Contacts of the helix formed by residues 460 - 473 (chain A) in PDB entry 6C90
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 460 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A LEU* 4.1 7.6 - - + -
440A GLN* 2.7 33.9 + - + +
441A VAL* 3.7 24.9 - - + -
458A GLY 4.0 0.2 + - - -
459A LEU* 1.3 70.8 - - - +
461A PRO* 1.3 72.8 - - + +
462A ILE* 4.3 3.4 - - + -
463A LEU* 2.8 25.8 + - + +
464A LYS* 3.0 10.6 + - - +
979A PHE* 3.7 21.8 - - + -
990A GLU* 4.0 8.1 - - + -
991A GLY* 4.4 0.8 - - - -
994A ILE* 3.4 26.5 - - + -
1034A ILE* 3.7 28.9 - - + -
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Residues in contact with PRO 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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459A LEU 3.2 7.8 - - - +
460A LEU* 1.3 81.6 - - + +
462A ILE* 1.3 58.7 + - - +
464A LYS* 3.2 15.1 + - + +
465A GLU* 2.9 44.8 + - + +
991A GLY* 4.8 2.7 - - - +
994A ILE* 3.6 32.3 - - + -
998A ARG* 3.7 38.1 - - - +
1034A ILE* 5.5 2.5 - - + +
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Residues in contact with ILE 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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427A ALA 3.5 26.5 - - - +
428A ILE* 4.2 4.7 - - + -
430A CYS* 3.6 20.6 - - - -
431A LEU* 4.0 20.4 - - + -
441A VAL* 5.8 0.4 - - + -
460A LEU* 3.0 2.2 + - + -
461A PRO* 1.3 80.1 - - - +
463A LEU* 1.3 72.4 + - + +
465A GLU* 4.4 7.6 - - - +
466A THR* 2.8 32.8 + - - +
1034A ILE* 4.0 28.7 - - + +
1037A ALA* 4.7 12.1 - - + -
1038A ALA 5.4 2.9 - - - +
1040A LEU* 3.5 21.0 - - + +
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Residues in contact with LEU 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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424A PHE* 3.7 35.9 - - + -
428A ILE* 4.5 11.0 - - + -
440A GLN* 3.6 45.3 - - + +
441A VAL* 3.9 12.6 - - + -
444A VAL* 4.1 10.3 - - + -
459A LEU* 5.1 4.0 - - + -
460A LEU* 2.8 27.1 + - + +
462A ILE* 1.3 81.2 - - + +
464A LYS* 1.3 59.8 + - - +
466A THR* 3.1 6.3 + - - +
467A ILE* 2.8 44.3 + - + +
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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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193A ALA* 5.6 7.2 - - - -
455A HIS* 3.1 45.1 - - + +
456A HIS 3.5 20.8 - - - +
457A GLY* 4.2 18.6 + - - -
459A LEU* 4.4 16.2 + - + +
460A LEU 3.0 11.2 + - - +
461A PRO* 3.6 17.8 - - + +
463A LEU* 1.3 77.2 - - - +
465A GLU* 1.3 58.7 + - + +
467A ILE* 3.4 6.7 + - - +
468A GLU* 2.9 40.1 + - - +
484A THR* 6.2 1.8 - - - +
995A ARG* 4.9 5.9 - - - +
1105A MLI 5.8 2.2 + - - -
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Residues in contact with GLU 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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193A ALA* 6.0 1.4 - - - +
196A ASN* 4.4 7.1 + - - -
461A PRO* 2.9 29.3 + - + +
462A ILE* 4.0 3.5 - - - +
464A LYS* 1.3 75.9 - - + +
466A THR* 1.3 66.1 + - - +
468A GLU* 3.3 13.2 + - - +
469A ILE* 3.0 28.9 + - - +
998A ARG* 5.7 2.1 + - - -
1038A ALA 4.3 1.7 - - - +
1039A SER* 3.0 29.5 + - - -
1040A LEU* 2.7 43.6 + - + +
1041A TYR* 4.0 17.6 - - + -
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Residues in contact with THR 466 (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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423A VAL* 4.4 14.5 - - + +
424A PHE* 4.1 28.7 - - + -
427A ALA* 3.4 12.2 - - + +
428A ILE* 5.6 0.7 - - - +
448A LEU* 4.9 1.6 - - + -
462A ILE* 2.8 21.4 + - - +
463A LEU* 3.1 13.2 + - - +
465A GLU* 1.3 76.8 - - - +
467A ILE* 1.3 58.7 + - - +
469A ILE* 3.3 6.3 + - - +
470A LEU* 2.9 45.7 + - + +
1040A LEU* 3.2 16.2 - - - +
688B ILE* 6.3 0.7 - - + -
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Residues in contact with ILE 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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444A VAL* 5.0 12.3 - - + -
448A LEU* 3.8 31.4 - - + -
454A ILE* 3.0 40.4 - - + +
455A HIS* 4.8 5.4 - - + -
459A LEU* 4.2 12.1 - - + -
463A LEU* 2.8 29.4 + - + +
464A LYS* 3.8 4.0 - - - +
466A THR* 1.3 70.7 - - - +
468A GLU* 1.3 62.3 + - - +
470A LEU* 4.4 1.1 - - - -
471A PHE* 2.9 28.1 + - - +
476A ILE* 3.4 20.6 - - + +
479A LEU* 3.8 18.8 - - + -
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Residues in contact with GLU 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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193A ALA* 5.6 3.6 - - - +
197A GLN* 2.9 24.0 + - - -
455A HIS* 2.8 34.1 + - + +
464A LYS* 2.9 33.7 + - - +
465A GLU* 3.6 5.9 - - - +
467A ILE* 1.3 78.1 - - - +
469A ILE* 1.3 57.1 + - - +
471A PHE* 3.3 2.5 + - - -
472A SER* 2.8 32.0 + - - -
485A PHE* 4.4 2.7 - - + -
491A MET* 3.7 26.0 - - + +
1041A TYR* 2.7 39.4 + - - +
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Residues in contact with ILE 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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423A VAL* 5.3 2.9 - - + -
465A GLU 3.0 17.9 + - - +
466A THR* 3.8 4.5 - - - +
468A GLU* 1.3 74.6 - - - +
470A LEU* 1.3 62.5 + - - +
472A SER* 3.0 23.0 + - - +
473A GLU* 3.2 13.9 + - + +
1040A LEU* 4.2 22.0 - - + -
1041A TYR* 3.9 23.8 - - + +
685B TYR* 4.1 31.2 - - + +
688B ILE* 4.1 32.5 - - + -
692B LEU* 4.3 11.4 - - + -
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Residues in contact with LEU 470 (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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420A VAL* 4.1 24.2 - - + +
423A VAL* 3.9 29.6 - - + -
424A PHE* 5.5 0.7 - - + -
448A LEU* 3.9 28.0 - - + -
466A THR* 2.9 28.0 + - + +
468A GLU 3.3 0.2 - - - -
469A ILE* 1.3 78.1 - - - +
471A PHE* 1.3 61.7 + - - +
473A GLU* 3.1 10.2 + - - -
475A LEU* 3.0 52.6 + - + +
476A ILE* 3.5 23.8 - - + -
692B LEU* 5.1 2.5 - - + -
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Residues in contact with PHE 471 (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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388A PRO* 4.6 7.9 - - + -
389A VAL 4.3 7.2 - - - -
390A ILE* 3.5 25.4 - - + -
467A ILE 2.9 17.2 + - - +
468A GLU* 3.8 4.5 - - - +
470A LEU* 1.3 76.5 - - - +
472A SER* 1.3 64.0 + - - +
474A GLY* 3.1 13.2 + - - -
476A ILE* 3.5 37.3 - - + +
479A LEU* 3.8 37.2 - - + -
485A PHE* 3.9 15.5 - + + -
491A MET* 3.7 22.7 - - + -
492A PRO 3.5 23.3 - - - +
493A ALA* 3.9 6.7 - - + -
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Residues in contact with SER 472 (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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468A GLU 2.8 16.3 + - - -
469A ILE* 3.0 20.4 + - - +
471A PHE* 1.3 78.6 - - - +
473A GLU* 1.3 66.9 + - - +
474A GLY 3.5 0.2 - - - -
490A ASN 4.2 6.5 - - - -
491A MET* 3.9 22.7 - - - +
697B ARG* 2.9 38.9 + - - +
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Residues in contact with GLU 473 (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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469A ILE* 3.2 18.8 + - + +
470A LEU* 3.1 5.6 + - - +
471A PHE 3.1 1.0 - - - -
472A SER* 1.3 89.8 + - - +
474A GLY* 1.3 57.7 + - - +
475A LEU* 3.4 5.1 + - + -
692B LEU* 3.8 26.9 - - + +
695B SER* 2.9 22.2 + - - +
696B PRO* 3.3 21.3 - - - +
697B ARG* 3.4 22.3 + - - +
698B ASN* 2.8 31.1 + - - +
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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