Contacts of the strand formed by residues 543 - 553 (chain A) in PDB entry 3DXD
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 PHE 543 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A VAL* 3.7 27.4 - - + -
541A GLN 3.8 6.3 - - - -
542A LYS* 1.3 74.4 - - - +
544A GLN* 1.3 57.7 + - - +
545A VAL* 3.3 16.6 + - + +
581A SER 3.2 1.0 - - - +
582A HIS* 2.5 34.0 - - - -
583A VAL* 3.0 25.9 + - + +
585A VAL* 3.9 8.7 - - + -
645A SER* 3.5 33.0 - - - -
646A LEU* 3.7 24.9 - - + -
649A ALA* 3.5 29.4 - - + -
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Residues in contact with GLN 544 (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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542A LYS* 4.0 5.6 + - - +
543A PHE* 1.3 68.1 - - - +
545A VAL* 1.3 65.1 + - - +
546A TYR* 6.3 0.2 - - - -
581A SER 3.3 9.2 + - - +
582A HIS* 2.8 29.5 + - - +
595A GLN* 3.2 48.5 + - - +
640A GLU 5.1 8.7 + - - +
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Residues in contact with VAL 545 (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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543A PHE* 4.0 21.8 - - + +
544A GLN* 1.3 80.8 + - - +
546A TYR* 1.3 70.8 + - - +
580A PRO* 3.5 4.2 - - - +
581A SER* 2.6 41.1 + - - +
583A VAL* 4.1 10.8 - - + -
637A PHE* 3.7 28.0 - - + -
638A TRP 3.5 11.0 - - - +
639A CYS* 3.6 29.8 - - + +
640A GLU 5.4 1.1 - - - +
646A LEU* 4.4 4.9 - - + -
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Residues in contact with TYR 546 (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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545A VAL* 1.3 81.1 - - - +
547A TYR* 1.3 60.1 + - - +
548A LEU* 4.2 0.4 - - + +
575A ARG 5.3 3.1 - - - -
578A TRP* 3.9 47.8 - + + -
579A THR 3.4 2.0 - - - +
580A PRO* 3.9 29.6 - - + -
581A SER* 4.1 0.9 - - - -
637A PHE* 3.1 9.2 - - - +
638A TRP* 2.9 56.8 + + + +
640A GLU* 4.9 12.1 - - + -
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Residues in contact with TYR 547 (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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546A TYR* 1.3 70.7 - - - +
548A LEU* 1.3 60.7 + - - +
549A GLY* 3.5 30.5 - - - -
550A ASN* 3.1 19.1 + - - +
578A TRP* 4.3 2.3 - - - -
579A THR* 2.8 40.2 + - - +
581A SER* 3.4 19.0 + - - +
592A ILE* 3.7 21.4 - - + +
601A LEU* 4.2 38.5 + - + -
635A HIS* 2.6 30.4 + - - -
636A MET 3.4 11.0 - - - -
637A PHE* 3.4 23.8 - + + -
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Residues in contact with LEU 548 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A TYR 4.6 0.9 - - - +
547A TYR* 1.3 74.2 - - - +
549A GLY* 1.3 56.9 + - - +
566A LEU* 4.3 16.2 - - + -
569A VAL* 3.4 30.8 - - + +
570A LEU* 4.0 21.1 - - + -
573A SER* 5.5 1.9 - - - +
578A TRP* 3.5 53.8 - - + +
620A THR* 5.1 0.7 - - + -
636A MET* 2.8 19.7 + - + +
637A PHE 3.7 24.2 - - - +
638A TRP* 3.9 18.8 - - + +
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Residues in contact with GLY 549 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A TYR* 3.3 27.5 - - - -
548A LEU* 1.3 81.0 - - - +
550A ASN* 1.3 61.0 + - - +
569A VAL* 5.4 0.9 - - - -
636A MET* 2.9 34.2 + - - +
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Residues in contact with ASN 550 (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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547A TYR* 3.1 25.2 + - - +
549A GLY* 1.3 74.3 - - - +
551A VAL* 1.3 70.9 + - - +
552A PRO* 5.9 0.2 - - - +
601A LEU 5.6 2.2 + - - -
633A CYS* 3.8 20.7 - - - -
634A CYS 3.1 13.0 - - - +
635A HIS* 3.7 15.5 - - - +
636A MET* 4.3 0.9 - - - -
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Residues in contact with VAL 551 (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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550A ASN* 1.3 80.3 - - - +
552A PRO* 1.4 77.4 - - + +
553A VAL* 4.4 0.4 - - + -
565A ALA* 3.7 24.2 - - + +
568A SER* 6.0 4.5 - - - -
569A VAL* 5.1 12.1 - - + +
633A CYS* 3.6 4.2 - - - -
634A CYS* 2.7 38.2 + - + +
636A MET* 3.6 24.2 - - + -
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Residues in contact with PRO 552 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551A VAL* 1.4 94.7 - - + +
553A VAL* 1.3 65.5 + - - +
632A PHE 3.4 11.2 - - - +
633A CYS* 4.4 2.2 - - + -
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Residues in contact with VAL 553 (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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551A VAL* 4.1 1.1 - - + +
552A PRO* 1.3 81.1 - - - +
554A ALA* 1.3 63.4 + - - +
555A LYS 3.6 17.0 + - - +
561A VAL* 3.5 25.8 - - + +
565A ALA* 4.2 15.0 - - + -
624A ILE* 3.8 13.7 - - + -
632A PHE* 3.0 36.6 + - + +
634A CYS* 3.6 29.6 - - + -
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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