Contacts of the helix formed by residues 449 - 469 (chain A) in PDB entry 6R7X
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 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A GLN 3.7 5.4 + - - -
448A GLU* 1.3 85.8 - - - +
450A PHE* 1.3 77.0 + - - +
452A PRO* 3.6 5.8 - - - +
453A TYR* 2.9 30.5 + - - +
532A SER* 2.7 41.6 + - - -
535A LEU* 4.7 2.9 - - - +
536A LYS* 4.1 17.5 - - - -
540A VAL* 4.1 3.6 - - - +
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Residues in contact with PHE 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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445A GLN* 3.2 37.1 + - + +
446A ILE* 4.1 14.1 - - + +
449A SER* 1.3 86.2 + - - +
451A LEU* 1.3 61.6 + - - +
453A TYR* 3.2 9.0 + + + +
454A TRP* 2.9 27.7 + - - +
528A THR* 6.2 0.2 - - - -
532A SER* 4.4 11.4 - - - -
535A LEU* 4.3 15.3 - - + -
707A UMQ 3.6 44.9 - - + -
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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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446A ILE* 3.2 23.0 + - + +
447A MET* 3.9 26.9 - - + -
450A PHE* 1.3 78.8 - - - +
452A PRO* 1.3 60.1 - - + +
454A TRP* 3.3 26.8 + - + +
455A LEU* 3.0 42.8 + - + +
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Residues in contact with PRO 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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446A ILE 4.0 0.7 - - - +
447A MET 3.9 15.0 - - - +
448A GLU 3.6 16.8 - - - +
449A SER 3.6 13.5 - - - +
450A PHE 3.9 0.4 - - - +
451A LEU* 1.3 94.8 - - + +
453A TYR* 1.3 55.9 + - - +
455A LEU* 3.5 9.5 + - + +
456A GLN* 2.9 29.8 + - - +
540A VAL* 3.7 22.0 - - + +
541A PHE* 5.9 3.4 - - + -
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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 SER 2.9 21.3 + - - +
450A PHE* 3.2 8.9 + + - +
452A PRO* 1.3 72.2 - - - +
454A TRP* 1.3 64.4 + - - +
456A GLN* 3.3 1.9 + - + +
457A ARG* 2.9 68.8 + - + +
535A LEU* 3.8 32.1 - - + -
539A ARG* 3.8 28.7 - - + -
540A VAL* 3.7 13.2 - - + +
707A UMQ 2.3 41.0 + - + +
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Residues in contact with TRP 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 PHE 2.9 16.0 + - - +
451A LEU* 3.3 25.8 + - + +
453A TYR* 1.3 80.8 - - + +
455A LEU* 1.3 74.4 + - + +
457A ARG* 3.3 13.4 + - + +
458A LYS* 3.0 43.5 + - + +
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Residues in contact with LEU 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* 3.0 34.9 + - + +
452A PRO* 3.9 7.6 - - + +
454A TRP* 1.3 94.0 - - + +
456A GLN* 1.3 57.4 + - - +
458A LYS* 3.4 16.3 + - + +
459A HIS* 2.9 29.0 + - - +
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Residues in contact with GLN 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 PRO 2.9 19.0 + - - +
453A TYR* 3.7 5.8 - - + +
454A TRP 3.3 0.2 - - - -
455A LEU* 1.3 73.9 - - - +
457A ARG* 1.3 60.8 + - - +
459A HIS* 4.4 12.7 - - - +
460A GLY* 2.8 25.3 + - - -
484A LEU* 4.0 18.4 + - - +
487A GLU 4.6 2.8 - - - +
488A MET* 3.4 46.9 - - + +
489A GLY 4.8 1.0 + - - -
539A ARG 3.3 25.6 - - - +
540A VAL* 3.8 14.3 - - + +
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Residues in contact with ARG 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* 2.9 61.2 + - + +
454A TRP* 3.3 12.5 + - + +
456A GLN* 1.3 74.1 - - - +
458A LYS* 1.3 59.2 + - - +
460A GLY* 3.8 0.8 - - - -
461A VAL* 3.0 44.7 + - + +
707A UMQ 3.9 26.1 + - - +
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Residues in contact with LYS 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 TRP* 3.0 31.5 + - + +
455A LEU* 3.6 22.7 - - + +
457A ARG* 1.3 76.8 - - - +
459A HIS* 1.3 57.4 + - - +
461A VAL* 3.4 7.2 + - - +
462A ARG* 3.0 60.3 + - + +
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Residues in contact with HIS 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 LEU 2.9 17.8 + - - +
456A GLN* 3.9 20.0 - - - +
458A LYS* 1.3 76.5 - - - +
460A GLY* 1.3 58.1 + - - +
462A ARG* 3.4 31.9 + - - +
463A VAL* 2.9 43.2 + - + +
484A LEU* 4.8 4.3 - - + -
487A GLU* 2.5 50.7 + - + +
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Residues in contact with GLY 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 GLN 2.8 17.8 + - - -
457A ARG* 3.8 1.8 - - - -
459A HIS* 1.3 74.6 - - - +
461A VAL* 1.3 58.3 + - - +
463A VAL* 4.0 0.7 - - - +
464A LYS* 2.9 38.0 + - - +
484A LEU* 3.7 24.8 - - - +
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Residues in contact with VAL 461 (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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457A ARG* 3.0 31.6 + - + +
458A LYS* 3.8 6.7 - - - +
459A HIS 3.4 0.2 - - - -
460A GLY* 1.3 74.4 - - - +
462A ARG* 1.3 58.4 + - - +
464A LYS* 3.4 6.7 + - - +
465A ARG* 2.9 34.2 + - + +
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Residues in contact with ARG 462 (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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458A LYS* 3.0 43.4 + - + +
459A HIS* 3.5 35.9 + - + +
461A VAL* 1.3 77.7 - - - +
463A VAL* 1.3 58.3 + - + +
465A ARG* 3.4 25.4 + - - +
466A LYS* 2.9 28.8 + - + +
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Residues in contact with VAL 463 (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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459A HIS* 2.9 31.4 + - + +
460A GLY 4.0 3.1 - - - +
462A ARG* 1.3 76.8 - - + +
464A LYS* 1.3 59.7 + - - +
466A LYS* 3.3 7.7 + - + +
467A VAL* 2.9 35.9 + - + +
480A GLU* 4.7 6.3 - - + +
483A ILE* 4.1 25.6 - - + -
484A LEU* 4.2 28.0 - - + +
487A GLU* 3.9 21.5 - - - +
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Residues in contact with LYS 464 (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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460A GLY 2.9 22.8 + - - +
461A VAL* 3.6 7.4 - - - +
463A VAL* 1.3 78.6 - - - +
465A ARG* 1.3 56.7 + - - +
467A VAL* 3.3 4.9 + - + +
468A GLN* 2.9 53.3 + - + +
480A GLU* 3.2 40.8 + - - +
484A LEU* 4.5 18.7 - - - +
707A UMQ 5.6 7.2 + - - -
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Residues in contact with ARG 465 (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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461A VAL* 2.9 21.9 + - + +
462A ARG* 3.9 26.1 + - - +
464A LYS* 1.3 76.5 - - - +
466A LYS* 1.3 63.1 + - - +
468A GLN* 4.4 10.8 - - + +
469A ALA* 3.7 19.1 + - - +
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Residues in contact with LYS 466 (chain A).
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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62A GLU 5.2 8.6 + - - -
63A THR* 5.2 5.5 - - - +
66A ASN* 3.9 11.7 + - - -
462A ARG* 2.9 18.4 + - + +
463A VAL* 3.6 8.5 - - + +
464A LYS 3.2 0.2 - - - -
465A ARG* 1.3 80.5 - - - +
467A VAL* 1.3 73.9 + - + +
469A ALA* 3.4 21.7 + - - +
470A LEU* 4.7 8.9 - - - +
479A TYR* 3.8 23.6 + - - -
483A ILE* 5.3 8.0 - - + +
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Residues in contact with VAL 467 (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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463A VAL* 2.9 30.8 + - + +
464A LYS* 3.3 5.6 + - - +
466A LYS* 1.3 86.2 - - + +
468A GLN* 1.3 65.8 + - + +
469A ALA 3.2 1.4 + - - -
470A LEU* 3.3 34.8 - - + +
476A ALA* 4.6 13.9 - - + -
479A TYR* 4.6 16.6 - - + -
480A GLU* 4.0 39.5 - - + +
483A ILE* 5.0 5.2 - - + -
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Residues in contact with GLN 468 (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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464A LYS* 2.9 36.6 + - + +
465A ARG* 4.4 10.0 - - - +
466A LYS 3.4 0.2 - - - -
467A VAL* 1.3 79.4 - - + +
469A ALA* 1.3 58.2 + - - +
470A LEU* 3.4 4.8 + - - +
480A GLU* 6.1 0.4 - - - +
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Residues in contact with ALA 469 (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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465A ARG 3.7 14.3 + - - +
466A LYS* 3.4 14.7 + - - +
467A VAL 3.2 0.8 - - - -
468A GLN* 1.3 74.9 - - - +
470A LEU* 1.3 62.4 + - - +
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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
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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