Contacts of the helix formed by residues 541 - 553 (chain A) in PDB entry 3KFL
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 541 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A ALA 2.7 17.5 + - - +
538A LYS* 4.0 3.7 + - - -
539A GLU 3.7 1.4 - - - -
540A PHE* 1.3 75.8 - - - +
542A ILE* 1.3 59.9 + - - +
543A ASP 3.5 2.2 - - - -
544A ALA* 3.4 5.8 + - - +
545A LEU* 3.0 28.2 + - - +
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Residues in contact with ILE 542 (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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290A GLU 3.0 27.6 - - - +
291A MET* 4.1 17.4 - - + +
292A ASN* 5.2 6.1 - - + +
534A VAL* 6.2 1.3 - - + -
537A ALA* 3.2 26.0 + - + +
538A LYS* 4.9 13.9 - - + +
541A GLY* 1.3 70.6 - - - -
543A ASP* 1.3 64.1 + - - +
545A LEU* 3.2 4.9 + - - +
546A LYS* 2.9 49.6 + - - +
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Residues in contact with ASP 543 (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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292A ASN* 5.2 0.9 + - - -
541A GLY 3.5 0.4 - - - -
542A ILE* 1.3 80.0 - - - +
544A ALA* 1.3 61.1 + - - +
546A LYS* 3.6 24.3 + - - +
547A TYR* 2.9 25.5 + - - +
685A MET* 3.3 38.5 - - + +
686A PRO* 3.9 4.9 - - - +
687A GLN* 3.0 20.1 + - - +
688A LYS* 2.7 48.1 + - + -
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Residues in contact with ALA 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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540A PHE 3.7 10.8 - - - +
541A GLY* 3.4 9.7 + - - +
542A ILE 3.3 0.4 - - - -
543A ASP* 1.3 78.2 - - - +
545A LEU* 1.3 55.8 + - - +
547A TYR* 3.5 3.1 + - - +
548A PHE* 3.0 28.2 + - - +
566A MET* 3.5 19.9 - - + +
570A LEU* 3.9 24.8 - - + +
574A LEU* 3.7 15.7 - - + +
730A PHE* 4.9 5.3 - - + -
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Residues in contact with LEU 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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226A ILE* 4.2 13.7 - - + -
291A MET* 4.0 15.3 - - + -
533A PRO 4.0 8.1 - - - +
536A LYS* 4.6 4.5 - - + +
537A ALA* 3.5 36.3 - - + +
540A PHE* 5.8 0.4 - - + -
541A GLY 3.0 13.4 + - - +
542A ILE 3.5 7.4 - - - +
544A ALA* 1.3 73.0 - - - +
546A LYS* 1.3 60.2 + - - +
548A PHE* 3.2 5.6 + - + +
549A LEU* 2.9 47.1 + - + +
561A TYR* 3.1 42.0 - - + +
566A MET* 3.5 9.5 - - + +
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Residues in contact with LYS 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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233A LEU* 3.6 28.6 - - + +
236A ASP* 4.5 3.2 + - - -
291A MET* 2.9 41.1 + - + -
292A ASN* 3.4 19.4 + - - +
293A TYR* 4.1 15.2 - - - -
542A ILE* 2.9 23.8 + - - +
543A ASP* 3.3 17.4 + - - +
545A LEU* 1.3 78.3 - - - +
547A TYR* 1.3 61.4 + - - +
549A LEU* 3.5 0.4 + - - -
550A MET* 3.1 28.8 + - - +
683A PRO 5.7 0.2 - - - +
684A VAL* 3.4 27.4 - - + +
686A PRO* 3.8 19.2 - - + +
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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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543A ASP 2.9 17.2 + - - +
544A ALA 3.7 4.7 - - - +
546A LYS* 1.3 75.8 - - - +
548A PHE* 1.3 58.8 + - - +
550A MET* 3.2 1.4 + - - +
551A ARG* 2.7 65.2 + - + +
569A ARG* 4.1 15.0 - - + -
573A GLU* 2.8 39.4 + - + +
574A LEU* 3.6 29.8 - - + -
633A LEU* 4.2 22.4 - - + +
637A PHE* 3.5 38.9 - + - +
684A VAL* 3.9 10.0 - - + +
685A MET* 3.9 17.9 - - + -
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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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516A TRP* 4.1 15.0 - + - -
544A ALA 3.0 17.2 + - - +
545A LEU* 3.2 4.2 + - + +
547A TYR* 1.3 84.0 - - + +
549A LEU* 1.3 62.0 + - + +
551A ARG* 4.7 0.9 - - - -
552A GLU* 2.8 70.1 + - + +
560A ASP 5.4 0.4 - - - -
561A TYR* 3.6 34.3 - + - -
562A SER* 3.9 19.5 - - - -
565A ASN* 3.6 13.0 - - + -
566A MET* 3.4 49.6 - - + +
569A ARG* 4.4 8.5 - - + +
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Residues in contact with LEU 549 (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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226A ILE* 4.1 28.9 - - + -
229A VAL* 4.5 11.2 - - + -
230A TYR* 3.7 20.4 - - + -
233A LEU* 3.9 22.9 - - + -
291A MET* 5.6 0.4 - - + -
516A TRP* 3.7 31.4 - - + +
545A LEU* 2.9 33.3 + - + +
546A LYS* 3.9 3.6 - - - +
548A PHE* 1.3 73.3 - - + +
550A MET* 1.3 56.9 + - - +
553A SER* 2.8 34.3 + - - -
561A TYR* 4.1 24.0 - - + -
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Residues in contact with MET 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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230A TYR* 3.3 39.7 - - + +
233A LEU* 3.7 28.5 - - + -
234A ILE* 3.8 15.0 - - + -
237A VAL* 4.3 6.3 - - + -
546A LYS 3.1 17.6 + - - +
549A LEU* 1.3 77.9 - - - +
551A ARG* 1.3 61.2 + - - +
553A SER* 3.6 9.9 + - - +
555A PHE* 5.7 2.5 - - + -
629A ILE* 3.9 37.3 - - + +
630A GLN* 3.4 22.0 + - - -
633A LEU* 3.6 20.4 - - + -
684A VAL* 4.2 9.9 - - + -
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Residues in contact with ARG 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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547A TYR* 2.7 53.9 + - + +
548A PHE 4.2 0.4 - - - +
550A MET* 1.3 72.8 - - - +
552A GLU* 1.3 58.3 + - - +
553A SER 3.2 1.8 - - - -
569A ARG* 3.6 46.3 - - - +
573A GLU* 4.2 10.7 + - - -
630A GLN* 3.0 39.5 + - - +
633A LEU* 4.1 16.6 - - + -
634A ILE* 3.6 41.8 - - - +
637A PHE* 6.2 0.4 - - - +
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Residues in contact with GLU 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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516A TRP* 4.3 12.1 - - + -
548A PHE* 2.8 53.1 + - + +
551A ARG* 1.3 74.1 - - - +
553A SER* 1.3 57.1 + - - +
554A ASN 4.1 0.5 + - - -
560A ASP 6.1 0.2 - - - +
565A ASN* 4.0 23.3 + - - +
569A ARG* 2.7 44.7 + - - +
630A GLN* 3.6 8.7 + - - -
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Residues in contact with SER 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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230A TYR* 2.9 22.5 + - - -
516A TRP* 3.6 20.4 - - - -
549A LEU 2.8 23.5 + - - -
550A MET* 3.6 13.9 + - - +
551A ARG 3.2 0.2 - - - -
552A GLU* 1.3 78.2 - - - +
554A ASN* 1.3 59.2 + - - +
555A PHE* 5.0 3.6 - - - -
630A GLN* 3.6 12.2 - - - +
812A EDO 3.7 16.4 - - - -
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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