Contacts of the helix formed by residues 435 - 444 (chain A) in PDB entry 1T5A
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 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432A THR* 2.6 29.7 + - - +
433A LYS 3.5 1.2 - - - -
434A SER* 1.3 73.2 - - - +
436A ARG* 1.3 62.9 + - - +
437A SER 3.3 2.7 - - - -
438A ALA* 2.9 9.2 + - - +
439A HIS* 2.9 37.4 + - - -
459A THR* 4.7 7.4 - - - -
463A ALA* 6.2 1.8 - - - -
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Residues in contact with ARG 436 (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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434A SER* 3.2 29.5 + - - +
435A GLY* 1.3 75.6 - - - +
437A SER* 1.3 63.9 + - - +
439A HIS* 3.0 18.3 + - + +
440A GLN* 3.0 34.7 + - - +
519A SER* 3.6 28.1 + - - -
520A GLY* 4.8 4.4 - - - +
532A FBP 4.1 6.2 + - - +
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Residues in contact with SER 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR* 4.9 2.3 - - - +
413A ALA* 5.1 0.5 - - - +
430A VAL* 3.9 18.2 - - - -
431A LEU 4.3 0.7 - - - -
432A THR* 4.2 2.5 - - - -
435A GLY 3.2 0.2 + - - -
436A ARG* 1.3 77.8 - - - +
438A ALA* 1.3 62.9 + - - +
440A GLN* 3.5 15.6 + - - +
441A VAL* 3.3 23.6 + - - +
512A LEU* 4.9 1.9 - - - +
520A GLY* 5.5 0.3 + - - -
522A THR* 2.6 35.7 + - - -
532A FBP 2.6 27.7 + - - -
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Residues in contact with ALA 438 (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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430A VAL* 4.0 11.3 - - + +
432A THR* 4.2 8.4 - - + -
435A GLY* 2.9 10.9 + - - +
437A SER* 1.3 76.8 - - - +
439A HIS* 1.3 69.2 + - - +
441A VAL* 3.1 7.1 + - - +
442A ALA* 3.0 19.9 + - - +
450A ILE* 4.3 9.1 - - + +
452A ALA* 3.8 28.9 - - + -
463A ALA* 6.4 0.2 - - + -
469A ILE* 3.9 16.0 - - + +
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Residues in contact with HIS 439 (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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266A LYS* 6.3 1.6 - - - -
434A SER 4.3 5.0 + - - -
435A GLY* 2.9 27.9 + - - -
436A ARG* 3.0 29.1 + - + +
438A ALA* 1.3 74.8 - - - +
440A GLN* 1.3 57.1 + - + +
442A ALA* 2.7 24.8 + - - +
443A ARG* 2.9 12.8 + - - +
459A THR 5.8 0.7 - - - -
462A GLN* 5.4 1.6 - - + -
463A ALA* 4.8 11.2 - - + -
466A TYR* 3.3 59.6 + + + -
469A ILE* 3.7 13.3 - - + +
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Residues in contact with GLN 440 (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 ASP* 3.9 5.9 + - - -
409A THR* 3.4 36.2 + - - +
410A GLU* 2.8 35.0 + - - +
413A ALA* 4.0 13.9 - - + +
436A ARG* 3.0 20.3 + - + +
437A SER* 3.6 15.7 + - - +
439A HIS* 1.3 76.2 - - + +
441A VAL* 1.3 61.8 + - - +
443A ARG* 3.2 16.5 - - - +
444A TYR* 3.1 24.4 - - - -
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Residues in contact with VAL 441 (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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413A ALA* 4.1 16.8 - - + +
416A ALA* 4.9 1.1 - - + -
417A VAL* 3.7 8.4 - - + +
428A ILE* 3.8 27.6 - - + -
430A VAL* 4.2 7.2 - - + -
437A SER 3.3 9.8 + - - +
438A ALA 3.1 8.6 + - - +
439A HIS 3.1 0.8 - - - -
440A GLN* 1.3 77.0 - - - +
442A ALA* 1.3 63.3 + - - +
444A TYR* 3.1 15.1 + - - +
446A PRO* 3.4 11.3 - - + +
450A ILE* 3.5 27.6 - - + -
512A LEU* 3.5 31.9 - - + -
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Residues in contact with ALA 442 (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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438A ALA 3.0 9.3 + - - +
439A HIS 2.7 11.7 + - - +
441A VAL* 1.3 73.7 - - - +
443A ARG* 1.3 54.4 + - - +
444A TYR 2.9 5.4 - - - -
445A ARG* 2.7 36.9 + - - +
446A PRO* 4.5 1.1 - - - -
450A ILE* 3.4 16.0 - - + +
466A TYR* 4.2 13.2 - - + -
467A ARG 3.3 24.2 - - - +
469A ILE* 4.1 9.4 - - + -
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Residues in contact with ARG 443 (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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318A ASN 4.7 5.8 + - - +
319A ARG 2.9 29.3 + - - -
320A ALA* 4.2 7.4 + - - +
321A GLY* 4.2 28.6 - - - +
398A LEU* 3.7 23.2 - - - +
402A ALA* 5.1 6.3 - - - +
403A PRO* 4.5 20.4 - - - +
410A GLU* 3.7 26.8 + - - -
439A HIS 2.9 10.7 + - - +
440A GLN* 3.2 24.0 - - - +
442A ALA* 1.3 75.2 - - - +
444A TYR* 1.3 76.3 + - + +
445A ARG* 3.2 12.5 + - - +
466A TYR* 5.7 1.7 - - + -
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Residues in contact with TYR 444 (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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395A PHE* 3.7 31.0 - + + -
398A LEU* 3.9 17.0 - - + +
399A ARG* 4.5 12.8 - - + -
402A ALA* 4.4 18.9 - - + +
410A GLU* 3.1 28.1 + - - -
413A ALA* 4.4 4.0 - - + -
414A VAL* 3.2 41.5 - - + +
417A VAL* 3.7 18.8 - - + +
440A GLN 3.1 22.4 - - - -
441A VAL 3.1 7.9 + - - +
442A ALA 2.8 1.6 + - - -
443A ARG* 1.3 93.3 + - + +
445A ARG* 1.3 70.6 + - - +
446A PRO* 3.5 2.7 - - - +
422B LYS* 3.3 23.6 + - - -
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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