Contacts of the strand formed by residues 461 - 465 (chain A) 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 GLY 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A THR* 3.3 2.1 - - - -
444A ALA 3.0 33.2 + - - +
455A PHE* 3.4 20.0 - - - -
459A GLY 3.9 0.2 + - - -
460A GLY* 1.3 73.4 - - - -
462A ALA* 1.3 59.6 + - - -
586A VAL 3.5 10.1 - - - -
587A GLY 3.7 7.9 - - - -
588A GLY 4.1 0.7 - - - -
590A LYS* 3.0 12.8 - - - +
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Residues in contact with ALA 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TRP* 3.8 29.8 - - + -
441A ALA* 4.3 7.4 - - + -
442A SER 3.1 10.1 - - - +
443A THR* 3.9 9.2 - - + -
455A PHE* 4.0 3.6 - - + -
461A GLY* 1.3 73.5 - - - -
463A LEU* 1.3 61.3 + - - +
584A PHE 3.9 0.2 - - - +
585A TYR* 3.5 5.2 - - - +
586A VAL* 2.8 43.2 + - + +
588A GLY 4.7 0.5 - - - +
590A LYS* 3.9 4.3 - - - +
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Residues in contact with LEU 463 (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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441A ALA* 3.1 4.3 - - - -
442A SER* 2.7 46.0 + - - +
462A ALA* 1.3 74.3 - - - +
464A TRP* 1.3 62.8 + - - +
465A PRO* 3.5 24.2 - - + +
468A GLN* 4.1 11.9 - - - +
583A HIS* 3.5 37.7 - - + +
584A PHE 3.6 2.2 - - - -
589A TYR 4.6 4.9 - - - +
590A LYS* 4.0 14.8 - - + +
591A ARG* 3.6 38.1 - - - +
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Residues in contact with TRP 464 (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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421A GLY* 3.9 22.7 - - - -
422A PHE 4.0 0.9 - - - -
423A LEU* 3.7 34.0 - - + +
434A ASP* 4.8 0.7 - - - -
439A VAL* 3.0 29.1 + - + +
440A ASN 3.5 21.6 - - - -
441A ALA* 3.8 7.6 - - + +
462A ALA 4.2 0.2 - - - -
463A LEU* 1.3 73.4 - - - +
465A PRO* 1.3 64.5 - - - +
466A VAL* 3.8 3.5 - - - +
475A TYR* 3.6 26.7 + + - -
484A LEU* 3.9 20.2 - - + -
583A HIS* 3.3 1.5 - - - +
584A PHE* 2.9 54.3 + + + +
586A VAL* 5.2 7.0 - - + -
605A VAL* 3.9 15.0 - - + -
607A LEU* 3.8 31.9 - - + -
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Residues in contact with PRO 465 (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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439A VAL* 4.1 6.3 - - + -
440A ASN 3.4 21.5 - - - +
442A SER* 5.3 0.7 - - - +
463A LEU* 3.5 15.0 - - + +
464A TRP* 1.3 87.8 - - + +
466A VAL* 1.3 59.1 + - - +
468A GLN* 3.7 23.8 - - + +
469A GLN* 3.0 38.8 + - + +
475A TYR* 3.7 8.3 - - - -
582A SER 4.1 0.4 - - - +
583A HIS* 3.9 8.5 - - + -
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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