Contacts of the helix formed by residues 444 - 458 (chain A) in PDB entry 1T9A
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 ARG 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A ILE* 4.6 9.9 + - - +
299A ALA 3.1 26.1 + - - -
300A LYS* 3.8 10.5 + - - +
302A PRO* 3.5 35.5 - - - +
327A ALA* 2.9 24.2 + - - +
328A GLN* 2.8 34.1 + - + +
329A ILE* 4.4 1.0 - - - +
441A VAL* 3.7 21.8 - - + +
443A GLU* 1.3 78.6 - - - +
445A SER* 1.3 60.0 + - - +
446A GLU 3.5 2.2 - - - -
447A TRP* 4.0 16.8 - - + -
448A PHE* 2.9 43.7 + - + +
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Residues in contact with SER 445 (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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443A GLU* 2.7 34.4 + - - +
444A ARG* 1.3 71.2 - - - +
446A GLU* 1.3 62.2 + - - +
448A PHE* 3.8 3.9 - - - +
449A ALA* 2.7 33.7 + - - +
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Residues in contact with GLU 446 (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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444A ARG 3.5 0.4 - - - -
445A SER* 1.3 76.5 - - - +
447A TRP* 1.3 58.6 + - - +
449A ALA* 3.2 5.7 + - - +
450A GLN* 2.8 32.7 + - - +
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Residues in contact with TRP 447 (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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300A LYS 4.1 8.3 - - - +
301A LYS* 3.6 58.6 - - + -
302A PRO* 3.0 27.8 + - + -
303A VAL* 3.7 19.1 - - + -
330A PRO* 3.7 20.5 - - + +
363A ALA* 3.7 25.6 - - + -
366A ASN* 4.1 10.5 - - + -
367A ALA 4.1 6.3 - - - -
444A ARG* 3.8 21.9 - - + +
445A SER 3.4 0.4 - - - -
446A GLU* 1.3 79.2 - - - +
448A PHE* 1.3 59.2 + + - +
450A GLN* 3.3 9.0 + - + +
451A ILE* 3.0 43.1 + - + +
454A TRP* 4.4 14.1 - + - -
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Residues in contact with PHE 448 (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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328A GLN* 3.5 50.7 - - + -
330A PRO* 3.8 22.0 - - + -
346A PRO 6.3 0.2 - - - -
347A LYS* 4.0 29.2 - - + -
444A ARG* 2.9 33.8 + - + +
445A SER* 4.0 3.1 - - - +
447A TRP* 1.3 80.2 - + - +
449A ALA* 1.3 61.4 + - - +
451A ILE* 3.4 7.5 + - + +
452A ASN* 2.8 43.7 + - - +
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Residues in contact with ALA 449 (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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445A SER 2.7 24.9 + - - +
446A GLU* 3.4 6.3 - - - +
448A PHE* 1.3 73.1 - - - +
450A GLN* 1.3 64.1 + - - +
452A ASN* 3.0 10.7 + - - +
453A LYS* 3.0 21.5 + - - +
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Residues in contact with GLN 450 (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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446A GLU 2.8 17.5 + - - +
447A TRP* 3.6 14.6 - - + +
449A ALA* 1.3 76.1 - - - +
451A ILE* 1.3 62.8 + - - +
453A LYS* 3.1 20.7 + - - +
454A TRP* 3.2 57.4 + - + +
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Residues in contact with ILE 451 (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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330A PRO* 3.5 34.5 - - + -
349A LEU* 3.5 27.1 - - + -
359A THR* 3.8 8.1 - - + -
363A ALA* 4.7 3.1 - - + -
447A TRP* 3.0 45.4 + - + +
448A PHE* 3.7 8.7 - - + +
449A ALA 3.2 0.2 - - - -
450A GLN* 1.3 75.2 - - - +
452A ASN* 1.3 59.3 + - - +
454A TRP* 3.2 26.8 + - + +
455A LYS* 3.0 37.3 + - - +
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Residues in contact with ASN 452 (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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346A PRO 5.4 1.0 - - - +
448A PHE* 2.8 32.1 + - - +
449A ALA* 3.0 8.0 + - - +
451A ILE* 1.3 73.3 - - - +
453A LYS* 1.3 65.5 + - - +
455A LYS* 3.3 25.7 + - - +
456A LYS* 3.2 22.2 + - - +
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Residues in contact with LYS 453 (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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449A ALA 3.0 11.6 + - - +
450A GLN* 3.1 20.6 + - - +
452A ASN* 1.3 75.6 - - - +
454A TRP* 1.3 65.0 + - + +
456A LYS* 3.2 7.9 + - - +
457A GLU* 3.0 23.2 + - - +
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Residues in contact with TRP 454 (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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359A THR* 3.4 22.8 + - + +
362A LEU* 3.4 39.4 - - + +
363A ALA* 3.8 23.3 - - - -
366A ASN* 3.5 38.4 - - + -
447A TRP* 4.4 4.5 - + - -
450A GLN* 3.2 44.1 + - + +
451A ILE* 3.2 30.8 + - + +
453A LYS* 1.3 79.1 - - + +
455A LYS* 1.3 54.1 + - - +
457A GLU* 3.1 1.7 + - + -
458A TYR* 2.7 46.5 + + + -
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Residues in contact with LYS 455 (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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345A ASP 5.1 0.4 + - - -
346A PRO* 2.9 29.9 + - - +
347A LYS 4.8 0.6 - - - -
348A SER 2.9 23.1 + - - -
349A LEU* 4.5 6.7 - - - +
359A THR* 3.5 17.9 - - + +
451A ILE* 3.0 34.0 + - - +
452A ASN* 3.3 25.6 + - - +
454A TRP* 1.3 77.0 - - - +
456A LYS* 1.3 61.3 + - - +
458A TYR 4.0 5.0 + - - -
459A PRO* 4.1 15.1 - - - +
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Residues in contact with LYS 456 (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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452A ASN 3.2 11.1 + - - +
453A LYS* 3.6 9.0 - - - +
454A TRP 3.2 0.6 - - - -
455A LYS* 1.3 77.6 - - - +
457A GLU* 1.3 61.1 + - - +
459A PRO* 3.6 10.9 - - - +
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Residues in contact with GLU 457 (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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453A LYS 3.0 16.9 + - - +
454A TRP* 3.8 4.5 - - + +
456A LYS* 1.3 77.8 - - - +
458A TYR* 1.3 84.9 + - + +
459A PRO* 3.4 6.4 - - - +
666A ASN* 4.9 2.4 - - - +
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Residues in contact with TYR 458 (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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357A CYS* 4.2 17.7 - - - -
358A ALA* 3.5 21.4 + - + +
359A THR* 4.3 4.0 + - - +
362A LEU* 3.7 31.4 - - + +
454A TRP* 2.7 34.3 + + + +
455A LYS 4.2 3.0 - - - +
456A LYS 3.5 0.2 - - - -
457A GLU* 1.3 94.2 - - + +
459A PRO* 1.3 66.1 - - - +
460A TYR* 5.9 0.2 - - - -
653A PRO* 5.9 1.7 - - + +
664A PHE* 3.8 26.3 - + - -
666A ASN* 3.7 27.6 - - - +
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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