Contacts of the strand formed by residues 628 - 633 (chain B) in PDB entry 1MWR
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 628 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ALA* 3.1 5.0 - - - +
350B ILE* 2.9 34.1 + - + +
352B PRO* 3.6 26.9 - - + +
532B LEU* 3.8 18.9 - - + +
535B TYR* 3.5 40.4 - - - +
536B SER* 3.6 12.8 - - - -
538B LEU* 4.7 1.1 - - + -
539B GLU* 4.0 15.5 - - + +
618B ILE* 4.3 8.5 - - + -
619B SER 3.3 14.6 - - - +
620B TYR* 3.7 33.2 - - + -
627B MSE 1.3 75.2 - - - +
629B MSE 1.3 61.2 + - - +
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Residues in contact with MSE 629 (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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336B ILE* 4.0 19.3 - - + -
348B THR 3.3 10.5 - - - +
349B ALA* 4.7 0.4 - - + -
532B LEU* 4.6 0.9 - - - -
617B PHE 3.8 0.8 - - - +
618B ILE* 3.0 9.2 - - - +
619B SER* 2.9 43.0 + - - +
627B MSE 3.5 28.0 - - + -
628B MSE 1.3 76.1 - - - +
630B ALA* 1.3 64.1 + - - +
631B ILE* 3.8 22.7 - - + -
649B SER* 3.3 48.9 - - - +
652B VAL* 3.7 19.7 - - + -
653B TYR* 4.2 7.4 - - + +
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Residues in contact with ALA 630 (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* 3.7 2.8 + - - +
347B GLY* 3.4 4.7 - - - -
348B THR* 2.8 46.9 + - - +
528B PRO 5.0 2.2 - - - +
531B ILE* 6.3 0.2 - - + -
532B LEU* 3.7 16.8 - - + -
616B TRP* 3.9 21.3 - - + -
617B PHE 3.6 4.3 - - - -
618B ILE* 4.1 12.1 - - + +
629B MSE 1.3 75.8 - - - +
631B ILE* 1.3 62.7 + - - +
632B ASN 4.1 0.2 - - - -
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Residues in contact with ILE 631 (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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336B ILE* 4.6 6.5 - - + -
340B MSE 4.3 14.1 - - + -
346B SER 3.8 1.1 - - - -
347B GLY* 4.1 13.7 - - - -
616B TRP* 3.4 4.7 - - - -
617B PHE 3.0 35.1 + - - +
629B MSE 3.8 40.2 - - + -
630B ALA* 1.3 81.8 - - - +
632B ASN* 1.3 61.7 + - - +
633B VAL* 4.3 12.8 - - + -
645B ASN* 3.3 30.0 - - + +
648B ILE* 4.3 24.0 - - + -
649B SER* 3.9 8.1 - - - +
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Residues in contact with ASN 632 (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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340B MSE 3.7 0.5 - - - +
345B GLY* 2.9 28.0 - - - -
346B SER* 3.0 29.0 + - - +
394B LYS* 6.2 1.6 - - - +
399B THR* 4.2 19.6 + - - +
528B PRO* 5.2 0.6 - - - +
614B ILE* 3.7 12.1 - - - +
615B GLY 3.0 16.4 - - - +
616B TRP* 3.1 47.0 + - + -
631B ILE* 1.3 74.9 - - - +
633B VAL* 1.3 67.7 + - - +
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Residues in contact with VAL 633 (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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340B MSE 4.0 17.7 - - + -
343B ASP* 3.8 23.1 - - + +
344B TYR 3.3 9.2 - - - +
345B GLY* 4.3 0.2 - - - -
614B ILE* 3.7 5.2 - - - +
615B GLY 2.9 33.2 + - - +
631B ILE* 4.3 7.4 - - + -
632B ASN* 1.3 83.3 - - - +
634B LYS* 1.3 74.7 + - - +
636B VAL* 3.2 9.6 - - + +
639B LYS* 5.2 2.9 - - + +
644B TYR* 4.2 24.9 - - + -
645B ASN* 3.5 14.3 + - - +
648B ILE* 4.6 3.6 - - + -
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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