Contacts of the helix formed by residues 510 - 519 (chain B) in PDB entry 1MWT
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 ASN 510 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509B ASP* 1.3 76.3 + - - +
511B GLU* 1.3 64.8 + - - +
512B ILE* 3.0 28.8 + - - +
513B LEU* 2.7 39.7 + - + +
514B LEU* 2.9 11.3 + - - +
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Residues in contact with GLU 511 (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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434B LYS* 2.8 39.4 + - - +
437B SER* 4.9 3.3 + - - -
438B TRP* 3.3 31.8 + - + +
472B LEU* 3.7 14.0 - - + +
509B ASP 3.2 11.3 + - - +
510B ASN* 1.3 70.0 + - - +
512B ILE* 1.3 52.8 + - + +
514B LEU* 3.0 12.3 + - + +
515B ALA* 2.7 34.7 + - - +
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Residues in contact with ILE 512 (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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438B TRP* 3.7 46.2 - - + +
441B TYR* 3.3 41.7 - - + -
510B ASN* 3.0 13.8 + - - +
511B GLU* 1.3 75.7 - - + +
513B LEU* 1.3 58.8 + - - +
515B ALA* 3.1 8.2 + - - +
516B ASP* 2.9 35.2 + - - +
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Residues in contact with LEU 513 (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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508B LEU* 4.1 31.4 - - + +
510B ASN* 2.7 34.7 + - + +
512B ILE* 1.3 72.9 - - - +
514B LEU* 1.3 52.1 + - - +
516B ASP* 3.3 5.4 + - - +
517B SER* 2.5 49.2 + - - +
522B GLY* 4.0 9.4 - - - -
523B GLU* 3.6 44.6 - - + +
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Residues in contact with LEU 514 (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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471B ALA* 3.4 41.9 - - + +
472B LEU* 4.1 12.8 - - + -
475B GLY* 3.7 4.3 - - - -
476B SER* 3.5 35.7 - - - +
479B PHE* 4.1 24.5 - - + -
508B LEU* 3.7 17.6 - - + +
509B ASP 5.9 0.4 - - - -
510B ASN 2.9 11.2 + - - +
511B GLU* 3.3 12.8 - - + +
513B LEU* 1.3 76.8 - - - +
515B ALA* 1.3 63.2 + - - +
517B SER* 3.3 1.6 + - - -
518B GLY 3.1 15.9 + - - -
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Residues in contact with ALA 515 (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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432B TRP* 5.8 0.2 - - + -
438B TRP* 3.6 24.9 - - + -
443B VAL* 4.2 12.8 - - + -
468B ALA* 3.2 44.8 - - + +
472B LEU* 4.2 5.8 - - + +
511B GLU 2.7 16.0 + - - +
512B ILE* 3.2 9.0 - - - +
514B LEU* 1.3 74.4 - - - +
516B ASP* 1.3 63.3 + - - +
518B GLY 3.2 6.2 + - - -
519B TYR* 3.4 2.1 - - - -
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Residues in contact with ASP 516 (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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441B TYR* 2.9 33.3 + - - -
443B VAL* 3.8 8.0 - - - +
512B ILE* 2.9 25.0 + - - +
513B LEU* 3.8 5.9 - - - +
515B ALA* 1.3 71.9 - - - +
517B SER* 1.3 64.7 + - - +
519B TYR* 3.0 32.2 + - + +
521B GLN* 2.8 46.6 + - - +
522B GLY* 3.8 2.5 - - - +
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Residues in contact with SER 517 (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 GLN* 3.2 17.3 - - - +
479B PHE* 4.0 21.7 - - - -
508B LEU* 3.6 7.8 - - - +
513B LEU* 2.5 39.7 + - - +
514B LEU* 3.4 9.0 - - - -
515B ALA 3.3 0.2 - - - -
516B ASP* 1.3 76.2 - - - +
518B GLY* 1.3 63.4 + - - +
520B GLY* 2.9 10.2 + - - -
522B GLY* 3.9 12.4 - - - +
523B GLU 4.5 1.7 + - - -
524B ILE* 4.1 12.2 - - - +
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Residues in contact with GLY 518 (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 GLN* 3.9 2.6 - - - +
406B LYS* 4.2 3.6 - - - -
409B THR* 2.7 31.9 + - - +
467B PHE* 3.8 16.6 - - - +
471B ALA* 3.8 20.2 - - - -
479B PHE* 4.5 2.4 - - - -
514B LEU 3.1 9.5 + - - -
515B ALA 3.2 6.9 + - - -
516B ASP 3.1 1.6 - - - -
517B SER* 1.3 77.0 - - - +
519B TYR* 1.3 57.6 + - - +
520B GLY 3.8 0.2 + - - -
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Residues in contact with TYR 519 (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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402B GLY 3.4 15.2 - - - +
403B SER* 3.7 8.1 + - - -
405B GLN* 4.3 2.0 - - - -
406B LYS* 3.5 28.3 - - + +
441B TYR* 3.3 11.4 + - - -
443B VAL* 3.4 28.2 - - + +
444B THR 4.9 2.2 + - - -
464B ASN* 3.2 47.3 - - + +
467B PHE* 4.6 0.9 - - + -
468B ALA* 3.8 0.2 - - + -
515B ALA 3.4 11.9 - - - -
516B ASP* 3.0 40.8 + - - -
518B GLY* 1.3 77.3 - - - +
520B GLY* 1.3 60.1 + - - +
521B GLN* 3.4 26.6 + - + +
708B PNM 3.9 10.1 - - - +
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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