Contacts of the strand formed by residues 555 - 560 (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 ILE 555 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B THR 3.7 0.7 - - - +
551B MET* 3.2 7.3 - - - -
552B ALA 2.8 37.5 + - - +
553B ASN* 2.9 21.5 + - + +
554B LYS* 1.3 77.1 - - + +
556B GLY* 1.3 64.1 + - - +
557B SER* 4.2 3.5 + - - +
569B GLY* 3.5 28.7 - - - +
570B GLN 3.3 17.3 - - - +
571B THR* 4.3 9.0 - - - +
572B VAL* 4.4 0.2 - - - -
611B GLN* 4.8 5.0 + - - +
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Residues in contact with GLY 556 (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* 4.2 7.9 - - - -
528B TYR* 3.7 11.3 - - - -
550B THR 3.3 8.1 - - - -
551B MET* 4.4 2.2 - - - -
555B ILE* 1.3 74.5 - - - +
557B SER* 1.3 62.3 + - - -
569B GLY* 3.0 20.4 + - - -
570B GLN 2.8 17.8 + - - +
572B VAL* 3.8 16.7 - - - +
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Residues in contact with SER 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B LEU* 3.8 2.8 - - - +
528B TYR* 4.6 0.4 - - - -
548B VAL 4.3 0.4 - - - -
549B LEU* 3.4 5.0 - - - -
550B THR* 2.9 45.3 + - - +
555B ILE* 4.6 4.2 + - - +
556B GLY* 1.3 76.8 + - - -
558B VAL* 1.3 63.4 + - - +
559B TYR* 3.7 20.5 + - - -
568B SER* 3.0 19.3 + - - -
569B GLY* 3.8 9.4 - - - -
611B GLN* 5.1 4.2 + - - -
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Residues in contact with VAL 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B LEU* 4.2 10.3 - - + -
515B GLY 4.3 5.8 - - - +
516B LEU* 4.3 16.6 - - + -
526B PRO* 4.0 16.8 - - + -
528B TYR* 4.2 15.0 - - + +
547B VAL* 5.1 0.4 - - + -
548B VAL 3.3 3.6 - - - +
549B LEU* 3.9 24.2 - - + -
557B SER* 1.3 77.8 - - - +
559B TYR* 1.3 69.3 + - - +
560B ILE* 4.7 0.2 - - + -
564B PRO* 3.6 3.8 - - - +
565B LEU* 2.9 52.2 + - + +
568B SER* 3.4 6.4 + - - -
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Residues in contact with TYR 559 (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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546B HIS 3.7 0.4 - - - +
547B VAL* 3.4 7.8 - - - +
548B VAL* 2.6 60.0 + - + +
550B THR* 4.1 8.8 + - + -
557B SER* 3.7 28.3 + - - -
558B VAL* 1.3 79.7 - - - +
560B ILE* 1.3 67.4 + - - +
562B GLY* 4.1 16.2 - - - +
563B GLU 3.3 10.1 - - - +
564B PRO* 3.3 41.3 - - + +
614B ALA* 5.9 4.4 - - + -
617B ILE* 3.8 29.9 - - + +
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Residues in contact with ILE 560 (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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516B LEU* 3.8 29.6 - - + -
524B TRP* 3.7 26.5 - - + +
545B TYR* 4.0 24.5 - - + -
546B HIS 3.4 2.5 - - - +
547B VAL* 3.9 13.9 - - + -
558B VAL* 4.7 0.7 - - + -
559B TYR* 1.3 80.4 - - - +
561B ASP* 1.3 82.1 + - + +
562B GLY 3.1 0.7 - - - -
563B GLU* 2.8 23.5 + - - +
565B LEU* 3.5 32.5 - - + +
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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