Contacts of the helix formed by residues 374 - 386 (chain B) in PDB entry 3BWE
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 GLY 374 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369B VAL 3.4 1.1 + - - +
370B GLU* 2.9 23.1 + - - -
372B LEU 3.6 1.0 - - - -
373B ASN* 1.3 80.6 - - - +
375B LYS* 1.3 64.3 + - - -
376B GLU 3.5 2.2 - - - -
377B VAL 4.3 0.2 - - - -
378B ALA* 3.1 24.9 + - - +
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Residues in contact with LYS 375 (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 GLU* 3.8 33.0 + - + +
374B GLY* 1.3 70.2 - - - -
376B GLU* 1.3 67.1 + - - +
378B ALA* 3.3 7.1 + - - +
379B ALA* 3.0 23.6 + - - +
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Residues in contact with GLU 376 (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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374B GLY 3.5 0.6 - - - -
375B LYS* 1.3 74.4 - - - +
377B VAL* 1.3 69.8 + - + +
379B ALA* 2.9 8.1 + - - +
380B GLN* 2.9 38.1 + - + +
612D LYS* 4.3 8.9 + - - +
613D GLY* 3.5 13.7 - - - +
645D GLN* 5.2 6.4 - - - +
646D CYS 4.8 2.9 - - - +
647D SER* 3.3 36.3 - - - -
649D ASP* 5.7 0.3 - - - +
676D ASN* 5.5 1.1 - - + -
677D LEU* 3.8 40.7 + - + +
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Residues in contact with VAL 377 (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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229B ALA* 4.1 15.9 - - - +
369B VAL* 4.3 7.4 - - + -
373B ASN* 3.6 43.5 - - + +
374B GLY 3.8 1.4 + - - +
376B GLU* 1.3 79.1 - - + +
378B ALA* 1.3 61.9 + - - +
380B GLN* 3.3 19.6 + - + +
381B VAL* 3.0 29.4 + - + +
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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
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366B LEU* 3.8 12.1 - - + +
369B VAL* 3.8 22.0 - - + -
370B GLU* 4.1 19.5 - - + +
374B GLY 3.1 21.6 + - - +
375B LYS* 3.4 7.6 - - - +
376B GLU 3.0 0.6 - - - -
377B VAL* 1.3 78.2 - - - +
379B ALA* 1.3 55.9 + - - +
381B VAL* 3.4 3.9 + - - +
382B LYS* 3.1 25.1 + - - +
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Residues in contact with ALA 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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375B LYS 3.0 14.1 + - - +
376B GLU* 2.9 6.5 + - - +
378B ALA* 1.3 75.0 - - - +
380B GLN* 1.3 65.5 + - - +
381B VAL 3.1 0.2 - - - -
382B LYS* 3.9 8.5 - - + +
383B ALA* 3.2 20.1 + - - +
676D ASN* 3.4 33.7 + - - +
680D GLN* 6.3 0.2 - - - +
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Residues in contact with GLN 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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376B GLU* 2.9 28.6 + - + +
377B VAL* 3.5 25.3 + - + +
379B ALA* 1.3 76.2 - - - +
381B VAL* 1.3 62.0 + - + +
383B ALA* 4.1 2.8 - - - +
384B PRO* 3.3 20.3 - - - +
1D PO4 3.4 28.4 + - - +
647D SER* 3.3 22.8 + - - +
648D ARG* 3.2 41.4 + - - +
676D ASN* 4.5 7.4 - - + +
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Residues in contact with VAL 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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225B VAL* 3.9 34.5 - - + +
228B ARG* 3.9 23.7 + - + +
229B ALA* 3.7 31.9 - - + -
366B LEU* 4.2 5.8 - - + -
369B VAL* 4.7 2.0 - - + -
377B VAL* 3.0 19.6 + - + +
378B ALA* 3.7 7.0 - - - +
380B GLN* 1.3 80.7 - - + +
382B LYS* 1.3 61.3 + - - +
384B PRO* 3.5 9.4 - - - +
385B LEU* 3.4 16.1 - - + +
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Residues in contact with LYS 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 LEU* 4.1 16.9 - - + +
378B ALA 3.1 16.6 + - - +
379B ALA* 3.4 8.3 + - + +
381B VAL* 1.3 77.1 - - - +
383B ALA* 1.3 68.2 + - - +
385B LEU* 3.1 26.1 + - - +
386B VAL 3.8 1.9 + - - -
387B LEU* 3.9 37.9 + - + +
388B LYS 5.9 3.7 - - - -
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Residues in contact with ALA 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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379B ALA 3.2 16.7 + - - +
380B GLN* 4.1 4.0 - - - +
382B LYS* 1.3 78.5 - - - +
384B PRO* 1.3 70.0 - - + +
386B VAL* 3.3 10.2 + - - -
387B LEU 5.1 0.2 + - - -
1D PO4 5.8 3.8 - - - +
676D ASN* 4.8 7.6 - - - +
728D LEU* 3.8 27.9 - - + +
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Residues in contact with PRO 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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126A HIS* 2.9 32.3 - - + +
128A LEU* 5.6 2.9 - - + -
158A PRO* 4.3 3.9 - - - +
228B ARG* 4.8 13.5 - - - +
380B GLN 3.3 16.6 - - - +
381B VAL 3.5 10.5 - - - +
383B ALA* 1.3 91.2 - - + +
385B LEU* 1.3 60.4 + - - +
386B VAL* 2.9 6.6 + - - -
584C PRO* 5.7 8.5 - - + -
728D LEU* 4.0 23.3 - - + -
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Residues in contact with LEU 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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17A MSE 4.2 6.1 - - + -
158A PRO* 3.5 25.3 - - + +
159A GLY 2.6 29.3 + - - +
225B VAL* 4.2 11.9 - - + -
228B ARG* 3.9 38.6 - - - +
362B PHE* 3.9 14.6 - - + -
366B LEU* 4.5 8.1 - - + -
381B VAL* 3.4 19.1 - - + +
382B LYS* 3.1 13.9 + - - +
384B PRO* 1.3 76.4 - - - +
386B VAL* 1.3 62.4 + - - +
387B LEU* 3.8 30.7 - - + -
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Residues in contact with VAL 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A HIS* 3.3 23.8 - - + +
127A PRO* 4.0 15.0 - - + -
145A ARG* 2.5 28.5 + - + +
156A ARG* 4.1 33.7 - - + +
157A GLY* 4.6 3.8 - - - -
159A GLY* 3.6 6.4 - - - -
160A THR* 3.9 5.2 - - + +
382B LYS 3.8 0.2 + - - -
383B ALA 3.3 12.0 + - - +
384B PRO 2.9 19.1 - - - +
385B LEU* 1.3 81.2 - - - +
387B LEU* 1.3 56.2 + - - +
728D LEU* 4.6 2.7 - - + -
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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