Contacts of the strand formed by residues 382 - 390 (chain B) in PDB entry 3MA2
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 GLU 382 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320B ARG* 2.4 48.2 + - - +
321B ALA 3.6 4.8 + - - -
322B LYS* 3.7 19.3 + - - +
343B THR* 2.5 32.9 + - - +
380B SER 4.0 6.1 - - - +
381B GLU* 1.3 75.0 - - - +
383B PHE* 1.3 55.4 + - - +
404B PRO* 3.4 8.5 - - - +
405B TRP* 2.9 33.3 + - + +
406B ASN* 4.6 8.7 + - - +
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Residues in contact with PHE 383 (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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320B ARG* 3.1 7.5 - - - -
321B ALA 2.8 34.8 + - - +
323B PHE* 3.9 23.1 - + + -
372B TYR* 4.7 2.0 - - - -
374B HIS* 3.3 35.7 - + - -
376B SER* 3.6 21.3 - - - -
378B ASN 5.4 0.4 - - - -
381B GLU* 3.5 33.7 - - + -
382B GLU* 1.3 78.0 - - - +
384B LEU* 1.3 61.5 + - - +
385B ILE* 3.6 8.6 + - + +
402B VAL* 4.3 7.9 - - + -
403B ALA* 3.3 25.4 - - - -
404B PRO* 3.6 25.8 - - + -
405B TRP 4.5 0.2 - - - -
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Residues in contact with LEU 384 (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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318B VAL* 3.8 12.8 - - + -
319B ILE 3.4 12.6 - - - +
320B ARG* 4.4 1.5 - - - +
346B TYR* 3.8 30.3 - - + -
383B PHE* 1.3 71.8 - - - +
385B ILE* 1.3 69.5 + - - +
386B ALA* 4.0 4.0 - - + +
401B PHE* 4.0 17.0 - - + -
402B VAL* 3.2 6.2 - - - +
403B ALA 2.8 32.4 + - - +
405B TRP* 3.9 22.9 - - + +
408B LEU* 4.5 7.9 - - + -
416B PHE* 3.7 41.7 - - + -
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Residues in contact with ILE 385 (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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317B LEU 3.8 1.6 - - - +
318B VAL* 3.5 2.4 - - - -
319B ILE* 2.8 42.8 + - + +
321B ALA* 3.7 28.7 - - + -
323B PHE* 3.9 26.9 - - + -
340B ILE* 4.4 10.3 - - + -
361B VAL* 5.0 3.4 - - + -
383B PHE* 4.0 12.8 - - + +
384B LEU* 1.3 80.3 - - - +
386B ALA* 1.3 64.4 + - - +
394B LEU* 4.3 15.9 - - + +
396B ILE* 3.7 30.1 - - + -
401B PHE 4.1 1.6 - - - -
402B VAL* 4.4 10.5 - - + +
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Residues in contact with ALA 386 (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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311B ALA* 4.3 18.4 - - + +
312B PHE 5.1 0.4 - - - +
315B SER* 3.4 18.6 + - - +
317B LEU 3.5 5.4 - - - -
318B VAL* 4.1 14.1 - - + +
384B LEU* 4.1 11.2 - - + -
385B ILE* 1.3 77.7 - - - +
387B GLY* 1.3 57.2 + - - +
396B ILE* 4.6 0.2 - - - -
400B SER* 3.6 22.9 + - - -
401B PHE* 3.2 19.2 + - + +
402B VAL* 4.8 0.2 - - - +
416B PHE* 5.5 0.9 - - + -
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Residues in contact with GLY 387 (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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315B SER* 3.1 4.9 - - - -
316B ASP 3.0 21.5 + - - -
317B LEU 3.0 14.0 + - - -
385B ILE* 4.1 1.4 - - - +
386B ALA* 1.3 74.7 - - - +
388B LYS* 1.3 66.0 + - - -
394B LEU* 3.8 11.6 - - - +
395B HIS 3.3 13.2 - - - -
396B ILE* 4.0 7.6 - - - +
400B SER* 4.7 2.9 - - - -
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Residues in contact with LYS 388 (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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193A ASP* 4.3 31.7 + - + +
195A GLU 5.6 2.0 + - - -
196A GLY 5.6 0.8 - - - -
197A GLY* 4.7 11.9 - - - +
314B ASN* 3.8 34.0 - - - +
315B SER* 4.3 2.7 - - - +
316B ASP* 3.4 13.2 - - - +
387B GLY* 1.3 78.9 - - - +
389B LEU* 1.3 65.4 + - - +
390B GLN* 6.3 0.2 - - + -
393B LEU 3.4 1.6 - - - +
394B LEU* 3.7 5.5 - - - +
395B HIS* 2.8 41.4 + - + +
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Residues in contact with LEU 389 (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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316B ASP* 2.8 29.3 + - + +
317B LEU* 3.7 37.5 - - + -
358B ILE* 6.3 0.2 - - + -
388B LYS* 1.3 74.0 - - - +
390B GLN* 1.3 59.2 + - - +
391B ASP 4.3 0.4 - - - -
392B GLY* 3.9 22.7 - - - +
393B LEU 3.3 20.2 - - - +
394B LEU* 4.1 1.1 - - + +
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Residues in contact with GLN 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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191A PRO* 4.1 27.2 - - - +
335B TYR* 4.7 5.5 + - - -
388B LYS 3.7 0.6 + - - -
389B LEU* 1.3 74.6 - - - +
391B ASP* 1.4 80.1 + - - +
393B LEU* 2.9 29.9 + - - +
395B HIS* 3.2 42.5 + - + +
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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