Contacts of the helix formed by residues 515 - 524 (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 SER 515 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ASP* 5.2 2.2 - - - -
513A HIS* 3.0 21.1 - - - +
514A GLU* 1.3 80.7 - - - +
516A ARG* 1.3 64.8 + - - +
517A ARG* 3.1 48.8 + - - +
518A ILE* 3.3 18.7 + - - +
519A ASP* 3.7 1.7 + - - +
582A GLN* 4.0 0.2 - - - -
586A GLU* 3.7 13.1 + - - -
593A ARG* 6.0 2.5 - - - -
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Residues in contact with ARG 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A THR* 3.5 25.6 + - - +
512A ARG* 3.8 11.2 - - - +
515A SER* 1.3 70.3 + - - +
517A ARG* 1.3 66.4 + - - +
519A ASP* 3.0 14.2 + - + +
520A ASN* 2.9 35.0 + - - +
579A GLU* 3.1 24.3 + - - +
582A GLN* 3.6 22.2 - - + +
583A LYS* 3.3 42.5 - - - +
586A GLU* 3.0 41.0 + - - +
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Residues in contact with ARG 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASP* 3.0 21.9 + - - +
214A ILE* 4.4 9.0 - - - +
215A ASP* 2.5 45.5 + - - -
373A THR* 3.4 51.6 - - - +
374A ALA* 4.5 1.3 - - - +
376A THR* 5.3 7.4 - - - +
377A GLU* 2.8 50.2 + - - +
515A SER* 3.1 27.6 + - - +
516A ARG* 1.3 77.9 - - - +
518A ILE* 1.3 59.1 + - + +
520A ASN* 3.3 3.8 + - - +
521A GLN* 3.0 25.4 + - - +
586A GLU* 5.9 0.8 - - - +
593A ARG* 4.9 5.1 - - - +
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Residues in contact with ILE 518 (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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210A ASP* 5.1 0.4 - - - +
211A SER* 5.3 4.9 - - - +
215A ASP* 4.2 18.6 - - - +
485A ASN* 4.1 21.3 - - + +
486A MET* 5.8 6.5 - - + -
513A HIS* 3.2 41.4 - - + +
515A SER* 3.3 17.7 + - - +
516A ARG 3.2 0.6 - - - -
517A ARG* 1.3 78.5 - - + +
519A ASP* 1.3 65.2 + - - +
521A GLN* 3.1 32.8 + - + +
522A LEU* 3.1 13.3 + - - +
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Residues in contact with ASP 519 (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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512A ARG* 2.8 39.9 + - - -
513A HIS* 2.4 53.6 + - - +
515A SER 4.0 5.8 - - - -
516A ARG* 3.0 16.4 + - + +
518A ILE* 1.3 75.0 - - - +
520A ASN* 1.3 58.8 + - - +
522A LEU* 3.2 6.6 + - - +
523A ARG* 3.0 41.7 + - - +
537A PHE* 3.6 16.2 - - + -
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Residues in contact with ASN 520 (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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101A LYS* 6.3 2.7 - - - -
373A THR* 4.2 13.8 - - + +
516A ARG* 2.9 30.9 + - - +
517A ARG* 3.7 5.2 - - - +
519A ASP* 1.3 75.2 - - - +
521A GLN* 1.3 60.0 + - - +
523A ARG* 2.9 34.5 + - + +
524A GLY* 2.9 25.1 + - - -
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Residues in contact with GLN 521 (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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102A THR* 4.9 5.6 + - - -
208A GLU* 4.2 14.7 + - - +
210A ASP* 3.1 19.2 + - - -
211A SER* 4.9 6.9 + - - -
371A THR* 4.4 1.5 + - - -
372A GLY* 5.6 2.9 - - - +
373A THR* 2.8 34.0 + - + +
486A MET* 5.9 1.4 - - - +
489A ARG* 4.9 12.8 - - - +
517A ARG 3.0 15.8 + - - +
518A ILE* 3.1 26.4 + - + +
520A ASN* 1.3 74.2 - - - +
522A LEU* 1.3 65.9 + - - +
524A GLY* 3.4 6.7 + - - +
525A ARG* 3.4 16.6 + - - +
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Residues in contact with LEU 522 (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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433A LEU* 4.3 7.0 - - + -
435A GLY* 3.7 34.8 - - - +
507A VAL* 3.5 26.1 - - + +
509A GLY* 3.7 24.0 - - - -
513A HIS* 4.6 9.9 - - + +
518A ILE 3.1 11.5 + - - +
519A ASP* 3.4 8.3 - - - +
521A GLN* 1.3 76.6 - - - +
523A ARG* 1.3 67.1 + - - +
525A ARG* 3.1 36.8 + - - +
537A PHE* 3.8 14.8 - - + -
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Residues in contact with ARG 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ARG* 3.4 25.5 - - - +
402A ASP* 3.8 31.9 - - - +
403A ARG 4.8 9.1 + - - -
405A ASP* 3.9 14.1 + - - -
507A VAL* 4.7 1.1 - - - -
512A ARG* 5.4 4.9 - - - +
519A ASP* 3.0 32.6 + - - +
520A ASN* 2.9 34.9 + - - +
522A LEU* 1.3 76.8 - - - +
524A GLY* 1.3 60.5 + - - +
525A ARG 3.2 1.4 + - - -
526A SER* 3.4 9.7 + - - -
535A THR* 3.6 28.6 + - - +
537A PHE* 3.4 30.7 - - + -
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Residues in contact with GLY 524 (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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101A LYS* 6.2 4.3 - - - -
102A THR* 3.2 35.5 - - - +
400A ARG* 4.1 12.1 - - - +
520A ASN 2.9 17.2 + - - -
521A GLN* 3.4 4.2 + - - -
522A LEU 3.2 1.0 - - - -
523A ARG* 1.3 73.2 - - - +
525A ARG* 1.3 59.1 + - - +
526A SER 3.0 12.4 + - - +
528A ARG* 5.5 1.4 + - - +
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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