Contacts of the helix formed by residues 497 - 517 (chain N) in PDB entry 6NR8
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 ASN 497 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90N ASP* 3.8 8.8 - - - +
151N VAL* 3.8 11.1 - - - +
155N SER* 3.3 17.0 + - - -
397N ALA* 3.0 41.4 + - - +
400N ASN* 4.7 6.5 - - + -
401N ALA* 3.4 26.0 - - - +
407N VAL* 4.7 2.4 - - - +
408N VAL* 3.9 0.7 - - - -
496N ASP* 1.3 75.2 - - - +
498N TYR* 1.3 60.0 + - - +
499N CYS 4.2 2.0 - - - +
500N VAL* 3.3 24.7 + - + +
501N LYS* 3.0 24.9 + - - +
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Residues in contact with TYR 498 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131N LEU 4.8 0.3 + - - -
134N LEU* 3.3 49.7 + - + +
135N GLU* 3.5 19.1 + - - -
138N LYS* 3.5 24.5 - - + -
401N ALA* 6.2 0.4 - - - +
404N ASP* 4.0 10.7 + - - +
406N CYS* 3.4 23.6 - - + +
407N VAL* 4.1 3.4 - - - +
408N VAL* 3.6 32.7 - - + +
496N ASP 3.5 3.4 + - - -
497N ASN* 1.3 70.1 - - - +
499N CYS* 1.3 59.3 + - - +
501N LYS* 4.1 4.0 - - + -
502N LYS* 2.7 71.3 + - + +
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Residues in contact with CYS 499 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87N ILE* 4.8 9.9 - - - -
88N THR* 3.4 17.1 + - - -
185N PRO* 5.0 4.9 - - - -
400N ASN* 3.4 40.4 - - + -
404N ASP* 3.1 24.6 + - - +
497N ASN* 3.2 1.0 - - + +
498N TYR* 1.3 74.3 - - - +
500N VAL* 1.3 63.8 + - - +
502N LYS* 4.3 15.2 + - - +
503N GLN* 3.3 23.1 + - - +
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Residues in contact with VAL 500 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N GLN* 4.2 10.1 + - - +
88N THR* 3.7 12.6 - - + -
90N ASP* 3.5 37.0 - - + +
91N GLY* 3.9 21.3 - - - -
94N SER* 5.0 8.7 - - - +
496N ASP* 6.0 2.0 - - + -
497N ASN* 3.3 24.8 + - + +
498N TYR 3.2 0.2 - - - -
499N CYS* 1.3 78.2 - - - +
501N LYS* 1.3 62.1 + - - +
503N GLN* 3.3 3.1 + - - +
504N LEU* 2.8 37.9 + - + +
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Residues in contact with LYS 501 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134N LEU* 3.8 24.0 - - + -
408N VAL* 3.8 24.4 - - + +
410N GLY* 4.5 4.2 - - - -
412N GLY 5.6 2.2 - - - +
414N VAL* 3.9 26.6 - - + +
415N GLU* 4.0 19.9 + - - +
496N ASP* 4.4 19.6 + - - -
497N ASN 3.0 14.9 + - - +
498N TYR* 3.1 6.0 + - + +
500N VAL* 1.3 79.8 - - - +
502N LYS* 1.3 62.7 + - - +
504N LEU* 3.4 26.8 + - + +
505N LEU* 3.3 28.6 - - + +
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Residues in contact with LYS 502 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131N LEU* 4.4 5.3 - - + +
134N LEU* 3.8 14.1 - - + +
135N GLU* 5.6 1.8 - - - +
404N ASP* 5.1 5.1 + - - -
498N TYR* 2.7 56.4 + - + +
499N CYS* 4.3 21.8 + - - +
501N LYS* 1.3 75.3 - - - +
503N GLN* 1.3 62.1 + - - +
504N LEU 3.3 0.7 + - - -
505N LEU* 3.5 9.4 + - - +
506N HIS* 3.1 31.9 + - + +
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Residues in contact with GLN 503 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83N ALA* 4.9 6.3 + - - +
84N GLN* 3.3 23.3 - - - +
87N ILE* 3.4 43.7 - - + +
88N THR* 4.2 8.1 - - - +
499N CYS* 3.3 19.7 + - - +
500N VAL 3.3 3.7 + - - +
502N LYS* 1.3 78.8 - - - +
504N LEU* 1.3 62.6 + - - +
506N HIS* 3.2 31.8 + - - +
507N SER* 3.3 21.4 + - - +
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Residues in contact with LEU 504 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N GLN* 4.3 5.6 + - - +
91N GLY 5.2 0.9 - - - +
94N SER* 4.3 13.9 - - - +
95N ASN* 3.7 37.5 - - + +
98N ILE* 4.5 16.6 - - + -
415N GLU* 5.6 3.1 - - - +
447N ILE* 6.4 1.6 - - + -
500N VAL* 2.8 21.9 + - + +
501N LYS* 3.5 31.2 - - + +
502N LYS 3.2 0.6 - - - -
503N GLN* 1.3 78.7 - - - +
505N LEU* 1.3 64.0 + - + +
507N SER* 3.5 3.1 + - - +
508N CYS* 3.3 41.8 + - - +
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Residues in contact with LEU 505 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127N LYS* 3.3 41.4 - - + +
130N ALA* 3.7 20.6 - - + -
131N LEU* 3.7 17.9 - - + +
134N LEU* 3.7 19.1 - - + -
440N PHE* 4.8 14.1 - - + -
444N LEU* 6.5 0.9 - - + -
501N LYS* 3.3 29.2 - - + +
502N LYS 3.5 6.7 + - - +
503N GLN 3.2 0.6 - - - -
504N LEU* 1.3 84.9 - - + +
506N HIS* 1.3 58.5 + - - +
508N CYS* 4.5 1.7 - - - +
509N THR* 2.4 34.7 + - - +
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Residues in contact with HIS 506 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127N LYS* 3.5 20.4 + - - +
131N LEU* 3.9 33.0 - - + +
502N LYS* 3.1 38.2 + - + +
503N GLN* 3.2 23.7 + - - +
505N LEU* 1.3 78.0 - - - +
507N SER* 1.3 61.7 + - - +
509N THR* 3.4 1.7 + - - -
510N VAL* 3.3 31.8 + - + +
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Residues in contact with SER 507 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N VAL* 4.5 24.8 - - - +
83N ALA* 6.1 2.2 - - - -
84N GLN* 3.7 17.7 + - - -
95N ASN* 4.5 7.6 - - - +
503N GLN* 3.3 21.5 + - - +
504N LEU* 3.5 6.2 + - - -
506N HIS* 1.3 78.9 - - - +
508N CYS* 1.3 68.7 + - - +
510N VAL* 3.4 19.8 - - - +
511N ILE* 3.5 14.9 - - - +
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Residues in contact with CYS 508 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95N ASN* 3.7 25.1 - - - -
98N ILE* 3.7 28.5 - - + -
99N ILE* 3.8 18.3 - - + +
102N LEU* 3.7 20.2 - - + +
440N PHE* 6.2 3.8 - - + -
504N LEU* 3.3 33.8 + - - +
505N LEU* 4.5 2.2 - - - +
507N SER* 1.3 84.7 + - - +
509N THR* 1.3 64.5 + - - +
510N VAL 3.4 0.2 - - - -
512N ALA* 3.8 10.2 + - - +
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Residues in contact with THR 509 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102N LEU* 5.3 2.7 - - - -
123N PHE* 4.0 33.8 + - + +
124N GLU* 4.2 17.0 - - - +
127N LYS* 3.4 23.0 - - - +
440N PHE* 5.1 8.7 - - - -
505N LEU* 2.4 26.9 + - - -
506N HIS 3.8 4.0 - - - -
507N SER 3.3 0.4 - - - -
508N CYS* 1.3 79.9 - - - +
510N VAL* 1.3 64.3 + - + +
512N ALA* 3.7 2.4 + - - +
513N THR* 2.8 32.6 + - - +
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Residues in contact with VAL 510 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N LYS* 6.2 1.1 - - - +
80N VAL* 4.9 8.1 - - + -
127N LYS* 5.0 7.4 - - - +
506N HIS* 3.3 21.5 - - + +
507N SER* 3.4 14.8 - - - +
509N THR* 1.3 81.7 - - + +
511N ILE* 1.3 62.5 + - + +
513N THR* 3.3 8.4 - - - +
514N ASN* 2.7 36.8 + - - +
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Residues in contact with ILE 511 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N LEU* 3.6 44.2 - - + +
77N ILE* 4.2 10.8 - - + +
79N LYS* 5.8 2.9 - - - +
80N VAL* 3.7 31.9 - - + -
99N ILE* 4.3 20.4 - - + -
507N SER 3.5 16.2 - - - +
508N CYS 4.1 5.6 - - - +
510N VAL* 1.3 77.7 - - - +
512N ALA* 1.3 62.8 + - - +
514N ASN* 2.9 14.3 + - + +
515N ILE* 2.8 42.4 + - + +
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Residues in contact with ALA 512 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99N ILE* 5.2 4.7 - - + -
102N LEU* 3.7 33.9 - - + -
103N LEU* 5.0 10.1 - - + +
123N PHE* 4.5 11.4 - - + -
508N CYS 3.8 6.0 + - - +
509N THR 3.7 2.6 + - - +
511N ILE* 1.3 79.3 - - + +
513N THR* 1.3 64.3 + - - +
515N ILE* 3.6 15.0 + - + +
516N LEU* 3.4 29.1 + - - +
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Residues in contact with THR 513 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120N THR* 3.7 31.5 + - + +
123N PHE* 4.4 6.8 - - - +
509N THR* 2.8 26.5 + - - +
510N VAL* 3.3 14.3 - - - +
512N ALA* 1.3 76.8 - - - +
514N ASN* 1.3 63.7 + - - +
516N LEU* 3.1 6.1 + - - +
517N LEU* 3.1 38.6 + - + +
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Residues in contact with ASN 514 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47K MET* 3.3 29.7 - - + +
59K MET* 6.0 0.2 - - + -
76N LEU* 6.3 2.7 - - + -
79N LYS* 4.9 12.7 - - - +
510N VAL* 2.7 35.6 + - - +
511N ILE* 2.9 17.6 + - + +
513N THR* 1.3 77.8 - - - +
515N ILE* 1.3 63.9 + - + +
517N LEU* 3.3 9.9 + - - +
518N VAL* 3.2 26.9 + - - +
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Residues in contact with ILE 515 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20N LEU* 3.4 19.0 - - + +
23N ASN* 4.8 10.8 - - + +
24N ILE* 4.0 16.8 - - + +
27N ALA* 5.5 4.9 - - + -
73N THR* 6.4 2.2 - - + -
76N LEU* 5.0 14.8 - - + -
77N ILE* 6.6 0.2 - - + -
99N ILE* 6.1 5.2 - - + -
103N LEU* 3.9 31.4 - - + -
511N ILE* 2.8 35.9 + - + +
512N ALA* 3.9 11.2 - - + +
513N THR 3.2 0.4 - - - -
514N ASN* 1.3 77.2 - - - +
516N LEU* 1.3 59.6 + - + +
518N VAL* 2.9 33.9 + - + +
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Residues in contact with LEU 516 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46K MET* 3.4 14.4 - - - +
20N LEU* 3.9 27.8 - - + -
24N ILE* 5.8 2.0 - - + -
103N LEU* 6.0 3.6 - - + -
106N ALA* 5.6 5.6 - - + -
110N ILE* 4.5 8.7 - - + -
116N PRO* 3.5 23.7 - - + +
119N ILE* 4.2 7.2 - - + -
120N THR* 3.3 31.9 - - - +
123N PHE* 3.6 32.5 - - + -
512N ALA 3.4 8.3 + - - +
513N THR 3.1 7.0 + - - +
515N ILE* 1.3 81.4 - - + +
517N LEU* 1.3 62.2 + - - +
518N VAL 3.3 0.7 - - - -
519N ASP* 3.7 11.3 - - - +
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Residues in contact with LEU 517 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K SER* 3.3 27.4 - - - +
46K MET* 3.2 21.3 - - + +
47K MET* 2.5 65.6 + - + +
61K ASN* 5.7 0.2 - - - +
117N ARG* 4.4 16.6 - - - +
120N THR* 5.2 4.0 - - + +
513N THR* 3.1 26.8 + - + +
514N ASN* 3.6 14.1 - - - +
515N ILE 3.2 0.6 - - - -
516N LEU* 1.3 79.3 - - - +
518N VAL* 1.3 59.2 + - - +
519N ASP 3.5 1.1 + - - -
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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
------------------------------------------------------------
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