Contacts of the strand formed by residues 389 - 397 (chain B) in PDB entry 4M5X
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 ALA 389 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ILE* 4.0 11.4 - - + -
333B GLN 3.3 16.4 - - - +
334B CYS* 3.7 10.3 - - - +
335B LYS* 4.1 4.2 - - - +
372B GLN* 3.7 4.3 - - - +
373B LEU* 2.7 42.0 + - + +
379B TYR* 3.9 25.8 - - + -
387B GLN 3.5 0.4 + - - +
388B GLU* 1.3 77.4 - - - +
390B GLU* 1.3 64.0 + - - +
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Residues in contact with GLU 390 (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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331B TYR* 3.9 6.0 - - + +
332B ILE* 3.3 4.3 - - - -
333B GLN* 2.8 53.8 + - + +
335B LYS* 2.5 45.2 + - + +
370B VAL* 3.5 19.9 - - + +
371B GLU 3.5 3.6 - - - -
372B GLN* 2.9 26.0 + - - +
373B LEU* 4.9 0.2 - - - -
389B ALA* 1.3 73.0 - - - +
391B LYS* 1.3 60.6 + - - +
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Residues in contact with LYS 391 (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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330B SER* 4.2 14.4 + - - +
331B TYR* 3.4 13.7 - - - +
332B ILE* 3.9 21.3 - - + +
370B VAL* 3.6 3.7 - - - -
371B GLU* 2.7 64.2 + - - +
373B LEU* 3.9 26.2 - - + -
390B GLU* 1.3 74.9 - - - +
392B GLY* 1.3 64.5 + - - +
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Residues in contact with GLY 392 (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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330B SER* 3.5 2.3 + - - -
331B TYR* 3.0 51.3 + - - +
369B ALA 4.4 9.6 - - - -
371B GLU* 5.8 0.2 - - - -
391B LYS* 1.3 80.3 - - - +
393B VAL* 1.3 68.4 + - - +
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Residues in contact with VAL 393 (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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328B MET* 4.2 26.5 - - + -
329B VAL 3.2 7.4 - - - +
330B SER* 4.3 15.7 - - - +
331B TYR* 3.7 1.9 - - - -
345B GLU* 4.9 2.0 - - - +
367B TYR* 3.6 45.9 + - + +
368B VAL* 3.6 27.0 + - + +
392B GLY* 1.3 79.3 - - - +
394B LYS* 1.3 68.7 + - - +
395B PHE* 5.6 0.2 - - + -
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Residues in contact with LYS 394 (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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328B MET* 3.3 6.8 - - - +
329B VAL* 2.8 44.3 + - + +
331B TYR* 3.7 32.4 + - + +
340B ARG* 4.4 11.4 - - - +
368B VAL* 4.6 6.3 - - + -
393B VAL* 1.3 78.6 - - - +
395B PHE* 1.3 66.8 + - - +
436B PHE 4.9 3.6 - - - +
438B GLN* 3.4 33.7 - - + +
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Residues in contact with PHE 395 (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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327B LYS 4.0 1.8 - - - -
328B MET* 3.9 13.0 - - + +
347B TYR* 3.5 28.0 - + - -
350B ILE* 3.6 26.0 - - + -
364B PHE* 3.9 29.4 - + - -
367B TYR* 3.8 24.9 - + - -
368B VAL* 3.8 25.6 - - + -
393B VAL* 5.6 0.4 - - + -
394B LYS* 1.3 74.2 - - - +
396B LEU* 1.3 61.2 + - - +
397B THR 4.4 2.9 - - - +
398B LEU* 4.1 10.1 - - + -
436B PHE* 3.5 26.8 + - + +
437B LEU* 3.6 15.2 - - + -
438B GLN* 2.9 30.5 + - - +
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Residues in contact with LEU 396 (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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327B LYS* 2.8 27.9 + - + +
328B MET 3.6 20.0 - - - +
329B VAL* 3.6 36.8 - - + +
344B ARG* 4.9 10.8 - - + -
395B PHE* 1.3 76.2 - - - +
397B THR* 1.3 66.6 + - + +
437B LEU* 3.8 12.9 - - - +
438B GLN* 3.6 23.7 + - + +
439B LYS 4.6 9.0 + - - +
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Residues in contact with THR 397 (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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325B ARG 4.8 1.0 + - - -
326B GLY* 3.6 5.4 - - - -
327B LYS* 2.9 52.6 + - + +
347B TYR* 2.8 23.4 + - - -
395B PHE* 4.4 2.4 - - - -
396B LEU* 1.3 85.9 - - + +
398B LEU* 1.3 62.7 + - - +
437B LEU* 4.4 4.7 - - - -
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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