Contacts of the helix formed by residues 549 - 562 (chain A) in PDB entry 1TF5
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 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A ARG* 1.3 106.7 - - + +
550A GLY* 1.3 69.6 - - - +
551A ALA 3.1 0.7 - - - -
552A GLU* 3.0 12.5 + - - +
553A ARG* 4.0 1.9 + - - +
581A SER* 3.7 12.2 + - - +
584A ARG* 3.1 63.7 - - + -
585A VAL* 3.7 22.7 - - + -
588A ASN* 2.8 28.0 - - - -
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Residues in contact with GLY 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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549A PHE* 1.3 80.9 - - - +
551A ALA* 1.3 61.6 + - - +
552A GLU 3.1 1.0 + - - -
553A ARG* 3.3 8.3 + - - +
554A THR* 3.2 24.6 + - - -
577A ALA* 4.5 10.3 - - - -
580A SER* 6.1 2.0 - - - -
581A SER* 2.9 6.3 + - - +
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Residues in contact with ALA 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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545A LEU* 3.5 24.9 - - + +
546A MET* 3.5 22.7 - - - +
548A ARG 4.5 1.6 - - - +
549A PHE 3.1 0.2 - - - -
550A GLY* 1.3 72.4 - - - +
552A GLU* 1.3 63.0 + - - +
554A THR* 3.5 5.6 + - - -
555A MET* 3.0 32.6 + - - +
577A ALA 4.2 3.8 + - - -
578A VAL* 4.8 9.2 - - + +
581A SER* 2.7 24.3 + - - +
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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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546A MET 3.6 8.0 + - - +
547A ARG* 4.1 19.5 - - - +
548A ARG 3.0 23.4 + - - +
549A PHE 3.0 5.8 + - - +
551A ALA* 1.3 79.8 - - - +
553A ARG* 1.3 64.9 + - - +
555A MET* 3.4 2.8 + - - +
556A ALA* 3.1 29.1 + - - +
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Residues in contact with ARG 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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549A PHE 4.0 2.1 + - - +
550A GLY* 3.3 10.7 + - - +
552A GLU* 1.3 83.1 - - + +
554A THR* 1.3 62.0 + - - +
556A ALA* 3.5 7.7 + - + +
557A MET* 3.2 22.3 + - + +
560A ARG* 4.9 3.2 + - - +
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Residues in contact with THR 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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550A GLY 3.2 14.9 + - - -
551A ALA* 3.9 4.0 - - - -
552A GLU 3.2 0.4 - - - -
553A ARG* 1.3 75.4 - - - +
555A MET* 1.3 71.9 + - + +
557A MET* 3.0 10.2 + - - +
558A LEU* 2.9 27.3 + - + +
573A MET* 5.0 10.2 - - + +
574A VAL* 4.1 37.2 - - + -
577A ALA* 3.6 18.9 - - + +
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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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407A ILE* 4.2 12.1 - - + -
541A MET* 3.4 39.5 - - + +
546A MET* 3.4 43.5 - - + +
551A ALA 3.0 24.8 + - - +
552A GLU* 3.9 2.9 - - - +
554A THR* 1.3 80.7 - - + +
556A ALA* 1.3 57.1 + - - +
558A LEU* 3.2 13.0 + - + +
559A ASP* 2.8 30.5 + - - +
574A VAL* 3.9 28.5 - - + -
578A VAL* 4.2 12.8 - - + -
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Residues in contact with ALA 556 (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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541A MET* 5.3 0.4 - - - -
552A GLU* 3.1 25.0 + - - +
553A ARG* 3.5 12.8 - - + +
555A MET* 1.3 77.2 - - - +
557A MET* 1.3 62.4 + - - +
559A ASP* 3.2 8.8 - - - +
560A ARG* 3.1 43.9 + - - +
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Residues in contact with MET 557 (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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553A ARG* 3.2 10.4 + - + +
554A THR* 3.0 12.8 + - - +
556A ALA* 1.3 77.1 - - - +
558A LEU* 1.3 79.4 + - + +
559A ASP 3.2 0.2 + - - -
560A ARG* 3.3 22.4 + - - +
561A PHE* 2.9 54.9 + - + -
573A MET* 5.3 12.3 - - - -
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Residues in contact with LEU 558 (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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407A ILE* 5.3 1.3 - - + -
541A MET* 4.9 2.2 - - - -
554A THR* 2.9 17.2 + - + +
555A MET* 3.7 37.5 - - + +
557A MET* 1.3 95.4 - - + +
559A ASP* 1.3 64.4 + - - +
561A PHE* 3.3 10.5 + - + +
562A GLY 3.2 14.2 + - - -
563A MET* 3.3 28.3 + - + +
569A ILE* 4.4 31.4 - - + -
573A MET* 6.0 1.3 - - + -
574A VAL* 4.0 27.4 - - + -
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Residues in contact with ASP 559 (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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409A ARG* 4.0 24.3 + - - -
541A MET* 3.6 23.1 - - + +
555A MET 2.8 13.3 + - - +
556A ALA* 3.2 13.0 - - - +
558A LEU* 1.3 77.2 - - - +
560A ARG* 1.3 61.3 + - + +
562A GLY* 2.9 21.3 + - - -
563A MET* 4.0 3.5 + - - +
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Residues in contact with ARG 560 (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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553A ARG* 4.9 3.6 + - - +
556A ALA* 3.1 31.9 + - - +
557A MET* 3.6 27.9 - - - +
559A ASP* 1.3 78.0 - - + +
561A PHE* 1.3 65.4 + - - +
562A GLY* 3.2 1.6 + - - -
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Residues in contact with PHE 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A MET* 2.9 37.6 + - + -
558A LEU* 3.3 20.0 - - + +
560A ARG* 1.3 76.8 - - - +
562A GLY* 1.3 60.6 + - - +
563A MET* 4.7 6.5 - - - -
569A ILE* 5.0 14.8 - - + -
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Residues in contact with GLY 562 (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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558A LEU 3.2 0.4 + - - -
559A ASP 2.9 12.9 + - - -
560A ARG 3.0 1.3 - - - -
561A PHE* 1.3 84.8 - - - +
563A MET* 1.3 58.1 + - - +
564A ASP* 2.6 23.8 - - - +
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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