Contacts of the strand formed by residues 377 - 382 (chain B) in PDB entry 5MJ6
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 LEU 377 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B SER* 4.2 11.4 - - - -
371B GLN 4.0 4.3 - - - +
372B ASP* 4.1 28.3 - - + +
375B GLY 3.7 1.9 + - - +
376B THR* 1.3 70.0 - - - +
378B VAL* 1.3 59.3 + - - +
379B SER* 3.6 15.2 + - - +
415B LYS 2.9 15.7 + - - +
416B LYS* 3.9 10.5 - - + +
417B LEU 3.2 20.1 + - - -
1O NAG 3.4 26.9 - - - +
2O NAG 4.1 27.4 - - - +
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Residues in contact with VAL 378 (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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370B SER* 3.2 0.7 - - - -
371B GLN 2.8 43.8 + - - +
373B VAL* 3.5 29.2 - - + -
376B THR* 4.0 4.5 - - + +
377B LEU* 1.3 71.4 - - - +
379B SER* 1.3 67.7 + - - +
380B ILE* 5.3 0.7 - - + -
394B LEU* 3.7 22.9 - - + +
397B THR* 3.8 25.4 - - + -
398B VAL* 4.7 3.8 - - + -
401B LEU* 3.7 19.1 - - + -
417B LEU* 3.5 19.7 - - + +
419B LEU* 5.0 2.5 - - + -
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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
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368B ASN* 5.1 1.3 - - - -
369B LEU 3.3 5.4 - - - -
370B SER* 2.9 26.2 + - - -
377B LEU* 3.6 16.5 + - - +
378B VAL* 1.3 78.4 + - - +
380B ILE* 1.3 65.2 + - - +
381B TYR* 3.9 16.4 - - - -
394B LEU* 5.0 0.2 - - - -
416B LYS* 5.7 0.2 - - - +
417B LEU 3.1 7.9 + - - +
418B ASP* 3.4 18.5 + - - +
419B LEU* 3.0 24.4 + - - +
1O NAG 4.8 1.8 + - - -
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Residues in contact with ILE 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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368B ASN* 3.4 3.3 - - - -
369B LEU* 2.9 32.2 + - + +
378B VAL* 5.3 0.4 - - + -
379B SER* 1.3 74.6 - - - +
381B TYR* 1.3 66.9 + - - +
387B ILE* 4.4 2.8 - - - +
390B VAL* 3.2 30.1 - - + -
393B ALA* 3.8 13.2 - - + -
394B LEU* 3.8 45.8 - - + +
397B THR* 3.9 13.9 - - - +
419B LEU* 3.3 26.0 - - + +
421B ALA* 5.9 0.2 - - + -
443B LEU* 3.8 20.0 - - + -
444B LEU* 6.0 0.2 - - + -
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Residues in contact with TYR 381 (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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326B THR* 4.7 9.5 - - + +
328B LEU* 3.6 41.4 - - + +
366B MET* 4.0 18.8 - - + -
367B LYS 3.5 15.7 - - - -
368B ASN* 3.8 21.1 + - + +
379B SER* 3.9 18.8 - - - -
380B ILE* 1.3 84.2 - - - +
382B ALA* 1.3 62.0 + - - +
387B ILE* 5.3 0.9 - - - -
390B VAL* 5.1 0.6 - - - +
418B ASP* 3.8 28.3 + - + -
419B LEU 2.8 7.3 + - - +
420B VAL* 3.7 25.7 - - + -
421B ALA* 3.1 24.7 + - - +
1O NAG 5.0 7.3 + - - -
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Residues in contact with ALA 382 (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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366B MET* 3.3 9.6 - - - -
367B LYS* 2.9 30.7 + - - +
381B TYR* 1.3 77.3 - - - +
383B VAL* 1.3 70.1 + - + +
386B LYS* 4.2 23.6 - - + +
387B ILE* 4.3 9.3 - - + +
390B VAL* 5.2 2.7 - - + -
420B VAL* 5.4 0.9 - - - -
421B ALA* 4.3 19.3 - - + +
444B LEU* 4.5 6.7 - - + -
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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