Contacts of the helix formed by residues 522 - 532 (chain B) in PDB entry 3NMW
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 MSE 522 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B SO4 3.8 13.2 - - - +
472B LEU* 5.4 0.4 - - - -
473B GLN* 4.1 9.9 - - + +
476B ALA* 3.5 35.4 - - + -
477B GLU* 3.7 32.8 - - + +
480B GLN* 3.9 13.5 - - - +
518B THR* 3.4 30.3 - - + +
519B LEU* 3.0 14.9 + - - +
520B CYS 3.2 0.4 - - - -
521B SER* 1.3 78.1 - - - +
523B LYS* 1.3 57.7 + - - +
524B GLY 3.3 3.1 - - - -
525B CYS* 3.0 9.9 + - + +
526B MSE 2.9 28.4 + - - +
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Residues in contact with LYS 523 (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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1B SO4 3.1 20.2 + - - +
520B CYS 3.6 10.2 + - - +
521B SER* 3.7 15.8 + - - +
522B MSE 1.3 71.1 - - - +
524B GLY* 1.3 57.5 - - - +
526B MSE 3.2 7.3 + - - +
527B ARG* 2.9 56.6 + - - +
558B ASN* 6.0 2.4 - - - +
561B LYS* 6.5 0.9 - - - +
562B THR* 3.0 41.4 + - + +
565B GLU* 5.6 4.7 - - - -
566B VAL* 4.5 2.7 - - + +
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Residues in contact with GLY 524 (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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1B SO4 2.8 21.9 + - - -
480B GLN* 3.6 17.9 - - - +
484B GLU* 4.5 6.0 - - - +
522B MSE 3.3 0.2 - - - -
523B LYS* 1.3 72.7 - - - +
525B CYS* 1.3 56.8 + - - +
527B ARG* 3.4 16.2 + - - +
528B ALA* 3.0 26.3 + - - +
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Residues in contact with CYS 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ALA* 3.5 26.2 - - - -
479B LEU* 5.1 6.7 - - - -
480B GLN* 3.4 31.3 + - - +
505B LEU* 5.2 0.7 - - - -
519B LEU* 3.8 23.1 - - + -
522B MSE 3.0 22.0 + - + +
524B GLY* 1.3 72.3 - - - +
526B MSE 1.3 62.3 + - - +
528B ALA* 3.1 3.5 + - - +
529B LEU* 2.8 42.9 + - - +
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Residues in contact with MSE 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B LEU* 3.6 19.3 - - - +
520B CYS* 3.9 17.9 - - - +
522B MSE 2.9 18.4 + - - +
523B LYS 3.2 7.2 + - - +
525B CYS* 1.3 77.0 - - - +
527B ARG* 1.3 62.2 + - - +
529B LEU* 3.3 15.5 + - + +
530B VAL* 3.1 28.8 + - - +
548B LEU* 3.8 18.2 - - + -
551B LEU* 3.7 22.7 - - + -
562B THR* 4.0 5.4 - - + -
563B LEU* 3.3 36.3 - - + -
566B VAL* 4.0 24.2 - - + -
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Residues in contact with ARG 527 (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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1B SO4 4.7 2.2 + - - -
523B LYS* 2.9 47.4 + - - +
524B GLY* 3.8 13.0 - - - +
525B CYS 3.3 0.2 - - - -
526B MSE 1.3 74.7 - - - +
528B ALA* 1.3 58.4 + - - +
530B VAL* 3.4 4.6 + - - +
531B ALA* 3.0 28.9 + - - +
566B VAL* 3.9 25.9 - - + +
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Residues in contact with ALA 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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479B LEU* 5.2 2.2 - - + -
480B GLN* 4.3 12.8 - - + +
483B CYS* 3.6 30.7 - - + -
484B GLU* 5.4 3.4 - - + +
524B GLY 3.0 15.8 + - - +
525B CYS* 3.1 11.9 + - - +
527B ARG* 1.3 73.2 - - - +
529B LEU* 1.3 65.6 + - - +
531B ALA* 3.2 10.0 + - - +
532B GLN* 3.1 26.3 - - - +
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Residues in contact with LEU 529 (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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479B LEU* 3.7 22.0 - - + -
505B LEU* 4.9 2.0 - - + -
519B LEU* 4.5 6.1 - - + -
525B CYS* 2.8 29.5 + - - +
526B MSE 3.5 31.6 - - + +
528B ALA* 1.3 75.5 - - + +
530B VAL* 1.3 64.3 + - - +
532B GLN* 2.9 15.7 + - - +
544B ILE* 3.1 52.4 - - + +
547B VAL* 4.1 29.8 - - + -
548B LEU* 4.8 9.6 - - + -
551B LEU* 4.7 1.1 - - + -
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Residues in contact with VAL 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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526B MSE 3.1 15.9 + - - +
527B ARG* 3.4 5.1 + - - +
529B LEU* 1.3 74.7 - - - +
531B ALA* 1.3 64.9 + - - +
533B LEU* 3.1 26.6 + - - +
534B LYS* 5.9 0.5 - - - +
548B LEU* 4.5 14.1 - - + -
566B VAL* 3.7 38.6 - - + +
567B GLY 4.2 1.3 - - - +
568B SER* 4.0 16.8 - - - -
571B ALA* 3.5 27.2 - - + +
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Residues in contact with ALA 531 (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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488B LEU* 3.6 24.6 - - + +
527B ARG 3.0 14.0 + - - +
528B ALA* 3.5 12.8 - - - +
529B LEU 3.1 0.2 - - - -
530B VAL* 1.3 78.7 - - - +
532B GLN* 1.3 68.0 + - - +
533B LEU 3.1 1.9 + - - -
534B LYS* 3.4 12.5 + - - +
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Residues in contact with GLN 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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479B LEU* 5.5 2.7 - - + -
483B CYS* 3.3 24.8 - - - +
487B GLY 5.1 0.9 - - - +
488B LEU* 3.6 16.9 - - - +
498B ARG* 2.9 36.0 + - - +
528B ALA 3.1 22.1 - - - +
529B LEU* 2.9 11.7 + - + +
531B ALA* 1.3 77.7 - - - +
533B LEU* 1.3 56.5 + - - +
534B LYS 3.1 6.1 - - - -
535B SER* 2.9 27.8 + - - +
540B LEU* 3.7 15.7 - - + +
541B GLN* 3.9 7.4 + - - +
544B ILE* 3.6 28.9 - - + -
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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