Contacts of the helix formed by residues 527 - 537 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A PHE 2.7 25.7 + - - -
396A GLN* 3.0 12.8 + - - +
397A ILE 3.0 24.3 + - - +
398A THR* 3.7 4.5 - - + +
492A ILE* 4.9 2.0 - - + -
498A PHE* 3.6 11.8 - - - +
499A TYR 3.9 19.1 - - - +
501A ALA* 4.7 1.4 - - - +
526A ILE* 1.3 80.5 - - - +
528A PRO* 1.3 71.7 - - - +
529A VAL* 2.8 37.4 + - - +
530A GLN* 3.1 19.6 + - + +
531A ILE* 3.1 11.2 + - - +
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Residues in contact with PRO 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A SER* 3.8 19.7 - - - +
348A THR* 3.8 27.1 - - + +
394A LYS 4.4 7.6 - - - +
395A PHE* 4.1 4.5 - - - +
397A ILE 3.5 8.5 - - - +
399A THR* 5.6 4.0 - - + -
526A ILE 3.9 2.4 - - - +
527A ASN* 1.3 100.3 - - - +
529A VAL* 1.3 57.2 + - + +
531A ILE* 3.2 6.5 + - + +
532A LEU* 2.9 30.1 + - - +
616A TRP* 4.1 30.7 - - + -
630A ALA* 4.9 2.7 - - + +
632A ASN* 5.5 0.7 - - + -
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Residues in contact with VAL 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A THR* 4.5 10.1 - - + -
350A ILE* 4.7 1.5 - - + +
357A LEU* 3.9 16.6 - - + -
360A LEU* 3.8 18.6 - - + -
395A PHE 4.5 3.8 - - - +
492A ILE* 5.8 1.1 - - + -
498A PHE* 3.4 37.0 - - + -
527A ASN* 2.8 18.2 + - - +
528A PRO* 1.3 69.3 - - - +
530A GLN* 1.3 59.1 + - - +
532A LEU* 3.3 7.9 + - + +
533A SER* 2.8 31.8 + - - +
547A PRO* 3.7 32.3 - - + -
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Residues in contact with GLN 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A LEU 4.9 0.4 + - - -
487A GLY* 3.0 33.7 + - - -
488A VAL* 3.8 7.6 - - + +
489A GLY 4.6 1.4 + - - +
490A GLU 5.0 1.4 + - - +
492A ILE* 3.7 27.8 - - + +
499A TYR 5.1 0.3 - - - +
501A ALA* 3.7 22.9 + - - +
526A ILE* 3.7 14.8 - - + -
527A ASN* 3.1 14.5 + - - +
529A VAL* 1.3 75.8 - - - +
531A ILE* 1.3 67.0 + - - +
533A SER* 3.0 10.3 + - - -
534A ILE* 2.9 34.2 + - + +
547A PRO* 6.1 0.4 - - - -
558A TRP* 3.2 26.7 - - + -
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Residues in contact with ILE 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A PRO* 3.7 25.8 - - + -
404A THR* 3.8 7.6 - - - +
408A LEU* 5.1 5.2 - - + -
526A ILE* 3.4 29.2 - - + +
527A ASN 3.1 8.3 + - - +
528A PRO* 3.2 6.7 + - + +
530A GLN* 1.3 76.5 - - - +
532A LEU* 1.3 62.3 + - + +
534A ILE* 3.1 8.9 + - - +
535A TYR* 3.0 35.6 + - + -
616A TRP* 3.7 31.4 - - + -
618A ILE* 3.4 30.1 - - + -
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Residues in contact with LEU 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A THR* 3.3 42.6 - - - +
349A ALA* 3.9 8.1 - - - +
350A ILE* 4.0 13.9 - - + +
357A LEU* 5.7 0.9 - - + -
528A PRO 2.9 14.4 + - - +
529A VAL* 3.6 11.2 - - + +
531A ILE* 1.3 75.8 - - - +
533A SER* 1.3 55.5 + - - +
535A TYR* 3.3 5.2 + - - +
536A SER* 2.6 34.5 + - - -
618A ILE* 3.9 16.4 - - + -
628A MET* 3.5 37.3 - - + +
629A MET 3.9 3.6 - - - -
630A ALA* 3.8 19.1 - - + -
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Residues in contact with SER 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ILE* 4.2 6.6 - - - +
529A VAL 2.8 19.4 + - - -
530A GLN* 3.2 13.7 - - - -
532A LEU* 1.3 75.9 - - - +
534A ILE* 1.3 58.4 + - - +
536A SER* 3.1 26.2 - - - -
544A ILE* 3.6 22.6 - - - +
545A ASN 4.6 2.9 + - - -
547A PRO* 3.7 29.1 - - - +
558A TRP* 4.1 17.2 - - - -
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Residues in contact with ILE 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A LEU* 3.3 41.3 - - + -
411A MET* 3.5 31.7 - - + +
486A LEU* 3.9 18.6 - - + +
488A VAL* 3.8 22.7 - - + -
526A ILE* 5.4 2.2 - - + -
530A GLN* 2.9 29.1 + - + +
531A ILE* 3.1 9.4 + - - +
533A SER* 1.3 73.9 - - - +
535A TYR* 1.3 67.1 + - + +
536A SER 3.1 1.9 + - - -
537A ALA* 3.3 12.3 + - - +
544A ILE* 3.7 19.2 - - + +
558A TRP* 6.1 1.1 - - + -
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Residues in contact with TYR 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A THR* 2.8 36.1 + - - -
407A ILE* 3.0 38.6 - - + +
408A LEU* 3.9 9.4 - - + -
411A MET* 5.0 1.6 - - - -
531A ILE* 3.0 37.3 + - + +
532A LEU* 3.8 9.0 - - - +
534A ILE* 1.3 75.4 - - - +
536A SER* 1.3 64.7 + - - +
538A LEU* 3.0 33.9 + - + +
575A MET* 4.0 22.4 - - + -
597A LYS* 3.7 10.4 - - + +
618A ILE* 3.6 31.9 - - + -
620A TYR* 5.8 0.2 - + - -
628A MET* 3.3 19.0 - - - +
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Residues in contact with SER 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ILE* 3.8 19.2 - - - +
352A PRO* 3.8 24.0 - - - +
355A GLY* 6.1 0.6 - - - -
532A LEU 2.6 23.0 + - - -
533A SER* 3.1 16.4 + - - -
534A ILE 3.1 0.2 - - - -
535A TYR* 1.3 77.8 - - - +
537A ALA* 1.3 51.7 + - - +
539A GLU* 2.7 27.5 + - - +
540A ASN* 3.1 12.8 + - - +
543A ASN 5.2 1.6 - - - -
544A ILE* 5.6 2.0 - - - -
545A ASN 5.7 1.8 - - - -
628A MET* 3.8 10.8 - - - -
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Residues in contact with ALA 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A MET* 4.3 4.5 - - + -
533A SER 3.9 2.0 + - - -
534A ILE 3.3 14.8 + - - +
535A TYR 3.1 0.6 - - - -
536A SER* 1.3 78.2 - - - +
538A LEU* 1.3 62.6 + - - +
539A GLU 3.1 0.7 + - - -
540A ASN* 3.2 3.0 + - - -
542A GLY* 3.0 43.1 + - - +
543A ASN 3.3 21.7 + - - +
544A ILE* 4.1 5.6 - - + -
562A ILE* 3.9 18.6 - - + -
563A ILE* 4.5 1.1 - - + -
568A ILE* 3.7 3.3 - - - +
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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