Contacts of the strand formed by residues 524 - 528 (chain B) in PDB entry 1MS4
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 TRP 524 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B VAL* 4.8 2.7 - - + -
490B ILE* 3.9 15.0 - - + -
500B LEU* 3.5 27.8 - - + -
516B LEU* 4.0 11.7 - - + -
517B SER 3.7 12.6 - - - +
518B TYR* 4.1 2.5 - - + -
523B GLN* 1.3 72.4 - - - +
525B GLN* 1.3 60.2 + - - +
526B PRO* 3.1 5.3 - - + +
535B PRO* 3.5 3.1 - - - +
536B THR 2.9 39.9 + - - +
537B GLY* 4.5 1.1 - - - -
538B SER 4.0 22.2 + - - +
539B TRP* 3.6 28.7 - + + -
545B TYR* 3.8 37.5 - + + -
560B ILE* 3.7 27.4 - - + +
565B LEU* 4.0 37.0 - - + -
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Residues in contact with GLN 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B ALA* 3.4 26.1 - - + +
516B LEU* 4.1 0.4 - - - -
517B SER* 2.7 47.0 + - - -
519B ASP* 2.8 41.0 + - + +
523B GLN 3.8 0.2 + - - -
524B TRP* 1.3 73.9 - - - +
526B PRO* 1.3 66.4 - - - +
527B ILE* 3.6 6.7 - - + +
533B VAL* 3.8 25.6 - - + +
535B PRO* 3.8 17.6 - - + +
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Residues in contact with PRO 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B GLY 3.5 6.7 - - - +
516B LEU* 4.0 4.7 - - + -
524B TRP* 3.1 14.1 - - + +
525B GLN* 1.3 85.7 - - - +
527B ILE* 1.3 59.8 + - - +
528B TYR* 3.5 36.9 - - + +
533B VAL* 3.7 15.1 - - - +
534B THR 3.9 16.4 + - - +
536B THR* 4.2 9.9 - - + -
558B VAL* 4.0 8.5 - - + -
565B LEU* 3.9 26.5 - - + -
566B GLU 5.6 1.6 - - - +
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Residues in contact with ILE 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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512B LYS* 3.7 40.8 - - + -
514B LEU* 3.2 23.6 - - - +
515B GLY* 2.7 29.6 + - - +
516B LEU 4.8 0.2 - - - +
517B SER* 3.5 25.6 - - - +
525B GLN* 3.6 9.9 - - + +
526B PRO* 1.3 78.9 - - - +
528B TYR* 1.3 63.0 + - - +
529B GLY 4.0 17.0 - - - +
531B THR 5.3 1.1 - - - +
533B VAL* 4.0 25.4 - - + -
558B VAL* 5.1 0.2 - - - +
585B TYR* 4.8 0.2 - - - +
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Residues in contact with TYR 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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514B LEU* 3.8 13.0 - - + -
526B PRO* 3.5 39.3 - - + +
527B ILE* 1.3 72.1 - - - +
529B GLY* 1.3 67.4 + - - +
531B THR* 3.0 35.6 + - + +
532B PRO 5.9 1.8 - - - -
533B VAL* 6.2 1.1 - - - +
556B GLY 3.7 25.4 - - - -
558B VAL* 4.2 19.5 - - + +
565B LEU* 4.6 3.5 - - - +
566B GLU 5.1 0.3 + - - -
567B GLY* 3.7 8.2 - - - -
568B SER* 3.3 27.0 + - - -
570B GLN* 3.3 46.0 - - + +
571B THR 4.4 2.8 - - - +
572B VAL* 4.0 15.0 - - + -
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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