Contacts of the helix formed by residues 434 - 448 (chain B) in PDB entry 1T4L
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 ASP 434 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B LEU 2.6 29.0 - - - +
430B ASN 3.2 14.4 - - - +
431B ALA 3.8 0.4 + - - -
432B LEU 3.1 3.2 - - - -
433B ARG* 1.3 109.7 + - - +
435B LYS* 1.3 55.7 + - - +
436B LYS* 3.1 2.5 - - + -
437B MET* 2.9 31.8 + - + +
438B LEU* 2.6 39.5 + - - +
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Residues in contact with LYS 435 (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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432B LEU 4.7 0.6 + - - -
433B ARG 3.9 2.4 + - - -
434B ASP* 1.3 71.3 - - - +
436B LYS* 1.3 92.2 + - + +
438B LEU* 3.5 11.8 - - - +
439B ASP* 2.8 34.5 + - - +
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Residues in contact with LYS 436 (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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434B ASP* 3.1 1.7 - - + -
435B LYS* 1.3 99.6 - - + +
437B MET* 1.3 53.8 + - - +
439B ASP* 3.7 4.5 - - - +
440B PHE* 2.7 36.4 + - - +
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Residues in contact with MET 437 (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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378B ILE* 5.4 2.0 - - - -
410B THR* 5.5 2.2 - - + -
412B LEU* 3.2 42.4 - - + -
431B ALA* 2.6 32.5 - - + +
434B ASP* 2.9 32.2 + - + +
436B LYS* 1.3 75.0 - - - +
438B LEU* 1.3 77.4 + - + +
440B PHE* 3.0 23.8 - - + +
441B TYR* 3.0 45.1 - - + -
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Residues in contact with LEU 438 (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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373B GLN* 3.1 39.3 - - + +
378B ILE* 3.2 29.1 - - + +
431B ALA* 3.5 19.7 - - + +
432B LEU* 3.4 28.9 - - - +
434B ASP 2.6 24.8 + - - +
435B LYS* 3.5 7.9 - - - +
437B MET* 1.3 77.0 - - + +
439B ASP* 1.3 64.1 + - - +
441B TYR* 2.8 17.5 + - - +
442B ALA* 3.1 8.5 + - - +
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Residues in contact with ASP 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B LYS 2.8 20.9 + - - +
436B LYS* 4.0 4.3 - - - +
438B LEU* 1.3 72.9 - - - +
440B PHE* 1.3 62.6 + - - +
442B ALA* 3.0 26.1 + - - +
443B LYS* 3.2 10.2 + - - +
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Residues in contact with PHE 440 (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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410B THR* 5.7 2.7 - - + -
436B LYS 2.7 21.3 + - - +
437B MET* 3.0 22.2 - - + +
438B LEU 3.0 0.2 - - - -
439B ASP* 1.3 78.0 - - - +
441B TYR* 1.3 96.2 + + - +
443B LYS* 3.5 20.5 + - - +
444B GLN* 3.0 56.2 + - + +
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Residues in contact with TYR 441 (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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378B ILE* 3.3 31.4 - - + -
380B TYR* 4.3 15.2 - + + -
383B LEU* 4.5 16.6 - - + -
406B VAL* 3.6 25.7 - - + +
408B ASP* 5.6 5.1 + - - +
410B THR* 3.6 15.4 + - - +
412B LEU* 4.1 3.8 - - + +
437B MET* 3.0 52.2 + - + -
438B LEU 2.8 5.1 + - - +
440B PHE* 1.3 99.1 - + - +
442B ALA* 1.3 56.3 + - - +
444B GLN* 3.4 23.1 - - - +
445B ARG* 2.7 39.4 + - - +
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Residues in contact with ALA 442 (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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377B LEU 5.9 1.3 - - - +
378B ILE* 5.0 4.4 - - + +
438B LEU 3.1 6.3 + - - +
439B ASP* 3.0 26.8 + - - +
441B TYR* 1.3 79.0 - - - +
443B LYS* 1.3 61.7 - - - +
445B ARG* 3.2 8.9 - - - +
446B ALA* 3.2 17.7 + - - +
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Residues in contact with LYS 443 (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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439B ASP* 3.2 9.2 + - - +
440B PHE* 3.8 23.5 + - - +
442B ALA* 1.3 75.0 - - - +
444B GLN* 1.3 72.0 + - - +
446B ALA* 2.8 19.9 + - + +
447B ALA* 2.9 16.5 + - + +
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Residues in contact with GLN 444 (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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380B TYR* 4.4 11.3 + - + -
408B ASP* 6.0 0.2 + - - -
440B PHE* 3.0 46.9 + - + +
441B TYR* 3.1 33.1 + - + +
443B LYS* 1.3 84.0 - - + +
445B ARG* 1.3 58.6 + - - +
447B ALA* 4.4 5.8 - - - -
448B ILE* 2.6 47.4 + - + +
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Residues in contact with ARG 445 (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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378B ILE* 4.7 5.4 + - - +
380B TYR* 3.2 52.0 - - + +
441B TYR* 2.7 17.0 + - + +
442B ALA* 3.2 13.9 - - - +
444B GLN* 1.3 73.2 - - - +
446B ALA* 1.3 60.3 + - - +
448B ILE* 2.6 39.5 - - - +
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Residues in contact with ALA 446 (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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442B ALA 3.2 7.0 + - - +
443B LYS* 2.8 12.8 + - + +
445B ARG* 1.3 82.4 - - - +
447B ALA* 1.3 64.4 + - - +
448B ILE 4.7 0.3 - - - +
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Residues in contact with ALA 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LYS* 2.9 16.1 + - + +
444B GLN* 3.0 9.3 + - - +
446B ALA* 1.3 80.0 - - - +
448B ILE* 1.3 72.4 + - - +
449B PRO* 3.1 8.2 - - + +
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Residues in contact with ILE 448 (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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380B TYR* 4.6 24.5 - - + +
381B ALA 5.8 1.3 - - - +
444B GLN* 2.6 37.1 + - + +
445B ARG* 2.6 51.0 - - - +
446B ALA 4.7 0.3 - - - +
447B ALA* 1.3 79.7 - - - +
449B PRO* 1.3 68.1 - - - +
450B ARG* 3.0 12.0 + - - +
451B SER 3.9 14.6 - - - +
452B GLU* 4.4 7.6 - - - +
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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