Contacts of the helix formed by residues 407 - 418 (chain B) in PDB entry 2PMW
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 THR 407 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405B GLU 4.3 5.2 - - - +
406B LEU* 1.3 76.9 - - - +
408B LEU* 1.3 66.8 + - - +
409B ALA 3.6 2.0 + - - -
410B GLU* 2.9 32.0 + - - +
411B LEU* 2.9 22.0 + - - +
480B ASP* 2.8 31.4 + - + +
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Residues in contact with LEU 408 (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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305B ALA* 4.6 11.2 - - + +
309B VAL 5.4 4.5 - - - +
310B VAL* 4.9 15.0 - - + -
311B LEU 5.9 0.7 - - - +
332B GLU* 3.3 43.7 - - + +
334B ILE* 4.4 25.1 - - + -
407B THR* 1.3 74.2 - - - +
409B ALA* 1.3 57.9 + - - +
411B LEU* 3.3 7.2 + - + +
412B ARG* 2.9 52.1 + - + +
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Residues in contact with ALA 409 (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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407B THR* 3.2 2.0 + - - -
408B LEU* 1.3 78.6 - - - +
410B GLU* 1.3 63.2 + - - +
412B ARG* 3.4 13.7 + - - +
413B GLN* 3.1 30.9 + - - +
478B ALA* 3.7 20.4 - - + -
480B ASP* 3.4 30.5 - - - +
481B GLU* 4.1 14.3 - - + +
528B LEU* 4.7 1.3 - - + -
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Residues in contact with GLU 410 (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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405B GLU 3.9 2.9 - - - +
406B LEU* 3.3 19.0 - - + +
407B THR* 2.9 41.6 + - - +
409B ALA* 1.3 77.5 - - - +
411B LEU* 1.3 62.1 + - - +
413B GLN* 3.6 1.6 + - - +
414B ARG* 3.1 45.3 + - - +
480B ASP* 4.3 7.1 - - - +
528B LEU* 3.9 25.7 - - + +
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Residues in contact with LEU 411 (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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310B VAL* 3.9 28.5 - - + -
334B ILE* 4.4 7.6 - - + -
396B ALA* 4.2 20.9 - - + +
399B MET* 3.7 38.1 - - + -
400B LEU* 4.4 16.6 - - + -
406B LEU* 4.2 18.3 - - + +
407B THR 2.9 15.1 + - - +
408B LEU* 3.6 9.2 - - + +
410B GLU* 1.3 76.4 - - - +
412B ARG* 1.3 59.6 + - - +
414B ARG* 3.3 2.3 + - - +
415B LEU* 3.0 36.4 + - + +
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Residues in contact with ARG 412 (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 PRO 3.7 20.3 + - - -
332B GLU* 4.1 6.7 - - - +
333B VAL 4.7 3.2 + - - -
334B ILE* 5.0 10.7 - - + +
360B ASP* 4.0 25.1 + - + +
408B LEU* 2.9 50.4 + - + +
409B ALA* 3.8 21.5 - - - +
410B GLU 3.4 0.2 - - - -
411B LEU* 1.3 78.2 - - - +
413B GLN* 1.3 58.3 + - - +
415B LEU* 3.5 11.4 + - + +
416B ILE* 3.1 45.1 + - + +
458B ARG* 3.7 44.9 - - - +
478B ALA* 5.0 5.1 - - - +
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Residues in contact with GLN 413 (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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409B ALA 3.1 22.2 + - - +
410B GLU 3.9 4.9 - - - +
411B LEU 3.3 0.2 - - - -
412B ARG* 1.3 77.2 - - - +
414B ARG* 1.3 58.1 + - - +
416B ILE* 3.7 7.5 - - - +
417B HIS* 2.9 29.6 + - - +
456B PHE* 3.4 29.1 + - + +
457B CYS 3.3 22.0 - - - +
458B ARG* 3.4 15.8 - - - +
481B GLU* 2.7 27.3 + - - +
526B CYS 3.0 24.4 + - - -
527B CYS* 4.1 2.0 - - - +
528B LEU* 3.8 19.6 - - + +
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Residues in contact with ARG 414 (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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399B MET* 4.2 12.1 - - - -
403B GLU* 3.0 33.0 + - - -
406B LEU* 3.6 32.0 - - - +
410B GLU* 3.1 35.7 + - - +
411B LEU 3.7 4.3 - - - +
412B ARG 3.2 0.6 - - - -
413B GLN* 1.3 77.3 - - - +
415B LEU* 1.3 66.0 + - - +
417B HIS* 4.2 3.6 - - - -
418B PHE* 2.8 54.4 + - + +
456B PHE* 3.6 33.6 - - + -
528B LEU* 4.3 4.0 - - - +
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Residues in contact with LEU 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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334B ILE* 3.7 36.1 - - + -
361B LEU* 4.2 19.0 - - + +
392B VAL* 4.1 23.6 - - + -
395B ILE* 4.0 15.9 - - + -
396B ALA* 5.0 5.6 - - + +
399B MET* 3.5 30.7 - - + +
411B LEU* 3.0 25.5 + - + +
412B ARG* 3.6 8.1 - - + +
414B ARG* 1.3 76.2 - - - +
416B ILE* 1.3 61.1 + - + +
418B PHE* 4.0 0.7 - - - +
419B SER* 2.8 29.4 + - - -
442B ALA* 5.2 1.4 - - + -
443B ALA 5.3 2.6 - - - +
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Residues in contact with ILE 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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360B ASP* 4.9 9.2 - - + +
361B LEU* 5.6 1.8 - - + -
412B ARG* 3.1 33.6 + - + +
413B GLN* 3.7 6.1 - - - +
415B LEU* 1.3 76.9 - - + +
417B HIS* 1.3 65.3 + - - +
419B SER* 3.3 14.7 + - - -
421B LYS* 3.2 19.4 + - - -
440B LEU* 4.0 29.4 - - + +
457B CYS 5.1 10.3 - - - +
458B ARG* 3.9 31.0 - - + +
651B ASP* 5.7 2.2 - - - +
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Residues in contact with HIS 417 (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 GLN 2.9 19.9 + - - +
414B ARG* 3.7 4.5 - - - +
416B ILE* 1.3 79.9 - - - +
418B PHE* 1.3 92.6 + + - +
419B SER 3.8 0.3 - - - +
421B LYS* 2.9 22.4 + - - +
454B GLN* 3.7 25.1 + - - -
455B LEU 5.9 0.7 - - - -
456B PHE* 3.3 33.8 - + + -
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Residues in contact with PHE 418 (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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163B PRO* 6.0 0.2 - - - +
399B MET* 4.3 6.3 - - + -
403B GLU* 6.1 0.2 - - - -
414B ARG* 2.8 51.1 + - + +
415B LEU 4.0 1.3 - - - +
417B HIS* 1.3 97.6 - + - +
419B SER* 1.3 64.1 + - - +
443B ALA* 3.3 35.1 - - - +
444B LEU 4.3 1.7 - - - +
445B PRO* 3.6 29.4 - - + -
446B PRO* 3.6 29.8 - - + -
454B GLN* 5.7 3.1 - - - -
456B PHE* 4.9 6.5 - + - -
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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