Contacts of the helix formed by residues 527 - 536 (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 527 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395B PHE 3.3 18.6 + - - -
396B GLN 3.0 27.7 + - - -
397B ILE 3.6 5.0 + - - -
398B THR* 3.4 7.2 - - + +
492B ILE* 4.3 2.0 - - + +
498B PHE* 3.5 17.6 - - - +
499B TYR 3.7 18.6 - - - +
526B ILE* 1.3 80.5 - - - +
528B PRO* 1.3 69.8 - - - +
529B VAL* 2.6 34.0 + - - +
530B GLN* 2.9 28.7 + - + +
531B ILE* 3.0 10.9 + - - +
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Residues in contact with PRO 528 (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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346B SER* 3.8 21.5 - - - +
348B THR* 3.9 22.6 + - + +
394B LYS 4.1 11.0 - - - +
395B PHE* 4.4 3.4 - - - +
397B ILE 3.3 17.5 - - - +
398B THR* 5.1 0.2 - - - -
399B THR* 5.3 4.3 - - - +
526B ILE 3.8 3.8 - - - +
527B ASN* 1.3 89.1 - - - +
529B VAL* 1.3 61.1 - - - +
531B ILE* 3.3 6.2 + - + +
532B LEU* 3.2 24.8 + - - +
616B TRP* 4.1 29.4 - - + -
630B ALA* 5.0 2.2 - - + +
632B ASN* 5.6 1.1 - - - +
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Residues in contact with VAL 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B THR* 4.1 13.5 - - + -
350B ILE* 4.9 1.7 - - + +
357B LEU* 4.0 13.7 - - + -
360B LEU* 3.8 21.3 - - + -
395B PHE 4.5 1.6 - - - +
492B ILE* 5.6 1.1 - - + -
498B PHE* 3.6 32.8 - - + -
527B ASN* 2.6 17.3 + - - +
528B PRO* 1.3 70.9 - - - +
530B GLN* 1.3 59.0 + - - +
532B LEU* 3.3 9.2 + - + +
533B SER* 2.8 30.5 + - - +
547B PRO* 3.7 34.5 - - + -
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Residues in contact with GLN 530 (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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486B LEU 4.9 1.0 + - - -
487B GLY* 2.7 37.2 + - - -
488B VAL* 3.7 6.4 - - + +
489B GLY 4.6 0.2 - - - +
490B GLU 4.7 1.3 + - - +
492B ILE* 3.9 26.5 - - + +
501B ALA* 3.6 28.4 + - - +
526B ILE* 3.8 12.2 - - + +
527B ASN* 2.9 16.2 + - + +
529B VAL* 1.3 77.8 - - - +
531B ILE* 1.3 63.6 + - - +
533B SER* 3.1 9.9 + - - -
534B ILE* 3.1 31.1 + - + +
558B TRP* 3.4 25.0 - - + -
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Residues in contact with ILE 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B PRO* 3.7 28.7 - - + -
404B THR* 4.0 7.6 - - - +
408B LEU* 5.9 5.4 - - + -
526B ILE* 3.5 31.6 - - + +
527B ASN 3.0 7.8 + - - +
528B PRO* 3.6 6.3 - - + +
529B VAL 3.2 0.2 - - - -
530B GLN* 1.3 77.0 - - - +
532B LEU* 1.3 62.1 + - + +
534B ILE* 3.2 7.6 + - - +
535B TYR* 3.0 40.4 + - + -
616B TRP* 3.7 29.2 - - + -
618B ILE* 3.5 28.9 - - + -
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Residues in contact with LEU 532 (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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348B THR* 3.5 44.4 - - - +
349B ALA* 4.0 3.6 - - - +
350B ILE* 3.9 20.1 - - + +
357B LEU* 6.4 0.2 - - + -
528B PRO 3.2 10.8 + - - +
529B VAL* 3.7 9.9 - - + +
530B GLN 3.3 0.2 - - - -
531B ILE* 1.3 79.3 - - + +
533B SER* 1.3 56.0 + - - +
535B TYR* 3.8 4.1 - - + +
536B SER* 2.9 31.4 + - - -
618B ILE* 4.0 15.5 - - + -
628B MET* 3.5 31.9 - - + +
629B MET 3.7 9.0 - - - +
630B ALA* 3.7 21.3 - - + -
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Residues in contact with SER 533 (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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350B ILE* 4.4 6.5 - - - +
529B VAL* 2.8 21.0 + - - +
530B GLN* 3.1 14.6 + - - -
532B LEU* 1.3 78.2 - - - +
534B ILE* 1.3 61.1 + - - +
536B SER* 2.7 20.1 + - - -
537B ALA 4.0 0.5 + - - -
544B ILE* 3.3 33.5 - - - +
545B ASN 4.8 2.2 + - - -
547B PRO* 3.7 27.6 - - - +
558B TRP* 4.2 10.4 - - - -
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Residues in contact with ILE 534 (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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408B LEU* 3.2 39.0 - - + -
411B MET* 3.6 24.6 - - + +
486B LEU* 3.7 30.3 - - + +
488B VAL* 3.9 21.8 - - + -
526B ILE* 5.6 1.1 - - + -
530B GLN* 3.1 21.9 + - + +
531B ILE* 3.8 7.4 - - - +
533B SER* 1.3 75.5 - - - +
535B TYR* 1.3 66.8 + - + +
537B ALA* 3.1 20.4 + - - +
544B ILE* 3.7 10.8 - - + -
558B TRP* 6.3 0.9 - - + -
562B ILE* 4.0 7.2 - - + -
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Residues in contact with TYR 535 (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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404B THR* 2.7 38.2 + - - -
407B ILE* 3.0 36.5 - - + +
408B LEU* 5.1 6.5 - - + -
411B MET* 5.1 2.0 - - - -
531B ILE* 3.0 48.4 + - + +
532B LEU* 3.9 7.2 - - - +
533B SER 3.4 0.2 - - - -
534B ILE* 1.3 74.3 - - + +
536B SER* 1.3 62.5 - - - +
537B ALA 3.0 7.6 + - - -
538B LEU* 3.0 32.9 + - + +
575B MET* 4.0 23.1 - - + -
597B LYS* 3.8 7.5 - - + +
618B ILE* 3.6 33.9 - - + -
620B TYR* 6.0 0.2 - + - -
628B MET* 3.4 15.7 - - - +
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Residues in contact with SER 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ILE* 4.8 8.4 - - - +
352B PRO* 3.5 31.7 + - - +
355B GLY* 6.1 0.7 - - - -
532B LEU 2.9 15.6 + - - -
533B SER* 2.7 26.7 + - - -
535B TYR* 1.3 74.1 - - - +
537B ALA* 1.3 64.5 + - - +
538B LEU 3.0 0.4 - - - -
539B GLU* 2.9 14.3 + - - +
540B ASN* 3.1 15.5 + - - +
543B ASN 5.1 1.4 + - - -
544B ILE* 5.1 2.3 - - - +
545B ASN 5.5 1.9 + - - -
628B MET* 3.3 14.8 - - - -
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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