Contacts of the helix formed by residues 365 - 375 (chain B) in PDB entry 3GWX
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 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350B ARG* 2.8 36.7 + - - +
354B ARG* 3.1 43.2 + - + +
361B SER 3.6 8.7 + - - +
362B ASP* 4.6 6.3 - - + -
364B ILE* 1.3 83.1 - - - +
366B PRO* 1.3 71.2 - - + +
367B LYS 2.9 1.9 + - - -
368B PHE* 2.9 20.4 + - + +
369B GLU* 3.3 32.0 + - - +
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Residues in contact with PRO 366 (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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362B ASP 3.6 22.4 - - - +
363B ILE 4.0 11.9 - - - +
364B ILE 3.5 0.7 - - - +
365B GLU* 1.3 94.9 - - + +
367B LYS* 1.3 65.1 + - - +
369B GLU* 3.2 35.3 - - - +
370B PHE* 3.3 7.6 + - - +
445B LEU* 4.7 6.5 - - + +
448B GLU* 3.2 29.6 - - - +
452B MET* 4.2 3.8 - - + -
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Residues in contact with LYS 367 (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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3B EPA 4.2 9.0 - - + -
327B PHE* 3.2 42.8 - - + -
330B LEU* 3.9 21.0 - - + +
363B ILE* 2.6 32.3 + - - +
364B ILE* 3.3 15.5 - - - +
365B GLU 2.9 0.6 + - - -
366B PRO* 1.3 81.1 - - - +
368B PHE* 1.3 58.2 + - + +
370B PHE* 2.7 29.3 + - - +
371B ALA* 2.7 14.9 + - - +
445B LEU* 3.4 32.7 - - + +
448B GLU* 4.8 0.8 + - - -
449B HIS* 3.1 22.9 + - - +
452B MET* 5.0 0.6 - - - +
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Residues in contact with PHE 368 (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 LEU* 5.4 2.0 - - + +
334B VAL* 3.2 35.7 - - + -
335B ASN 3.3 21.5 - - - -
338B GLY 3.5 19.5 - - - -
339B LEU* 3.9 10.5 - - + -
350B ARG* 3.7 53.8 - - + +
353B LEU* 4.3 20.2 - - + -
364B ILE* 3.4 19.8 + - + -
365B GLU* 2.9 11.6 + - - +
367B LYS* 1.3 76.2 - - + +
369B GLU* 1.3 54.1 + - - +
371B ALA* 3.1 5.5 + - - +
372B VAL* 2.7 42.1 + - + +
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Residues in contact with GLU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ARG* 4.5 6.7 - - - +
365B GLU* 3.3 24.8 - - - +
366B PRO* 3.2 29.9 - - - +
367B LYS 3.1 0.4 - - - -
368B PHE* 1.3 78.9 - - - +
370B PHE* 1.3 63.2 + - - +
372B VAL* 3.5 8.2 + - - +
373B LYS* 3.5 38.6 + - - +
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Residues in contact with PHE 370 (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 PHE 3.9 19.3 - - - -
328B ALA* 4.4 4.0 - - - -
331B ALA* 5.5 0.4 - - + -
366B PRO 3.3 7.3 + - - +
367B LYS 2.7 16.1 + - - +
369B GLU* 1.3 72.7 - - - +
371B ALA* 1.3 68.5 + - - +
372B VAL 3.0 0.7 + - - -
373B LYS* 3.2 7.6 + - + +
374B PHE* 2.8 62.5 + + + +
438B LYS* 4.2 12.1 - - + -
441B ASP* 4.0 25.4 - - + -
442B LEU* 3.4 39.7 - - + -
445B LEU* 4.2 22.9 - - + -
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Residues in contact with ALA 371 (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 PHE 5.6 0.7 - - - +
330B LEU* 4.8 4.9 - - + -
331B ALA* 3.7 26.6 - - + +
334B VAL* 3.4 31.6 - - + -
367B LYS 2.7 14.6 + - - +
368B PHE* 3.5 9.6 - - - +
370B PHE* 1.3 75.8 - - + +
372B VAL* 1.3 64.5 + - - +
375B ASN* 2.9 30.1 + - - -
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Residues in contact with VAL 372 (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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334B VAL* 5.6 2.5 - - + -
335B ASN 5.6 0.7 - - - +
336B LYS* 5.3 12.6 - - + -
350B ARG* 4.2 19.1 - - - +
368B PHE* 2.7 38.5 + - + +
369B GLU* 3.6 9.0 - - - +
370B PHE 3.0 0.2 + - - -
371B ALA* 1.3 76.9 - - + +
373B LYS* 1.3 68.8 + - + +
375B ASN* 3.0 11.2 + - - +
376B ALA* 3.5 8.1 + - - +
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Residues in contact with LYS 373 (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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369B GLU* 3.5 27.1 + - - +
370B PHE* 3.2 7.5 + - + +
372B VAL* 1.3 83.6 - - + +
374B PHE* 1.3 59.0 + - - +
376B ALA* 2.9 31.4 + - - +
377B LEU* 3.9 6.2 + - - +
438B LYS* 4.6 14.7 - - - +
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Residues in contact with PHE 374 (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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230B LYS* 5.4 4.0 + - - -
328B ALA* 4.0 17.3 - - + -
331B ALA* 3.7 18.4 - - + -
332B SER* 6.0 0.7 - - - -
370B PHE* 2.8 49.9 + + + +
371B ALA* 4.0 3.6 - - - +
373B LYS* 1.3 77.8 - - - +
375B ASN* 1.3 61.8 + - - +
376B ALA 3.2 0.7 + - - -
377B LEU* 3.6 17.9 + - + +
378B GLU 4.6 0.7 + - - -
379B LEU* 3.8 25.2 + - + +
384B LEU* 4.2 17.5 - - + -
387B PHE* 3.8 33.9 - + - -
435B LEU* 4.2 10.5 - - + -
438B LYS* 3.8 21.5 - - + +
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Residues in contact with ASN 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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230B LYS* 3.1 29.0 + - - +
234B ARG* 3.8 9.6 - - - +
331B ALA* 2.7 40.8 + - - +
334B VAL* 4.1 8.9 + - - +
371B ALA 2.9 22.7 + - - +
372B VAL* 3.0 7.7 + - - +
374B PHE* 1.3 75.1 - - - +
376B ALA* 1.3 63.1 + - - +
377B LEU 3.2 1.6 - - - -
378B GLU* 3.3 17.9 + - - +
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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