Contacts of the helix formed by residues 488 - 511 (chain A) in PDB entry 6FF7
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 ASP 488 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PRO* 5.5 0.2 - - - +
113A ILE* 6.1 5.4 - - + -
114A ARG 4.7 0.2 - - - -
115A ASP* 4.6 7.4 - - - +
116A VAL* 5.1 1.8 - - - +
487A LEU* 1.3 81.0 - - - +
489A TRP* 1.3 65.5 + - - +
490A VAL* 3.5 2.9 - - + +
491A GLU* 3.7 16.8 + - + +
492A VAL* 3.4 19.1 + - - +
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Residues in contact with TRP 489 (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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107A PRO* 5.8 3.6 - - + -
113A ILE* 3.3 25.7 + - - +
114A ARG* 3.4 16.7 + - + +
116A VAL* 5.3 5.2 - - + -
488A ASP* 1.3 72.9 - - - +
490A VAL* 1.3 61.1 + - - +
492A VAL* 3.1 8.9 + - - +
493A GLY* 3.0 24.1 + - - -
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Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TYR* 5.3 5.8 - - + -
488A ASP* 3.5 2.3 - - + +
489A TRP* 1.3 76.3 - - - +
491A GLU* 1.3 60.5 + - - +
493A GLY* 4.4 1.6 - - - +
494A LEU* 2.9 33.5 + - - +
558A VAL* 5.8 3.1 - - - +
561A HIS* 5.5 8.7 - - + +
562A VAL* 5.1 20.2 - - + +
565A ARG* 5.8 5.8 - - + -
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Residues in contact with GLU 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TYR* 4.9 17.4 - - + +
487A LEU* 5.0 6.3 - - + -
488A ASP* 3.7 24.6 + - + +
489A TRP 3.2 0.6 - - - -
490A VAL* 1.3 77.3 - - - +
492A VAL* 1.3 56.4 + - - +
494A LEU* 3.8 3.2 - - - +
495A GLN* 2.8 31.8 + - - +
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Residues in contact with VAL 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 6.4 1.8 - - + -
118A VAL* 5.7 9.2 - - + -
127A SER* 5.5 11.6 - - - +
129A VAL* 5.4 12.3 - - + -
487A LEU* 5.6 3.3 - - + +
488A ASP 3.4 10.5 + - - +
489A TRP* 3.1 11.2 + - - +
491A GLU* 1.3 78.8 - - - +
493A GLY* 1.3 57.1 + - - +
495A GLN* 3.3 6.7 + - - +
496A VAL* 2.9 29.8 + - - +
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Residues in contact with GLY 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 6.3 3.1 - - - -
489A TRP 3.0 13.6 + - - -
490A VAL* 3.9 2.2 - - - -
492A VAL* 1.3 74.5 - - - +
494A LEU* 1.3 59.0 + - - +
496A VAL* 3.3 4.4 + - - +
497A CYS* 3.0 29.5 + - - +
558A VAL* 4.3 19.9 - - - +
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Residues in contact with LEU 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO* 4.2 26.6 - - + +
178A TYR* 5.1 11.4 - - + +
490A VAL 2.9 21.1 + - - +
491A GLU* 4.2 3.6 - - - +
493A GLY* 1.3 71.4 - - - -
495A GLN* 1.3 56.8 + - - +
497A CYS* 4.1 5.2 - - - +
498A ARG* 2.9 31.6 + - - +
558A VAL* 4.6 4.8 - - - +
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Residues in contact with GLN 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 6.5 1.1 - - + -
70A ILE* 6.5 0.9 - - + -
127A SER* 4.9 14.1 - - - -
491A GLU 2.8 21.1 + - - +
492A VAL* 3.4 8.3 - - - +
493A GLY 3.2 0.2 - - - -
494A LEU* 1.3 77.9 - - - +
496A VAL* 1.3 57.2 + - - +
498A ARG* 3.3 6.6 + - - +
499A GLN* 2.9 29.5 + - - +
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Residues in contact with VAL 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ALA* 5.4 11.7 - - + +
99A VAL* 6.4 1.3 - - - -
102A LEU* 6.1 4.7 - - + -
127A SER* 5.2 15.9 - - - +
492A VAL 2.9 16.2 + - - +
493A GLY* 4.2 3.4 - - - +
495A GLN* 1.3 76.6 - - - +
497A CYS* 1.3 58.6 + - - +
499A GLN* 3.8 6.0 - - - +
500A GLY* 2.9 24.8 + - - -
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Residues in contact with CYS 497 (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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175A PRO* 5.6 7.0 - - + -
493A GLY 3.0 17.1 + - - +
494A LEU* 4.2 5.2 - - - +
496A VAL* 1.3 77.0 - - - +
498A ARG* 1.3 59.1 + - - +
500A GLY* 3.3 1.8 + - - -
501A TYR* 2.9 28.8 + - - +
551A LEU* 5.5 4.0 - - - +
554A THR 5.8 1.3 - - - +
555A LYS* 4.8 23.6 - - + +
558A VAL* 5.8 2.0 - - + -
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Residues in contact with ARG 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 6.3 2.9 - - + -
175A PRO* 5.6 6.8 - - + +
494A LEU 2.9 21.2 + - - +
495A GLN* 3.5 7.4 - - - +
497A CYS* 1.3 75.7 - - - +
499A GLN* 1.3 57.3 + - - +
501A TYR* 3.3 6.8 + - - +
502A ASN* 2.9 29.3 + - - +
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Residues in contact with GLN 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 5.9 0.5 - - - +
124A GLY 4.6 7.9 - - - +
125A ALA 3.7 23.6 - - - +
126A ILE* 5.2 3.8 - - + -
127A SER 6.0 0.4 - - - +
495A GLN 2.9 17.0 + - - +
496A VAL* 3.9 7.0 - - - +
498A ARG* 1.3 73.8 - - - +
500A GLY* 1.3 59.8 + - - +
502A ASN* 3.3 8.8 + - - +
503A MET* 2.9 29.5 + - - +
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Residues in contact with GLY 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A MET* 6.6 0.2 - - - -
496A VAL 2.9 17.5 + - - -
497A CYS* 3.7 2.7 - - - -
498A ARG 3.3 0.2 - - - -
499A GLN* 1.3 74.1 - - - +
501A TYR* 1.3 59.1 + - - +
503A MET* 3.4 4.1 + - - +
504A LEU* 2.9 32.4 + - - +
551A LEU* 5.8 8.7 - - - -
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Residues in contact with TYR 501 (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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497A CYS 2.9 16.9 + - - +
498A ARG* 3.3 7.4 + - - +
500A GLY* 1.3 75.9 - - - +
502A ASN* 1.3 56.2 + - - +
504A LEU* 4.5 2.9 - - - +
505A ASN* 2.9 37.3 + - + +
519A ASP 5.7 2.2 - - - +
520A TYR* 5.5 13.9 - - + +
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Residues in contact with ASN 502 (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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74A GLY 4.6 15.7 - - - +
75A ASP* 5.6 7.4 - - - +
76A MET* 5.6 8.0 - - + +
88A TYR* 4.6 13.3 - - + +
498A ARG 2.9 18.0 + - - +
499A GLN* 3.3 10.1 + - - +
501A TYR* 1.3 74.4 - - - +
503A MET* 1.3 57.1 + - - +
505A ASN* 5.3 1.6 - - - -
506A LEU* 3.3 23.0 - - - +
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Residues in contact with MET 503 (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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88A TYR* 3.9 26.9 - - + +
89A LEU* 4.8 8.0 - - - +
91A ALA* 5.7 0.7 - - + -
92A LEU* 5.1 12.1 - - + -
499A GLN 2.9 15.3 + - - +
500A GLY* 4.2 3.8 - - - +
501A TYR 3.2 0.2 - - - -
502A ASN* 1.3 77.8 - - - +
504A LEU* 1.3 59.1 + - - +
505A ASN 3.3 1.8 - - - -
506A LEU* 3.8 2.4 - - - +
507A LEU* 3.0 29.1 + - - +
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Residues in contact with LEU 504 (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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500A GLY 2.9 18.7 + - - +
501A TYR* 4.4 2.7 - - - +
503A MET* 1.3 76.9 - - - +
505A ASN* 1.3 58.5 + - - +
507A LEU* 4.2 7.7 - - - +
508A ILE* 4.1 13.0 + - - +
518A LEU* 4.8 11.0 - - + +
548A ARG* 6.2 5.2 - - + -
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Residues in contact with ASN 505 (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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501A TYR* 2.9 17.8 + - + +
502A ASN* 5.3 1.1 - - - -
504A LEU* 1.3 78.2 - - - +
506A LEU* 1.3 59.7 + - - +
507A LEU 3.3 0.7 - - - -
508A ILE* 3.2 8.8 + - - +
509A HIS* 2.9 25.7 + - - +
518A LEU* 5.0 18.2 - - + +
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Residues in contact with LEU 506 (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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76A MET* 6.0 4.5 - - + -
85A LYS* 5.5 13.2 - - + +
88A TYR* 6.0 0.4 - - + -
89A LEU* 6.2 5.8 - - + +
502A ASN* 3.3 22.5 + - - +
503A MET* 3.3 5.8 + - - +
505A ASN* 1.3 77.8 - - - +
507A LEU* 1.3 58.7 + - - +
509A HIS* 3.7 10.1 - - + +
510A ARG* 2.9 29.6 + - - +
255Z C 5.2 1.8 + - - +
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Residues in contact with LEU 507 (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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89A LEU* 6.1 3.4 - - + +
503A MET 3.0 16.4 + - - +
504A LEU* 4.2 9.2 - - - +
506A LEU* 1.3 75.9 - - - +
508A ILE* 1.3 56.8 + - - +
510A ARG* 3.3 5.3 + - - +
511A LYS* 3.0 30.4 + - - +
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Residues in contact with ILE 508 (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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504A LEU 4.1 6.8 + - - +
505A ASN* 3.2 14.3 + - - +
507A LEU* 1.3 78.7 - - - +
509A HIS* 1.3 62.3 - - - +
511A LYS* 3.4 12.1 + - - -
512A ASN 3.4 10.0 + - - -
513A LEU* 3.5 22.5 + - + +
514A ASN 4.5 3.2 + - - +
516A LEU* 5.0 18.2 - - + +
518A LEU* 6.1 2.9 - - + -
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Residues in contact with HIS 509 (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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505A ASN 2.9 16.3 + - - +
506A LEU* 3.8 10.5 - - + +
507A LEU 3.3 0.4 - - - -
508A ILE* 1.3 77.7 - - - +
510A ARG* 1.3 57.2 + - - +
512A ASN* 3.9 4.4 + - - +
514A ASN 6.0 0.7 - - - +
254Z G 3.1 26.7 + - - +
255Z C 4.1 11.4 - - - +
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Residues in contact with ARG 510 (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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506A LEU 2.9 17.9 + - - +
507A LEU* 3.8 5.6 - - - +
508A ILE 3.3 0.2 - - - -
509A HIS* 1.3 74.7 - - - +
511A LYS* 1.3 58.2 + - - +
512A ASN* 3.1 11.6 + - - +
254Z G 3.9 6.8 + - - -
255Z C 4.1 25.5 + - - +
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Residues in contact with LYS 511 (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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646 U 6.1 0.7 - - - +
507A LEU 3.0 17.5 + - - +
508A ILE* 3.4 5.7 + - - +
510A ARG* 1.3 74.3 - - - +
512A ASN* 1.3 68.7 + - - +
513A LEU* 3.3 6.5 + - + +
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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
------------------------------------------------------------
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