Contacts of the helix formed by residues 441 - 460 (chain A) in PDB entry 6AH0
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 VAL 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A PRO* 1.3 66.5 - - - +
442A LYS* 1.3 53.6 + - - +
443A VAL 2.3 6.3 + - - -
444A ARG* 2.2 41.1 + - - +
445A VAL 3.3 4.1 + - - -
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Residues in contact with LYS 442 (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 PRO* 3.1 3.3 - - - +
441A VAL* 1.3 75.8 - - - +
443A VAL* 1.3 59.5 + - - +
445A VAL* 3.5 3.6 + - - +
446A SER* 3.3 14.9 + - - -
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PRO 3.4 7.9 + - - -
441A VAL 2.3 11.1 + - - -
442A LYS* 1.3 67.9 - - - +
444A ARG* 1.3 64.0 + - - +
446A SER* 3.0 4.5 + - - +
447A TYR* 2.9 19.8 + - - -
610A HIS* 6.4 1.3 - - - +
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Residues in contact with ARG 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLY 5.6 1.2 - - - +
440A PRO 4.3 1.4 + - - -
441A VAL* 2.2 23.5 + - - +
443A VAL* 1.3 67.5 - - - +
445A VAL* 1.3 60.6 + - - +
447A TYR* 3.2 3.4 + - - +
448A GLN* 3.1 18.0 + - - -
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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
----------------------------------------------------------
441A VAL 3.3 6.9 + - - -
442A LYS* 3.5 4.2 + - - +
443A VAL 3.1 0.6 - - - -
444A ARG* 1.3 77.0 - - - +
446A SER* 1.3 61.6 + - - +
448A GLN* 3.1 4.1 + - - +
449A LYS* 3.0 19.8 + - - -
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Residues in contact with SER 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LYS 3.3 10.2 + - - -
443A VAL* 3.0 8.7 + - - +
445A VAL* 1.3 76.4 - - - +
447A TYR* 1.3 60.7 - - - +
449A LYS* 3.2 2.3 + - - +
450A LEU* 3.1 20.1 + - - -
607A ASP* 4.9 17.5 - - - +
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Residues in contact with TYR 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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275A GLY 6.0 1.3 - - - -
276A GLY* 5.7 1.1 - - - -
277A PRO 5.3 2.3 - - - -
431A TYR* 5.4 9.3 - - - +
443A VAL 2.9 13.1 + - - -
444A ARG* 3.2 4.6 + - - +
446A SER* 1.3 75.7 - - - +
448A GLN* 1.3 62.2 + - - +
450A LEU* 3.4 2.4 + - - +
451A LEU* 3.2 18.4 + - - -
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Residues in contact with GLN 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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276A GLY 4.8 1.9 - - - -
277A PRO* 3.7 30.0 - - - +
278A LYS 5.0 1.8 - - - +
444A ARG 3.1 13.0 + - - -
445A VAL* 3.1 4.6 + - - +
447A TYR* 1.3 75.3 - - - +
449A LYS* 1.3 63.2 + - - +
451A LEU* 3.2 3.6 + - - -
452A LYS* 3.1 17.5 + - - -
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Residues in contact with LYS 449 (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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445A VAL 3.0 13.6 + - - -
446A SER* 3.2 4.0 + - - +
448A GLN* 1.3 77.4 - - - +
450A LEU* 1.3 62.6 + - - +
452A LYS* 3.1 12.0 + - - +
453A TYR* 3.2 10.0 + - - -
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Residues in contact with LEU 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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431A TYR* 6.6 0.7 - - - +
446A SER 3.1 13.4 + - - -
447A TYR* 3.4 3.1 + - - +
449A LYS* 1.3 76.6 - - - +
451A LEU* 1.3 61.1 + - - +
453A TYR* 3.2 3.7 + - - +
454A TYR* 3.1 18.2 + - - -
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Residues in contact with LEU 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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277A PRO* 6.0 3.1 - - - -
447A TYR 3.2 13.0 + - - -
448A GLN 3.2 4.6 + - - -
450A LEU* 1.3 72.5 - - - +
452A LYS* 1.3 65.9 + - - +
454A TYR* 3.2 2.9 + - - +
455A VAL* 2.9 21.8 + - - -
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Residues in contact with LYS 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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448A GLN 3.1 9.2 + - - -
449A LYS* 3.1 9.1 + - - +
451A LEU* 1.3 77.9 - - - +
453A TYR* 1.3 62.0 + - - +
455A VAL* 3.3 1.3 + - - +
456A LEU* 3.0 20.1 + - - -
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Residues in contact with TYR 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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449A LYS 3.2 12.9 + - - -
450A LEU* 3.2 4.0 + - - +
452A LYS* 1.3 75.8 - - - +
454A TYR* 1.3 61.6 - - - +
456A LEU* 3.3 1.3 + - - +
457A ASN* 3.0 20.6 + - - -
27B U 4.5 18.1 + - - +
28B A 5.5 6.1 - - - -
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Residues in contact with TYR 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 LEU 3.1 13.9 + - - -
451A LEU* 3.2 5.1 + - - +
453A TYR* 1.3 75.4 - - - +
455A VAL* 1.3 61.3 + - - +
457A ASN* 3.4 2.8 + - - +
458A ALA* 3.1 18.7 + - - -
27B U 5.1 2.0 + - - -
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Residues in contact with VAL 455 (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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451A LEU 2.9 14.0 + - - -
452A LYS* 3.8 2.7 - - - +
454A TYR* 1.3 77.3 - - - +
456A LEU* 1.3 57.4 + - - +
458A ALA* 3.2 3.6 + - - +
459A LEU* 2.9 25.5 + - - -
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Residues in contact with LEU 456 (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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452A LYS 3.0 13.7 + - - -
453A TYR* 3.3 2.9 + - - +
454A TYR 3.2 0.2 - - - -
455A VAL* 1.3 77.6 - - - +
457A ASN* 1.3 61.5 + - - +
459A LEU* 3.2 3.1 + - - +
460A LYS* 3.0 21.3 + - - -
27B U 5.8 0.2 - - - -
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Residues in contact with ASN 457 (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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453A TYR 3.0 14.0 + - - -
454A TYR 3.9 2.5 - - - -
456A LEU* 1.3 76.4 - - - +
458A ALA* 1.3 61.3 - - - +
460A LYS* 3.2 11.3 + - - +
461A HIS* 3.7 10.0 + - - -
24B G 4.9 2.6 + - - -
27B U 4.7 25.8 + - - -
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Residues in contact with ALA 458 (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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454A TYR 3.1 14.4 + - - -
455A VAL 3.2 3.8 + - - -
457A ASN* 1.3 76.9 - - - +
459A LEU* 1.3 61.2 + - - +
460A LYS 3.3 0.5 + - - -
461A HIS* 3.8 7.1 + - - -
24B G 5.5 1.0 + - - -
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Residues in contact with LEU 459 (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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455A VAL 2.9 14.4 + - - -
456A LEU* 3.2 4.0 + - - +
458A ALA* 1.3 77.0 - - - +
460A LYS* 1.3 58.1 + - - +
461A HIS 3.3 5.0 + - - -
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Residues in contact with LYS 460 (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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456A LEU 3.0 14.7 + - - -
457A ASN* 3.2 4.8 + - - +
458A ALA 3.2 1.4 - - - -
459A LEU* 1.3 76.3 - - - +
461A HIS* 1.3 56.7 + - - +
462A ARG* 3.1 9.0 + - - -
24B G 5.7 0.5 + - - -
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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