Contacts of the helix formed by residues 413 - 425 (chain B) in PDB entry 2W3S
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 VAL 413 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380B PRO* 4.8 11.0 - - + -
411B ASP 2.9 17.9 + - - +
412B CYS* 1.3 73.6 - - - +
414B LEU* 1.3 63.9 + - - +
415B GLY 3.3 2.5 - - - -
416B GLU* 3.1 10.6 + - + +
417B LEU* 3.1 30.0 + - + +
624B TYR* 4.4 15.7 - - + -
650B ASP* 4.9 2.7 - - + -
713B TRP* 3.5 36.1 - - + +
715B GLN* 3.3 27.1 - - - +
726B LYS* 6.0 0.4 - - - +
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B SER* 3.2 38.4 - - - +
376B PHE* 3.9 14.4 - - + -
412B CYS* 3.2 18.1 + - - -
413B VAL* 1.3 78.8 - - - +
415B GLY* 1.3 63.0 + - - +
417B LEU* 4.4 6.1 - - + -
418B VAL* 3.0 40.1 + - + +
452B PRO* 3.9 11.4 - - + -
453B VAL 3.9 2.0 - - - +
624B TYR* 3.6 30.3 - - + -
625B GLY 3.4 31.4 - - - +
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Residues in contact with GLY 415 (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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373B ALA* 6.4 0.2 - - - -
376B PHE* 3.7 21.0 - - - +
377B TYR 5.6 1.2 + - - -
379B PRO* 6.0 8.3 - - - +
412B CYS* 5.0 1.8 + - - -
413B VAL 3.3 1.0 - - - -
414B LEU* 1.3 78.7 - - - +
416B GLU* 1.3 59.8 + - - +
418B VAL* 3.9 2.8 - - - +
419B THR* 3.1 26.2 + - - -
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Residues in contact with GLU 416 (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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413B VAL* 3.1 10.3 + - - +
415B GLY* 1.3 73.3 - - - +
417B LEU* 1.3 57.1 + - - +
419B THR* 3.1 8.9 + - - -
420B ARG* 2.8 54.4 + - + +
713B TRP* 3.5 24.3 - - + -
715B GLN* 5.4 1.8 + - - -
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B VAL* 3.1 24.7 + - + +
414B LEU* 3.8 8.1 - - + +
416B GLU* 1.3 76.7 - - - +
418B VAL* 1.3 51.2 + - - +
420B ARG* 3.1 4.3 + - - +
421B LEU* 2.7 36.3 + - + +
624B TYR* 4.8 1.6 - - + -
625B GLY* 3.9 14.1 - - - +
626B ALA* 3.6 24.0 - - + +
648B LEU* 3.2 49.6 - - + +
650B ASP* 4.4 5.6 - - + -
713B TRP* 3.7 46.4 - - + -
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ALA* 5.3 7.9 - - + -
376B PHE* 3.7 28.5 - - + -
414B LEU* 3.0 26.9 + - + +
415B GLY 3.9 4.3 - - - +
417B LEU* 1.3 76.2 - - - +
419B THR* 1.3 55.7 + - - +
421B LEU* 3.8 6.3 - - - +
422B GLN* 2.8 52.1 + - - +
450B LEU* 3.9 18.8 - - + -
452B PRO* 5.0 0.9 - - + -
626B ALA* 3.8 24.5 - - + -
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Residues in contact with THR 419 (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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415B GLY 3.1 17.1 + - - -
416B GLU* 3.1 13.2 + - - -
418B VAL* 1.3 76.7 - - - +
420B ARG* 1.3 64.1 + - - +
422B GLN* 3.2 11.7 + - - +
423B LYS* 3.1 45.4 + - + +
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Residues in contact with ARG 420 (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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416B GLU* 2.8 41.9 + - + +
417B LEU* 3.5 8.1 - - - +
419B THR* 1.3 74.8 - - - +
421B LEU* 1.3 63.3 + - - +
423B LYS* 3.6 10.6 + - + +
424B SER* 3.1 28.6 + - - +
648B LEU* 3.8 21.9 - - + +
712B LEU 5.7 1.0 + - - -
713B TRP* 3.3 33.1 - - - +
714B ASP 5.3 3.4 + - - +
715B GLN* 5.8 0.8 - - - +
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Residues in contact with LEU 421 (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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417B LEU 2.7 19.8 + - - +
418B VAL* 3.8 4.7 - - - +
420B ARG* 1.3 73.3 - - - +
422B GLN* 1.3 56.0 + - - +
424B SER* 3.1 9.9 + - - +
425B ALA* 2.8 38.7 + - - +
450B LEU* 4.7 2.9 - - + -
626B ALA* 3.3 44.2 - - + +
627B ALA* 3.9 1.6 - - - +
628B ILE* 3.8 19.1 - - + -
646B ASP* 3.3 34.8 - - + +
647B ILE 3.8 2.7 - - - +
648B LEU* 3.6 28.7 - - + +
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Residues in contact with GLN 422 (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 ALA* 3.9 14.1 - - - +
418B VAL* 2.8 34.7 + - - +
419B THR* 3.2 8.7 + - - +
421B LEU* 1.3 78.0 - - - +
423B LYS* 1.3 61.1 + - + +
425B ALA 3.6 0.2 + - - -
426B ASN 3.2 2.8 + - - -
427B PHE* 2.9 74.3 + - + +
450B LEU* 3.5 20.5 - - + +
628B ILE* 4.4 2.0 - - + -
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Residues in contact with LYS 423 (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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419B THR* 3.1 44.8 + - + +
420B ARG* 3.7 9.2 - - - +
422B GLN* 1.3 75.6 - - - +
424B SER* 1.3 59.6 + - - +
426B ASN* 3.0 21.6 + - - +
427B PHE 5.1 0.2 - - - +
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Residues in contact with SER 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ARG* 3.1 20.5 + - - +
421B LEU* 3.1 21.0 + - - +
423B LYS* 1.3 76.8 - - - +
425B ALA* 1.3 57.8 + - - +
426B ASN* 3.7 1.2 + - - +
644B ARG* 4.4 4.7 + - - -
646B ASP* 4.6 2.3 - - - +
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Residues in contact with ALA 425 (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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421B LEU* 2.8 22.6 + - + +
422B GLN 4.1 1.8 - - - +
424B SER* 1.3 72.0 + - - +
426B ASN* 1.3 69.8 + - - +
427B PHE* 4.3 2.2 - - + +
430B ARG* 3.1 23.4 + - - +
628B ILE* 3.8 18.2 - - + -
644B ARG* 3.3 13.7 + - - +
646B ASP* 3.7 30.7 - - + -
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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