Contacts of the helix formed by residues 430 - 439 (chain A) in PDB entry 1LJ1
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 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A THR 5.0 0.7 + - - -
249A GLY* 3.0 17.5 + - - -
250A GLY 3.5 1.4 + - - -
251A ALA* 3.2 31.5 + - - +
426A ARG 4.8 0.7 - - - -
427A LYS 5.0 1.5 + - - -
429A LEU* 1.4 70.1 - - - +
431A LYS* 1.3 57.4 + - - +
433A ASP* 2.8 40.3 + - - +
434A LYS* 4.1 5.2 + - - +
325B LYS* 5.7 7.8 + - - -
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Residues in contact with LYS 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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167A LEU 5.6 0.6 + - - -
168A ALA 4.9 2.8 + - - -
169A ALA* 3.9 18.1 - - + +
250A GLY 3.3 15.4 + - - +
251A ALA* 4.5 1.5 - - - +
252A GLY* 3.5 33.5 - - - +
377A THR* 4.1 12.8 - - + -
429A LEU* 3.1 10.3 + - + -
430A SER* 1.3 80.2 + - - +
432A ILE* 1.3 62.7 + - - +
434A LYS* 2.8 35.1 + - + +
435A TYR* 3.6 25.4 + - + +
804A HEM 2.7 40.5 + - - +
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Residues in contact with ILE 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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380A VAL* 3.8 31.4 - - + -
421A PHE* 3.6 33.0 - - + -
425A VAL* 3.9 25.1 - - + +
426A ARG* 3.8 33.2 - - + +
429A LEU* 2.9 25.8 + - + +
431A LYS* 1.3 76.5 - - - +
433A ASP* 1.3 62.3 + - - +
435A TYR* 3.0 23.9 + - + +
436A ILE* 3.3 16.6 + - + +
497A ILE* 5.7 0.2 - - + -
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Residues in contact with ASP 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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426A ARG* 3.1 44.1 + - - +
427A LYS* 6.0 0.2 - - - -
430A SER* 2.8 31.3 + - - +
432A ILE* 1.3 70.8 - - - +
434A LYS* 1.3 59.0 + - + +
436A ILE* 3.4 10.9 + - - +
437A GLY* 2.9 25.8 + - - -
331B LYS* 5.1 8.4 + - - -
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Residues in contact with LYS 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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61A HIS* 6.5 0.9 - - - -
430A SER 4.5 4.0 - - - +
431A LYS* 2.8 31.2 + - + +
433A ASP* 1.3 79.4 - - + +
435A TYR* 1.4 58.1 + - - +
437A GLY* 3.4 0.6 + - - -
438A LEU* 3.0 24.6 + - - +
804A HEM 3.4 69.0 + - + +
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Residues in contact with TYR 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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169A ALA* 4.7 1.9 - - - +
374A VAL* 5.4 1.6 - - + -
375A MET* 3.6 19.7 + - - +
376A VAL* 3.6 30.1 - - + -
377A THR* 2.7 34.6 + - - +
380A VAL* 4.0 16.8 - - + -
431A LYS* 3.6 24.3 + - + +
432A ILE* 3.0 22.3 + - + +
434A LYS* 1.4 73.5 - - - +
436A ILE* 1.3 66.8 + - - +
438A LEU* 3.4 6.0 + - + +
439A GLY 3.2 4.3 + - - -
440A VAL* 3.2 43.6 + - + +
441A ALA* 3.9 3.5 + - + -
497A ILE* 4.4 14.8 - - + -
804A HEM 3.7 29.1 + - + -
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Residues in contact with ILE 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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426A ARG* 3.7 30.1 - - - -
432A ILE* 3.3 21.3 + - + +
433A ASP* 3.6 15.0 - - - +
435A TYR* 1.3 76.9 - - - +
437A GLY* 1.3 62.6 + - - +
439A GLY* 3.1 14.7 + - - -
441A ALA* 3.8 28.0 - - + +
495A TYR* 3.8 20.9 - - + -
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Residues in contact with GLY 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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54A HIS* 3.6 39.9 - - - +
433A ASP 2.9 15.7 + - - -
434A LYS* 3.4 4.7 + - - -
435A TYR 3.3 0.2 - - - -
436A ILE* 1.3 78.2 - - - +
438A LEU* 1.3 59.9 + - - +
439A GLY* 3.3 1.2 + - - -
804A HEM 4.6 9.0 - - - -
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Residues in contact with LEU 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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54A HIS 5.8 0.2 - - - -
86A HIS* 4.1 12.3 - - + +
88A PHE* 4.1 23.9 - - + -
372A GLY* 4.5 7.4 - - - -
374A VAL* 3.7 30.3 - - + -
434A LYS 3.0 16.1 + - - +
435A TYR* 3.7 9.2 - - + +
436A ILE 3.3 0.6 - - - -
437A GLY* 1.3 74.8 - - - +
439A GLY* 1.3 59.2 + - - +
440A VAL* 3.9 25.8 - - + +
804A HEM 3.8 36.3 - - + +
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Residues in contact with GLY 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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371A LYS* 2.7 31.7 + - - +
435A TYR 3.2 0.4 + - - -
436A ILE 3.1 16.5 + - - -
437A GLY 3.2 1.9 - - - -
438A LEU* 1.3 78.2 - - - +
440A VAL* 1.3 58.0 + - - +
441A ALA 3.6 3.4 - - - -
442A PRO* 4.9 3.6 - - - +
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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