Contacts of the helix formed by residues 544 - 555 (chain A) in PDB entry 1K4T
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 GLU 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A ARG* 3.9 24.8 + - - +
465A TRP* 3.7 36.1 - - + -
480A TYR* 3.7 16.1 + - + +
484A LYS* 6.1 0.2 - - - -
542A PRO 5.4 0.3 - - - +
543A VAL* 1.3 83.9 - - - +
545A LYS* 1.3 66.2 + - - +
546A ARG* 3.4 3.4 - - + +
547A VAL* 3.2 7.1 + - + +
548A PHE* 3.2 17.5 + - - +
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Residues in contact with LYS 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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523A TYR* 3.3 50.9 + - + +
543A VAL 3.7 1.6 + - - -
544A GLU* 1.3 71.8 - - - +
546A ARG* 1.3 62.4 + - + +
548A PHE* 3.0 5.5 + - - +
549A LYS* 2.9 53.8 + - + +
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Residues in contact with ARG 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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465A TRP* 4.3 29.8 - - + -
466A LYS* 2.8 57.4 - - + +
473A ARG* 5.4 7.2 - - - +
544A GLU* 3.4 1.8 - - + +
545A LYS* 1.3 84.1 - - + +
547A VAL* 1.3 53.0 + - - +
549A LYS* 3.6 13.1 + - - +
550A ASN* 2.7 40.5 + - - +
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Residues in contact with VAL 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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465A TRP* 3.5 48.5 - - + +
477A VAL* 4.3 12.8 - - + -
480A TYR* 4.0 26.7 - - + -
481A PHE* 4.3 3.4 - - + -
543A VAL* 4.2 8.5 - - + -
544A GLU* 3.2 12.5 + - + +
545A LYS 3.2 0.6 - - - -
546A ARG* 1.3 73.9 - - - +
548A PHE* 1.3 62.0 + - - +
550A ASN* 3.2 7.5 + - - +
551A LEU* 2.8 53.0 + - + +
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Residues in contact with PHE 548 (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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514A LEU* 3.7 17.6 - - + +
515A HIS 3.5 48.2 - - - -
516A PRO* 3.7 14.4 - - + -
523A TYR* 3.6 46.9 - + + -
524A VAL 3.6 7.0 - - - -
525A VAL* 4.3 9.9 - - + -
543A VAL* 4.0 3.6 - - + +
544A GLU 3.2 9.2 + - - +
545A LYS 3.0 8.9 + - - +
547A VAL* 1.3 80.3 - - - +
549A LYS* 1.3 64.7 + - - +
551A LEU* 3.3 7.8 + - - +
552A GLN* 3.1 61.6 + - + +
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Residues in contact with LYS 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A TYR* 3.8 21.2 + - - -
545A LYS* 2.9 49.7 + - + +
546A ARG* 3.9 15.9 - - - +
547A VAL 3.3 0.2 - - - -
548A PHE* 1.3 75.7 - - - +
550A ASN* 1.3 62.6 + - - +
552A GLN* 3.4 22.7 + - - +
553A LEU* 3.4 29.9 + - + +
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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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465A TRP* 3.2 38.1 + - - +
473A ARG* 2.9 38.4 + - - -
477A VAL* 4.1 9.7 - - + +
546A ARG* 2.7 28.8 + - - +
547A VAL 3.2 4.5 + - - +
549A LYS* 1.3 77.1 - - - +
551A LEU* 1.3 58.5 + - - +
553A LEU* 3.0 10.1 + - - +
554A PHE* 3.0 53.5 + - + -
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Residues in contact with LEU 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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477A VAL* 3.9 23.3 - - + -
481A PHE* 3.8 25.1 - - + -
512A ILE* 4.5 7.0 - - + -
514A LEU* 3.9 17.7 - - + -
525A VAL* 3.7 33.9 - - + -
547A VAL* 2.8 28.5 + - + +
548A PHE* 3.3 5.6 + - - +
550A ASN* 1.3 74.8 - - - +
552A GLN* 1.3 62.6 + - - +
554A PHE* 3.2 14.6 + - + +
555A MET* 3.1 29.1 + - - +
564A LEU* 4.4 15.3 - - + -
565A PHE* 4.6 0.2 - - + -
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Residues in contact with GLN 552 (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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514A LEU* 3.5 23.3 - - + -
548A PHE* 3.1 42.4 + - + +
549A LYS* 3.6 25.8 + - - +
550A ASN 3.2 0.2 - - - -
551A LEU* 1.3 75.9 - - - +
553A LEU* 1.3 64.7 + - + +
555A MET* 3.6 4.9 + - - +
556A GLU* 3.5 18.7 + - - +
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Residues in contact with LEU 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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470A MET* 4.3 23.9 - - + +
473A ARG* 4.5 17.5 - - - +
549A LYS* 3.4 16.8 + - + +
550A ASN* 3.0 12.6 + - - +
552A GLN* 1.3 78.7 - - + +
554A PHE* 1.3 70.6 + - + +
555A MET 3.1 2.0 - - - -
556A GLU* 3.2 22.9 + - + +
558A LYS* 5.8 0.2 - - - -
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Residues in contact with PHE 554 (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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470A MET* 3.6 28.3 - - + -
473A ARG* 3.9 7.2 - - + -
474A GLN* 3.5 49.8 - - + +
477A VAL* 3.8 24.9 - - + -
550A ASN* 3.0 38.1 + - + -
551A LEU* 3.2 13.7 + - + +
553A LEU* 1.3 79.0 - - + +
555A MET* 1.3 60.1 + - - +
556A GLU 3.4 0.2 - - - -
558A LYS* 2.9 34.0 + - - +
564A LEU* 3.6 22.7 - - + +
565A PHE* 3.9 18.4 - + - -
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Residues in contact with MET 555 (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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509A VAL* 3.7 36.5 - - + +
512A ILE* 3.3 48.0 - - + +
513A ASN* 5.1 1.1 - - - -
514A LEU* 3.6 28.0 - - + +
551A LEU 3.1 11.2 + - - +
552A GLN* 3.9 5.8 - - - +
553A LEU 3.1 0.8 - - - -
554A PHE* 1.3 75.9 - - - +
556A GLU* 1.3 64.2 + - - +
557A ASN 3.7 1.6 + - - -
558A LYS* 3.9 15.2 + - - +
564A LEU* 3.5 18.4 - - + -
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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