Contacts of the strand formed by residues 554 - 561 (chain B) in PDB entry 3P1X
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 ARG 554 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545B SER* 3.8 2.9 + - - +
546B GLU* 3.3 4.9 - - - -
547B THR* 3.0 45.9 + - - +
548B GLY* 5.6 0.2 - - - -
552B ASP 4.7 2.2 - - - +
553B LYS* 1.3 75.9 - - - +
555B PHE* 1.3 61.8 + - - +
556B VAL* 5.3 3.4 - - + -
570B GLY 3.7 5.4 - - - -
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Residues in contact with PHE 555 (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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543B LEU* 4.2 11.0 - - + -
545B SER 3.3 2.2 - - - -
546B GLU* 3.5 40.8 - - + -
553B LYS* 3.5 27.4 - - + -
554B ARG* 1.3 76.5 - - - +
556B VAL* 1.3 62.6 + - - +
557B MSE 5.7 0.2 - - + -
569B ALA* 3.1 8.1 - - - +
570B GLY 2.9 32.5 + - - +
571B SER 3.5 16.8 - - - -
572B ASN* 3.4 29.6 - - - +
573B LYS* 3.8 33.0 - - + +
576B ALA* 3.8 14.3 - - + +
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Residues in contact with VAL 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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543B LEU* 3.4 5.1 - - - +
544B ILE* 2.8 36.3 + - + -
545B SER* 2.9 32.8 + - - +
554B ARG* 5.3 4.5 - - + -
555B PHE* 1.3 79.5 - - - +
557B MSE 1.3 64.9 + - - +
567B GLN* 4.1 29.4 - - + +
568B GLY 3.4 9.0 - - - +
569B ALA* 4.0 13.5 - - + -
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Residues in contact with MSE 557 (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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541B TYR* 3.0 40.4 - - + +
542B GLU 3.5 3.8 - - - +
543B LEU* 3.6 34.3 - - + -
544B ILE* 4.4 0.9 - - - -
555B PHE* 5.7 0.2 - - + -
556B VAL* 1.3 75.5 - - - +
558B GLU* 1.3 60.8 + - - +
567B GLN* 3.0 8.4 - - - +
568B GLY 2.8 30.7 + - - -
573B LYS* 4.2 10.3 - - - +
576B ALA* 3.6 31.2 - - + +
577B LYS* 3.0 45.3 - - + +
580B ALA* 4.3 4.3 - - + -
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Residues in contact with GLU 558 (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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540B LYS 3.7 0.9 - - - +
541B TYR* 3.4 4.1 - - - -
542B GLU* 2.8 41.3 + - + +
544B ILE* 3.3 31.9 - - + +
557B MSE 1.3 74.6 - - - +
559B VAL* 1.3 65.0 + - - +
565B LYS* 3.9 44.6 + - + +
566B PHE 3.2 10.1 - - - +
567B GLN* 3.3 26.0 + - + +
580B ALA* 4.9 0.4 - - - -
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Residues in contact with VAL 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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532B LEU* 4.7 1.8 - - + -
539B LEU* 3.9 24.7 - - + -
540B LYS 3.4 16.8 - - - +
541B TYR* 3.7 30.5 - - + -
558B GLU* 1.3 79.0 - - - +
560B GLU* 1.3 67.9 + - - +
561B VAL* 4.1 15.0 - - + -
564B GLN 3.7 0.9 - - - +
565B LYS* 3.6 0.5 - - - -
566B PHE* 2.8 43.8 + - + +
580B ALA* 4.0 19.1 - - + +
581B ALA 4.6 0.4 - - - +
584B ALA* 4.7 1.8 - - + -
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Residues in contact with GLU 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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539B LEU* 3.7 15.4 - - - +
540B LYS 4.2 4.8 + - - -
559B VAL* 1.3 74.6 - - - +
561B VAL* 1.3 65.8 + - - +
563B GLY* 3.8 18.8 + - - +
564B GLN 3.3 18.4 - - - +
565B LYS* 2.9 37.0 - - + -
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Residues in contact with VAL 561 (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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532B LEU* 4.2 4.7 - - + -
536B ARG* 4.1 22.2 - - + -
539B LEU* 3.8 22.7 - - + -
559B VAL* 4.1 11.4 - - + -
560B GLU* 1.3 79.5 - - - +
562B ASP* 1.3 84.1 + - - +
563B GLY 3.2 1.3 - - - -
564B GLN* 2.8 24.7 + - - +
566B PHE* 4.1 3.8 - - + -
584B ALA* 4.1 20.9 - - + -
588B LEU* 3.9 23.2 - - + +
589B PHE* 4.3 9.4 - - + -
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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