
377B THR* 1.3 62.4 + - - +
393B VAL* 4.6 3.8 - - + -
397B ILE* 3.6 41.1 - - + -
400B LEU* 5.2 3.8 - - + -
434B SER 3.8 0.5 - - - +
435B MET* 3.2 6.2 - - - -
436B TRP* 2.9 54.1 + - + +
438B LEU* 4.8 11.4 - - + -
462B PHE* 3.8 19.7 - - + -
482B ILE* 3.7 26.2 - - + -
483B GLU 3.5 14.8 - - - +
484B ALA* 3.9 8.7 - - + -
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Residues in contact with THR 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B VAL* 4.4 13.2 + - - +
376B LEU* 1.3 73.2 - - - +
378B ALA* 1.3 61.3 + - - +
379B SER* 4.2 10.4 + - - +
433B VAL* 3.7 27.8 - - + -
434B SER 3.6 2.7 - - - +
435B MET* 4.4 11.8 - - + +
481B LYS* 4.1 0.3 - - - +
482B ILE* 3.6 5.0 - - - +
483B GLU* 3.0 48.9 + - - +
484B ALA* 5.5 0.2 - - - -
485B THR* 5.4 3.3 + - - -
495B TYR* 5.3 4.0 - - - -
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Residues in contact with ALA 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LEU* 3.8 0.8 + - + -
377B THR* 1.3 72.3 - - - +
379B SER* 1.3 62.9 + - - +
386B HIS* 3.5 6.9 - - - -
389B TRP* 4.2 16.2 - - + +
390B VAL* 5.0 4.5 - - + -
393B VAL* 4.3 13.9 - - + -
433B VAL* 3.5 0.9 - - - -
434B SER* 2.8 39.7 + - - +
436B TRP* 3.7 28.7 - - + -
481B LYS 3.7 4.7 - - - +
482B ILE* 4.8 2.2 - - + +
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Residues in contact with SER 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B THR* 4.2 11.1 + - - +
378B ALA* 1.3 76.4 - - - +
380B ALA* 1.3 63.4 + - - +
386B HIS* 4.4 0.7 - - - -
389B TRP* 3.1 14.9 - - - +
431B ASN* 4.6 8.3 - - - -
432B TYR 3.3 9.4 - - - -
433B VAL* 3.4 18.7 - - - +
479B GLY 4.2 1.8 - - - -
480B MET* 3.3 0.7 - - - -
481B LYS* 3.0 51.6 + - - +
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Residues in contact with ALA 380 (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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379B SER* 1.3 78.1 - - - +
381B SER* 1.3 67.3 + - - +
382B THR 4.5 0.4 - - - -
385B ASN* 4.0 9.4 - - + -
386B HIS* 3.6 40.4 - - + +
389B TRP* 4.8 1.1 - - + -
431B ASN* 3.8 9.7 - - - +
432B TYR* 3.0 24.8 + - - -
479B GLY 3.8 13.5 - - - +
480B MET* 4.2 7.0 - - + -
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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
------------------------------------------------------------
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