Contacts of the helix formed by residues 430 - 439 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B THR 4.9 1.0 + - - -
249B GLY* 3.0 17.8 + - - -
250B GLY 3.4 1.9 + - - -
251B ALA* 3.3 30.3 + - - +
426B ARG 4.7 1.1 - - - -
427B LYS 5.0 2.1 + - - -
429B LEU* 1.3 71.0 - - - +
431B LYS* 1.3 55.6 + - - +
432B ILE 3.1 0.2 - - - -
433B ASP* 2.9 37.8 + - - +
434B LYS* 4.0 5.0 + - - +
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Residues in contact with LYS 431 (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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61B HIS* 6.3 0.2 - - - +
167B LEU 5.7 0.8 + - - -
168B ALA 5.0 2.6 + - - -
169B ALA* 4.1 14.4 - - + +
250B GLY 3.3 18.1 + - - +
251B ALA* 4.7 1.8 - - - +
252B GLY* 3.5 32.9 - - - +
377B THR* 4.2 9.2 - - + -
429B LEU* 3.1 9.4 + - + -
430B SER* 1.3 76.7 + - - +
432B ILE* 1.4 57.2 + - - +
434B LYS* 2.8 39.2 + - + +
435B TYR* 3.7 24.7 + - + +
804B HEM 2.5 42.9 + - - +
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Residues in contact with ILE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B VAL* 3.9 26.2 - - + -
421B PHE* 3.7 29.4 - - + -
425B VAL* 3.9 30.1 - - + +
426B ARG* 4.0 24.5 - - + -
429B LEU* 3.0 33.9 + - + +
431B LYS* 1.4 77.5 - - - +
433B ASP* 1.4 62.9 + - - +
435B TYR* 3.0 24.5 + - + -
436B ILE* 3.2 17.4 + - + +
497B ILE* 5.7 0.2 - - + -
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Residues in contact with ASP 433 (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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426B ARG* 3.1 43.7 + - - +
430B SER* 2.9 26.5 + - - +
432B ILE* 1.4 76.3 - - - +
434B LYS* 1.3 60.6 + - + +
436B ILE* 3.4 11.2 + - + +
437B GLY* 3.0 24.1 + - - -
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Residues in contact with LYS 434 (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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61B HIS* 6.5 0.4 - - - -
430B SER 4.6 3.4 - - - +
431B LYS* 2.8 31.1 + - + +
433B ASP* 1.3 80.6 - - + +
435B TYR* 1.4 55.8 + - - +
437B GLY* 3.4 1.1 + - - -
438B LEU* 3.0 24.6 + - - +
804B HEM 3.5 68.9 + - + +
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Residues in contact with TYR 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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169B ALA* 4.7 1.9 - - - +
374B VAL* 5.4 3.4 - - + -
375B MET* 3.6 20.9 + - - +
376B VAL* 3.6 28.4 - - + -
377B THR* 2.8 35.3 + - + +
380B VAL* 4.1 12.6 - - + -
431B LYS* 3.8 25.3 - - + +
432B ILE* 3.0 22.9 + - + +
434B LYS* 1.4 73.7 - - - +
436B ILE* 1.4 64.8 + - - +
438B LEU* 3.3 5.8 + - + +
439B GLY 3.2 4.0 + - - -
440B VAL* 3.1 42.6 + - + +
441B ALA* 3.9 3.5 + - + -
497B ILE* 4.4 14.8 - - + -
804B HEM 3.8 27.8 + - + -
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Residues in contact with ILE 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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426B ARG* 3.6 30.7 - - - -
432B ILE* 3.2 20.6 + - + +
433B ASP* 3.6 14.1 - - - +
435B TYR* 1.4 77.8 - - - +
437B GLY* 1.3 63.1 + - - +
439B GLY* 3.0 15.1 + - - -
441B ALA* 4.0 26.0 + - + +
495B TYR* 3.9 20.2 - - + +
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Residues in contact with GLY 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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54B HIS* 3.7 39.7 + - - +
433B ASP 3.0 14.8 + - - -
434B LYS* 3.4 4.0 + - - -
436B ILE* 1.3 78.4 - - - +
438B LEU* 1.3 59.2 + - - +
439B GLY* 3.2 1.2 + - - -
804B HEM 4.7 8.1 - - - -
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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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54B HIS 5.8 0.4 - - - -
86B HIS* 4.1 17.9 - - + +
88B PHE* 4.1 16.8 - - + -
371B LYS* 5.3 1.2 + - - -
372B GLY* 4.7 7.4 - - - -
374B VAL* 3.7 30.5 - - + -
434B LYS 3.0 17.1 + - - +
435B TYR* 3.6 9.6 - - + +
436B ILE 3.3 0.4 - - - -
437B GLY* 1.3 74.5 - - - +
439B GLY* 1.3 59.0 + - - +
440B VAL* 4.2 23.4 - - + +
804B HEM 3.8 37.6 - - + +
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Residues in contact with GLY 439 (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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371B LYS* 3.0 28.4 + - - +
436B ILE 3.0 14.7 + - - -
437B GLY 3.1 1.9 - - - -
438B LEU* 1.3 79.2 - - - +
440B VAL* 1.3 61.3 + - - +
441B ALA 3.5 2.9 + - - -
442B PRO* 5.0 2.9 - - - +
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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