Contacts of the helix formed by residues 516 - 531 (chain B) in PDB entry 3TNF
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 516 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512B SER 5.0 0.7 - - - -
513B ILE* 2.5 21.6 + - - +
515B ASP* 1.3 77.9 - - - +
517B PRO* 1.3 60.7 - - - +
518B GLU* 3.8 6.4 + - - +
519B LYS* 3.0 52.4 + - - +
520B GLN* 2.6 24.0 + - - +
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Residues in contact with PRO 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515B ASP 3.8 7.0 - - - +
516B SER* 1.3 85.8 - - - +
518B GLU* 1.3 76.8 + - + +
519B LYS 3.3 0.2 - - - -
520B GLN* 3.2 18.6 + - - +
521B LYS* 3.1 25.6 + - - +
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Residues in contact with GLU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B SER* 4.0 7.6 - - - +
517B PRO* 1.3 87.5 - - + +
519B LYS* 1.3 67.9 + - + +
521B LYS* 4.0 6.9 - - - +
522B LYS* 3.1 23.0 + - - +
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Residues in contact with LYS 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B GLU* 4.5 13.9 + - - +
512B SER* 2.6 32.7 + - - +
513B ILE* 3.7 18.8 - - + -
516B SER* 3.0 37.7 + - - +
518B GLU* 1.3 78.6 - - + +
520B GLN* 1.3 63.7 + - - +
522B LYS* 3.0 9.0 + - - +
523B ALA* 2.9 24.2 + - - +
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Residues in contact with GLN 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B TYR* 3.6 19.3 + - + -
510B TRP* 2.9 30.9 - - + -
513B ILE* 3.6 33.0 + - + -
514B LYS 4.3 7.1 + - - +
516B SER 2.6 25.2 + - - +
517B PRO* 3.2 22.1 + - - +
519B LYS* 1.3 80.9 - - - +
521B LYS* 1.3 57.3 + - - +
523B ALA 3.4 1.3 + - - +
524B GLU* 3.1 35.2 + - - +
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Residues in contact with LYS 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASP 5.3 8.0 + - - -
517B PRO 3.1 13.7 + - - +
518B GLU* 4.1 8.3 - - - +
519B LYS 3.2 0.2 - - - -
520B GLN* 1.3 74.3 - - - +
522B LYS* 1.3 60.8 + - - +
524B GLU* 3.3 12.8 + - + +
525B HIS* 3.0 63.3 + - + +
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Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLN* 6.1 0.4 - - - +
518B GLU 3.1 14.0 + - - +
519B LYS* 3.0 12.5 + - - +
521B LYS* 1.3 76.8 - - - +
523B ALA* 1.3 55.7 + - - +
524B GLU 3.1 0.2 - - - -
525B HIS* 3.3 10.8 + - + +
526B ASP* 2.9 65.7 + - - +
529B LYS* 5.1 9.7 - - - +
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Residues in contact with ALA 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B TYR* 3.4 16.4 - - + -
503B LEU 2.8 46.3 + - - +
504B LEU* 3.5 22.9 - - + -
519B LYS 2.9 14.3 + - - +
520B GLN* 3.8 4.5 - - - +
521B LYS 3.3 0.2 - - - -
522B LYS* 1.3 76.8 - - - +
524B GLU* 1.3 57.7 + - - +
526B ASP* 3.9 4.0 - - - -
527B PHE* 3.3 11.1 + - - +
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Residues in contact with GLU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B LYS* 3.0 48.9 + - - +
501B PHE 3.5 20.7 + - - +
502B TYR* 3.7 11.9 - - + -
520B GLN* 3.1 21.0 + - - +
521B LYS* 3.7 15.7 - - + +
522B LYS 3.1 0.4 - - - -
523B ALA* 1.3 78.0 - - - +
525B HIS* 1.3 65.1 + - + +
526B ASP 3.3 0.2 - - - -
527B PHE* 3.4 4.5 + - - +
528B HIS* 2.9 27.5 + - - +
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Residues in contact with HIS 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASP 5.1 1.4 + - - -
128A LYS* 4.7 20.9 - - + -
129A ARG 3.9 20.4 + - - -
130A GLN* 3.6 26.9 - - + +
521B LYS* 3.0 52.7 + - + +
522B LYS* 3.8 12.6 + - - +
524B GLU* 1.3 77.1 - - + +
526B ASP* 1.3 67.6 + - - +
528B HIS* 3.1 9.5 + + + +
529B LYS* 3.0 31.0 + - + +
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Residues in contact with ASP 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B GLN* 5.4 2.8 + - - -
503B LEU* 3.6 34.8 - - + +
522B LYS* 2.9 59.6 + - - +
523B ALA* 3.9 2.9 - - - +
525B HIS* 1.3 79.8 - - - +
527B PHE* 1.3 62.0 + - - +
529B LYS* 3.5 24.9 + - - +
530B LEU* 3.8 12.8 - - - +
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Residues in contact with PHE 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B LEU* 3.8 26.5 - - + -
486B TYR* 4.9 13.9 - + - -
494B ILE* 3.9 21.3 - - + -
501B PHE* 3.5 48.0 - + + +
503B LEU* 3.7 10.9 - - - +
523B ALA 3.3 16.9 + - - +
524B GLU 3.8 5.2 - - - +
525B HIS 3.2 0.2 - - - -
526B ASP* 1.3 81.5 - - - +
528B HIS* 1.3 67.1 + - - +
530B LEU* 3.1 39.8 + - + +
531B GLN* 3.9 1.7 + - - +
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Residues in contact with HIS 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASP* 5.1 1.4 + - - -
91A THR* 3.0 44.9 + - + -
92A ASN* 6.1 0.2 - - + -
125A VAL* 5.7 1.3 - - + -
128A LYS* 3.8 34.9 - - + +
130A GLN* 4.1 7.9 - - - -
524B GLU 2.9 18.2 + - - +
525B HIS* 3.1 8.3 + + + +
527B PHE* 1.3 82.9 - - + +
529B LYS* 1.3 63.4 + - - +
531B GLN* 3.2 44.2 + - - +
532B TYR* 5.5 4.8 - + - -
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Residues in contact with LYS 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A THR 5.1 1.6 - - - +
92A ASN* 3.2 42.5 + - - +
93A GLU* 3.9 5.5 - - - +
94A LYS* 4.0 12.3 - - - +
130A GLN* 3.3 31.8 - - - +
522B LYS* 5.1 8.1 - - - +
525B HIS* 3.0 20.1 + - - +
526B ASP* 3.7 22.9 - - - +
527B PHE 3.2 0.4 - - - -
528B HIS* 1.3 77.0 - - - +
530B LEU* 1.3 67.0 + - + +
531B GLN 3.3 0.3 + - - -
532B TYR 4.2 4.9 + - - -
533B GLU* 4.0 11.8 - - - +
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Residues in contact with LEU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B LYS* 5.4 0.7 + - - -
486B TYR* 4.4 22.3 - - + -
487B PRO* 4.1 21.1 - - + +
488B ILE* 3.7 24.2 - - + -
494B ILE* 3.9 9.2 - - + -
503B LEU* 4.2 11.9 - - + -
526B ASP 3.8 10.3 - - - +
527B PHE* 3.1 41.6 + - + +
529B LYS* 1.3 80.1 - - + +
531B GLN* 1.3 64.2 + - - +
533B GLU* 2.8 31.7 + - + +
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Residues in contact with GLN 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 5.2 0.9 - - - -
484B LYS* 4.3 14.7 + - - -
486B TYR* 5.5 5.8 - - - -
527B PHE* 3.9 1.7 + - + +
528B HIS* 3.2 40.9 + - - +
529B LYS 3.2 0.4 - - - -
530B LEU* 1.3 77.8 - - - +
532B TYR* 1.3 103.2 + - + +
533B GLU 3.8 1.6 + - - +
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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