Contacts of the helix formed by residues 443 - 456 (chain B) in PDB entry 4LOU
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 PRO 443 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU 5.1 3.4 - - - +
26A LEU 5.9 0.7 - - - +
28A ARG* 3.2 66.2 - - + +
29A ASP* 4.8 2.5 - - + -
203B GLU* 4.9 0.7 - - - +
402B ILE 4.0 13.7 - - - +
403B ARG* 4.0 23.3 - - + -
442B LYS* 1.3 83.6 - - + +
444B LEU* 1.3 51.6 + - - +
445B TYR 3.5 1.3 - - - -
446B SER* 2.9 11.8 + - - +
447B ALA* 2.7 33.5 + - - +
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Residues in contact with LEU 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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269B PHE* 5.8 1.3 - - + -
270B ASN* 3.5 26.9 - - + +
273B VAL* 4.0 30.3 - - + -
274B LEU* 4.1 24.7 - - + -
348B PHE* 4.7 7.4 - - + -
356B ILE* 4.8 18.4 - - + -
360B MET* 5.8 0.9 - - - -
401B SER* 3.0 24.0 + - - +
402B ILE* 4.1 7.9 - - + +
442B LYS 2.9 6.6 + - - -
443B PRO* 1.3 68.5 - - - +
445B TYR* 1.3 64.5 + - + +
446B SER 3.0 0.2 + - - -
447B ALA* 3.1 7.3 + - + +
448B ILE* 2.7 41.6 + - + +
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Residues in contact with TYR 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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107B SER* 3.8 22.5 + - - -
109B ILE* 3.5 39.9 - - + +
110B PRO* 3.8 21.5 - - + +
113B GLU* 3.0 24.3 - - - +
199B PHE* 4.5 3.1 - + - -
203B GLU* 3.9 11.8 + - - +
348B PHE* 4.8 5.2 - + - -
356B ILE* 3.4 36.7 + - + +
357B PHE* 4.0 19.7 - + - -
402B ILE* 3.8 34.2 - - + +
443B PRO 3.5 0.6 - - - -
444B LEU* 1.3 87.7 - - + +
446B SER* 1.3 57.6 + - - +
448B ILE* 4.0 4.5 - - + -
449B LEU* 3.5 17.5 + - - +
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Residues in contact with SER 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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25A LEU* 3.9 38.4 - - - +
28A ARG* 3.4 24.8 + - - -
113B GLU* 4.1 9.2 + - - -
203B GLU* 4.3 2.5 + - - -
443B PRO* 2.9 20.7 + - - +
445B TYR* 1.3 78.9 + - - +
447B ALA* 1.3 59.2 + - - +
448B ILE 3.2 0.9 - - - -
449B LEU* 3.9 3.5 - - - +
450B ALA* 3.0 28.8 + - - +
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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
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25A LEU 5.3 0.4 + - - -
26A LEU* 5.1 8.6 - - + +
270B ASN* 5.9 0.7 - - - +
274B LEU* 4.1 22.4 - - + -
442B LYS* 4.5 19.3 - - + +
443B PRO 2.7 17.4 + - - +
444B LEU* 3.4 13.7 - - + +
446B SER* 1.3 73.2 - - - +
448B ILE* 1.3 60.4 + - - +
450B ALA* 3.4 6.8 - - - +
451B ARG* 3.3 29.2 + - - +
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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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110B PRO* 3.5 30.1 - - + -
273B VAL* 5.2 0.4 - - + -
274B LEU* 4.0 21.3 - - + -
277B GLN* 4.1 23.6 - - - +
348B PHE* 4.2 24.2 - - + -
444B LEU* 2.7 36.2 + - + +
445B TYR* 4.7 4.0 - - + -
447B ALA* 1.3 69.6 - - - +
449B LEU* 1.3 66.1 + - - +
450B ALA 3.0 2.6 + - - -
451B ARG* 3.2 7.5 + - - +
452B THR* 3.2 28.8 + - - +
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Residues in contact with LEU 449 (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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21A LEU* 5.4 1.1 - - + -
25A LEU* 3.6 27.6 - - + -
110B PRO* 3.1 31.1 - - + +
111B GLU* 5.0 0.9 - - - -
113B GLU* 4.2 11.9 - - + +
114B GLY* 3.6 31.6 - - - +
117B GLU* 5.3 7.0 - - + -
120B ARG* 4.4 12.8 - - + -
445B TYR 3.5 17.5 + - - +
446B SER* 3.7 4.5 + - - +
448B ILE* 1.3 79.4 - - - +
450B ALA* 1.3 61.3 + - - +
452B THR* 3.5 8.3 + - + -
453B LEU* 3.1 34.5 + - + +
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Residues in contact with ALA 450 (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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22A ILE* 4.1 17.7 - - + +
25A LEU* 4.1 12.5 - - + +
26A LEU* 4.1 28.9 - - + -
446B SER 3.0 19.1 + - - +
447B ALA* 3.4 8.5 - - - +
448B ILE 3.0 0.6 - - - -
449B LEU* 1.3 74.0 - - - +
451B ARG* 1.3 64.0 + - + +
452B THR 3.0 4.3 - - - -
453B LEU* 3.1 7.5 + - - +
454B ALA* 3.1 20.9 + - - +
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Residues in contact with ARG 451 (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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26A LEU* 6.3 1.3 - - + -
274B LEU* 3.2 44.9 + - + +
277B GLN* 3.0 28.9 + - - +
278B ASP* 3.2 32.4 + - - -
447B ALA 3.4 14.6 - - - +
448B ILE* 3.2 7.6 + - - +
450B ALA* 1.3 77.3 - - + +
452B THR* 1.3 60.8 + - - +
453B LEU 3.4 0.2 - - - -
454B ALA* 3.4 10.7 - - - +
455B LYS* 3.4 26.0 + - - +
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Residues in contact with THR 452 (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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110B PRO* 6.4 0.7 - - - -
111B GLU* 4.2 11.9 - - - +
120B ARG* 3.1 33.1 + - - +
448B ILE* 3.2 22.5 + - - +
449B LEU* 3.9 10.5 - - + +
450B ALA 3.0 0.8 - - - -
451B ARG* 1.3 79.2 - - - +
453B LEU* 1.3 62.3 + - + +
454B ALA 3.2 0.2 - - - -
455B LYS* 3.9 6.4 + - - +
456B GLN* 3.4 21.5 + - - +
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Residues in contact with LEU 453 (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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18A ARG* 3.7 22.2 - - + +
21A LEU* 4.0 27.1 - - + -
22A ILE* 3.6 29.0 - - + +
25A LEU* 4.2 14.6 - - + -
119B GLN* 3.9 32.1 - - + +
120B ARG* 4.4 12.8 - - + -
449B LEU* 3.1 25.0 + - + +
450B ALA 3.1 2.4 + - - +
452B THR* 1.3 76.5 - - - +
454B ALA* 1.3 61.7 + - - +
456B GLN* 3.4 16.6 + - - +
457B GLU* 3.5 15.8 - - - +
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Residues in contact with ALA 454 (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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22A ILE* 4.0 11.9 - - + +
450B ALA 3.1 11.9 + - - +
451B ARG* 3.4 15.7 - - - +
452B THR 3.2 0.2 - - - -
453B LEU* 1.3 74.7 - - - +
455B LYS* 1.3 66.4 + - + +
456B GLN 3.1 1.1 - - - -
457B GLU* 3.3 17.8 + - - +
458B ALA* 3.4 14.7 + - - +
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Residues in contact with LYS 455 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281B HIS* 4.8 20.2 + - - -
451B ARG 3.4 13.2 + - - +
452B THR* 4.3 6.1 - - - +
454B ALA* 1.3 74.5 - - + +
456B GLN* 1.3 56.7 + - - +
457B GLU 3.0 10.7 + - - -
458B ALA* 3.3 24.4 + - - +
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Residues in contact with GLN 456 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ARG* 3.1 43.8 + - - +
119B GLN 3.9 17.8 - - - +
120B ARG* 4.6 15.7 - - - +
452B THR 3.4 17.7 + - - +
453B LEU* 3.7 17.0 - - + +
454B ALA 3.1 1.6 - - - -
455B LYS* 1.3 75.6 - - - +
457B GLU* 1.3 56.7 + - - +
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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