Contacts of the helix formed by residues 429 - 438 (chain A) in PDB entry 1SLY
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 TRP 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424A PHE* 4.3 17.4 + + - -
427A GLN* 2.9 61.7 + - + +
428A TRP* 1.3 72.5 - - - +
430A ASP* 1.3 62.7 + - - +
432A SER* 3.3 17.9 + - - -
433A VAL* 3.4 12.3 + - - +
450A PRO* 3.4 30.6 - - + +
451A LEU 4.2 11.5 + - - +
452A ALA* 3.4 28.5 - - + -
453A TYR* 3.5 40.8 - + + -
454A ASN 5.6 0.7 - - - -
481A TRP* 4.3 9.4 - - + +
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Residues in contact with ASP 430 (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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392A MET* 3.8 11.3 - - - +
397A ASP* 3.0 30.7 - - - +
428A TRP 4.2 0.7 - - - +
429A TRP* 1.3 75.7 + - - +
431A LEU* 1.3 75.6 + - + +
433A VAL* 3.4 2.7 + - - +
434A GLN* 3.0 29.4 + - - +
480A ALA 3.7 14.8 - - - +
481A TRP 3.3 26.0 + - - +
482A ASN* 3.3 26.8 + - + +
483A PRO* 4.6 0.2 - - - -
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Residues in contact with LEU 431 (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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388A VAL* 4.2 11.4 - - + -
392A MET* 3.5 38.6 - - + -
397A ASP 5.2 1.3 - - - +
400A ALA* 4.5 3.1 - - + -
401A ARG* 4.6 10.1 - - + +
404A TRP* 3.0 42.2 + - + +
423A ALA* 4.0 8.5 - - + -
428A TRP* 2.9 30.8 + - + +
430A ASP* 1.3 91.2 + - - +
432A SER* 1.3 57.3 + - - +
434A GLN* 3.4 22.8 + - - +
435A ALA* 3.0 17.7 + - - +
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Residues in contact with SER 432 (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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420A ALA* 3.5 9.4 + - - +
423A ALA* 3.8 8.3 - - - +
424A PHE* 3.4 36.6 - - - +
428A TRP 3.2 10.1 + - - -
429A TRP* 3.4 13.7 - - - -
431A LEU* 1.3 75.2 - - - +
433A VAL* 1.3 62.0 + - - +
435A ALA* 3.4 4.2 + - - +
436A THR* 3.2 23.2 + - - -
447A GLU* 3.0 28.5 + - - +
450A PRO* 5.0 2.5 - - - -
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Residues in contact with VAL 433 (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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429A TRP 3.4 12.9 + - - +
430A ASP 3.8 6.5 - - - +
431A LEU 3.4 0.6 - - - -
432A SER* 1.3 73.3 - - - +
434A GLN* 1.3 64.1 + - - +
436A THR* 3.2 12.5 - - + +
437A ILE* 3.0 33.3 + - + +
447A GLU 3.8 4.0 - - - +
448A ARG* 3.4 21.5 - - - +
450A PRO* 3.9 14.1 - - + -
476A ARG* 3.9 25.8 - - - +
480A ALA* 4.1 21.1 - - + +
481A TRP* 4.1 13.0 - - + -
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Residues in contact with GLN 434 (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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401A ARG* 3.3 42.5 - - - +
404A TRP* 3.6 15.2 - - + -
405A ALA* 3.9 12.1 + - - +
408A VAL* 5.5 1.6 - - + +
430A ASP* 3.0 16.2 + - - +
431A LEU* 3.4 32.2 - - - +
433A VAL* 1.3 76.3 - - - +
435A ALA* 1.3 56.5 + - - +
437A ILE* 3.2 9.2 + - + +
438A ALA* 2.9 31.9 + - + +
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Residues in contact with ALA 435 (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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404A TRP* 3.9 13.1 - - + +
408A VAL* 4.3 14.3 - - + +
416A GLN* 4.1 10.3 - - - +
420A ALA* 3.8 32.1 - - + +
431A LEU 3.0 15.3 + - - +
432A SER 3.4 0.6 + - - +
434A GLN* 1.3 75.8 - - - +
436A THR* 1.3 54.0 + - - +
438A ALA* 3.8 6.5 - - - +
439A GLY* 2.8 31.2 + - - -
441A LEU* 4.2 5.4 - - - +
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Residues in contact with THR 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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420A ALA* 4.6 3.5 - - - +
432A SER 3.2 11.6 + - - -
433A VAL* 3.2 15.5 - - + +
435A ALA* 1.3 77.1 - - - +
437A ILE* 1.3 65.7 + - + +
440A LYS* 3.1 6.1 + - - -
441A LEU* 2.8 43.1 + - - +
442A TRP* 4.0 2.8 - - + -
444A HIS* 4.4 2.6 + - - +
447A GLU* 4.1 13.7 + - - +
448A ARG* 3.2 52.8 - - + +
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Residues in contact with ILE 437 (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 VAL* 3.0 30.0 + - + +
434A GLN* 3.7 10.1 - - + +
436A THR* 1.3 78.2 - - + +
438A ALA* 1.3 64.7 + - - +
440A LYS* 2.9 28.4 + - - +
442A TRP* 4.0 23.3 - - + -
448A ARG* 5.2 1.8 - - - +
476A ARG* 5.2 5.8 - - - +
480A ALA* 5.5 4.7 - - + -
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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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408A VAL* 4.0 28.0 - - + -
409A LYS* 6.0 1.1 - - - -
413A LYS* 4.0 6.8 + - - -
416A GLN* 4.4 6.3 - - - +
434A GLN* 2.9 18.8 + - + +
435A ALA 3.8 3.1 - - - +
437A ILE* 1.3 81.1 - - - +
439A GLY* 1.3 58.0 + - - +
440A LYS* 3.4 9.7 + - - +
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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