Contacts of the helix formed by residues 438 - 454 (chain A) in PDB entry 6AGF
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 LEU 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A VAL* 5.1 2.4 - - + +
256A LEU* 4.4 19.7 - - + +
257A THR* 3.6 43.1 - - - +
260A CYS* 3.9 28.7 - - + -
261A LEU* 5.2 2.2 - - + +
264A PHE* 5.7 1.1 - - + -
403A MET* 4.4 11.4 - - - -
433A LEU* 4.2 8.3 - - + +
434A GLY* 3.3 28.5 + - - +
437A TYR* 1.3 86.2 - - + +
439A ILE* 1.3 65.2 + - - +
441A LEU* 3.4 15.8 + - + +
442A ILE* 3.5 20.4 + - - +
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Residues in contact with ILE 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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403A MET* 3.9 35.7 - - + +
434A GLY 4.5 0.7 - - - +
435A SER* 3.3 29.2 - - - +
436A PHE* 4.0 3.1 + - - +
437A TYR 3.2 0.6 - - - -
438A LEU* 1.3 80.8 - - - +
440A ASN* 1.3 61.3 + - - +
441A LEU 3.1 0.8 + - - -
442A ILE* 3.2 11.3 + - + +
443A LEU* 2.9 46.3 + - + +
1593A TYR* 5.6 3.8 - - + -
1911A 6OU 4.0 44.0 - - + +
1914A 9Z9 6.4 0.2 - - + -
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Residues in contact with ASN 440 (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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436A PHE* 2.8 31.4 + - - +
437A TYR 3.3 6.4 + - - +
439A ILE* 1.3 78.3 - - - +
441A LEU* 1.3 59.9 + - - +
443A LEU* 3.7 18.0 - - - +
444A ALA* 3.6 9.9 - - - +
1593A TYR* 3.1 44.5 - - - +
1596A ILE* 3.8 27.3 - - + +
1597A ILE* 4.1 12.8 - - + +
1600A ASN* 3.6 17.8 + - - -
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL* 3.9 15.8 - - + +
256A LEU* 5.4 4.5 - - + -
437A TYR* 3.3 51.2 + - + +
438A LEU* 3.4 12.5 + - + +
439A ILE 3.1 1.0 - - - -
440A ASN* 1.3 84.0 - - - +
442A ILE* 1.3 65.0 + - - +
443A LEU 3.3 1.1 - - - -
444A ALA* 3.5 0.8 + - - +
445A VAL* 3.2 37.9 + - + +
1471A LEU* 3.7 39.5 - - + -
1596A ILE* 5.0 0.4 - - + -
1600A ASN* 3.8 22.0 - - - +
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Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 5.0 6.5 - - + -
253A VAL* 3.7 19.7 - - + -
254A MET* 4.1 20.9 - - + -
257A THR* 4.7 10.1 - - + +
403A MET* 5.4 1.3 - - + -
438A LEU 3.5 17.2 + - - +
439A ILE* 3.2 14.1 + - + +
441A LEU* 1.3 77.5 - - - +
443A LEU* 1.3 58.4 + - + +
446A VAL* 3.2 35.9 + - + +
794A LEU* 4.8 0.5 - - - +
1911A 6OU 3.7 67.5 - - + +
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Residues in contact with LEU 443 (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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439A ILE* 2.9 27.4 + - + +
440A ASN* 3.7 21.8 - - - +
441A LEU 3.3 0.4 - - - +
442A ILE* 1.3 79.7 - - - +
444A ALA* 1.3 56.5 + - - +
445A VAL 3.5 0.2 - - - -
446A VAL* 4.5 3.4 - - - +
447A ALA* 3.5 20.4 + - - +
794A LEU* 4.4 18.0 - - + +
798A LEU* 5.1 1.9 - - - +
1593A TYR* 5.1 0.7 - - + -
1597A ILE* 4.2 10.3 - - + -
1911A 6OU 3.8 35.4 - - - +
1914A 9Z9 3.5 58.0 - - + +
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Residues in contact with ALA 444 (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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440A ASN 3.6 17.8 + - - +
441A LEU 3.5 4.8 + - - +
442A ILE 3.4 0.2 - - - -
443A LEU* 1.3 77.3 - - - +
445A VAL* 1.3 62.6 + - + +
447A ALA* 3.9 2.2 - - - -
448A MET* 3.3 28.6 + - + +
1597A ILE* 4.0 21.3 - - + -
1600A ASN* 3.9 26.2 - - + +
1601A PHE* 3.4 10.2 - - + -
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Residues in contact with VAL 445 (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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249A LYS* 3.7 28.2 - - + +
250A LEU* 3.7 19.0 - - + +
253A VAL* 3.8 19.3 - - + -
441A LEU* 3.2 28.1 + - + +
444A ALA* 1.3 79.9 - - + +
446A VAL* 1.3 62.2 + - - +
447A ALA 3.2 0.7 - - - -
448A MET* 3.9 19.0 - - + +
449A ALA* 3.0 27.5 + - - +
1471A LEU* 5.0 5.4 - - + -
1600A ASN* 6.2 0.4 - - + -
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Residues in contact with VAL 446 (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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246A SER* 4.7 12.7 - - - +
250A LEU* 3.9 20.4 - - + -
442A ILE* 3.2 22.7 + - + +
443A LEU 4.9 0.9 - - - +
445A VAL* 1.3 77.7 - - - +
447A ALA* 1.3 56.4 + - - +
449A ALA* 3.3 4.6 + - - +
450A TYR* 2.7 30.3 + - + +
791A LEU* 4.6 13.7 - - + -
794A LEU* 3.3 33.7 - - + -
795A ASN* 3.7 21.5 - - - +
798A LEU* 4.0 7.0 - - + -
1911A 6OU 5.4 0.2 - - + -
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Residues in contact with ALA 447 (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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443A LEU 3.5 10.5 + - - +
444A ALA 3.9 1.3 - - - +
445A VAL 3.2 0.4 - - - -
446A VAL* 1.3 77.4 - - - +
448A MET* 1.3 60.6 + - - +
450A TYR* 3.9 0.5 - - - +
451A ALA* 2.9 33.4 + - - +
798A LEU* 3.2 25.6 - - + +
802A LEU* 5.9 0.7 - - - +
1601A PHE* 3.9 12.6 - - + -
1914A 9Z9 3.4 34.7 - - + +
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Residues in contact with MET 448 (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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444A ALA 3.3 24.0 + - - +
445A VAL* 4.1 19.3 - - + +
446A VAL 3.4 0.2 - - - -
447A ALA* 1.3 78.8 - - - +
449A ALA* 1.3 60.2 + - - +
451A ALA* 4.2 3.0 - - - +
452A GLU* 3.4 27.9 + - - +
1600A ASN* 3.8 22.9 - - + +
1601A PHE* 3.5 31.6 - - + +
1604A ALA* 3.8 27.1 - - + -
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER* 4.4 22.7 - - - +
249A LYS* 3.8 36.0 - - + +
445A VAL 3.0 20.1 + - - +
446A VAL 3.9 2.9 - - - +
448A MET* 1.3 75.3 - - - +
450A TYR* 1.3 65.2 + - - +
452A GLU* 3.8 4.5 + - - +
453A GLN* 3.2 22.2 + - - +
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Residues in contact with TYR 450 (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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246A SER* 5.3 4.2 - - - -
446A VAL* 2.7 22.4 + - + +
447A ALA 3.9 2.9 - - - +
449A ALA* 1.3 73.1 - - - +
451A ALA* 1.3 54.0 + - - +
452A GLU 3.1 0.4 - - - -
453A GLN* 2.9 10.1 + - + +
454A ASN* 2.7 53.4 + - + +
700A LEU* 4.9 5.4 - - - +
703A LEU* 5.5 6.6 - - + +
795A ASN* 4.0 23.3 - - - +
798A LEU* 4.2 18.6 - - + -
799A ALA* 3.4 34.0 + - + +
802A LEU* 3.7 40.0 - - + +
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Residues in contact with ALA 451 (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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447A ALA 2.9 18.2 + - - +
448A MET* 4.2 3.4 - - - +
450A TYR* 1.3 78.1 - - + +
452A GLU* 1.3 57.1 + - - +
454A ASN* 4.1 10.4 - - - +
455A GLU* 3.4 20.8 + - - +
802A LEU* 4.4 22.0 - - + -
1601A PHE* 6.5 1.6 - - + -
1914A 9Z9 6.3 2.2 - - + -
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Residues in contact with GLU 452 (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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249A LYS* 4.9 11.6 - - - +
448A MET 3.4 20.7 + - - +
449A ALA* 4.1 6.4 - - - +
450A TYR 3.1 0.6 - - - -
451A ALA* 1.3 78.5 - - - +
453A GLN* 1.3 59.3 + - - +
454A ASN 3.4 0.2 - - - -
455A GLU* 3.5 10.3 + - - +
456A ALA* 3.1 27.3 + - + +
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Residues in contact with GLN 453 (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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242A ALA* 4.9 16.9 - - + +
245A GLN* 3.9 27.5 - - + +
449A ALA 3.2 17.1 + - - +
450A TYR* 2.9 11.0 + - + +
452A GLU* 1.3 74.9 - - - +
454A ASN* 1.3 65.1 + - - +
456A ALA* 3.4 15.7 + - - +
457A THR* 3.3 24.1 - - + +
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Residues in contact with ASN 454 (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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450A TYR* 2.7 39.8 + - + +
451A ALA* 4.2 6.7 - - - +
453A GLN* 1.3 73.3 - - - +
455A GLU* 1.3 58.3 + - - +
457A THR* 2.9 25.0 + - - -
458A LEU* 3.6 20.0 + - - +
802A LEU* 3.7 40.4 + - - +
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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
------------------------------------------------------------
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