Contacts of the helix formed by residues 508 - 522 (chain W) in PDB entry 6NE3
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 MET 508 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54J G 3.4 49.1 - - - +
55J C 3.3 12.3 - - - +
451W MET* 5.7 1.3 - - - -
454W ARG* 6.1 4.7 - - + +
455W LYS* 4.5 25.6 - - + -
458W ASN* 4.4 15.1 - - - +
462W LEU* 5.3 4.0 - - + -
506W SER* 3.1 20.9 + - - -
507W GLN* 1.3 82.7 - - + +
509W THR* 1.3 64.0 + - - +
510W ARG* 4.9 13.9 - - + +
511W VAL* 3.2 22.3 + - + +
512W LEU 3.2 6.4 + - - -
578W ASP* 6.1 0.2 - - - +
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Residues in contact with THR 509 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J C 2.7 40.5 + - + +
56J T 3.9 21.8 - - - +
506W SER 5.7 0.4 - - - -
507W GLN 4.3 4.0 - - - +
508W MET* 1.3 70.3 - - - +
510W ARG* 1.3 65.4 + - - +
512W LEU* 3.2 19.6 + - - +
513W ASP* 2.9 24.9 + - - +
528W ARG* 5.8 2.7 + - - -
530W ASP* 4.2 13.7 - - + +
558W SER* 5.1 4.3 - - - +
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Residues in contact with ARG 510 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG* 3.5 13.9 - - - +
20B LYS 3.2 38.1 + - - +
21B VAL* 3.4 30.0 - - - +
55J C 4.4 1.9 + - - +
462W LEU* 3.7 23.6 - - + +
508W MET* 3.3 13.4 - - + +
509W THR* 1.3 79.8 + - - +
511W VAL* 1.3 60.2 - - - +
513W ASP* 3.2 12.8 + - - +
514W ILE* 2.9 31.8 + - + +
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Residues in contact with VAL 511 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458W ASN* 3.8 17.3 - - + +
459W HIS* 5.3 3.8 - - + +
462W LEU* 3.7 28.5 - - + -
485W MET* 5.1 4.9 - - + -
506W SER* 3.3 20.4 - - - +
508W MET* 3.2 21.6 + - + +
510W ARG* 1.3 75.3 - - - +
512W LEU* 1.3 58.0 + - - +
514W ILE* 3.2 4.8 + - - +
515W LEU* 2.9 37.6 + - + +
577W TYR* 3.7 29.6 - - + -
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Residues in contact with LEU 512 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506W SER* 3.6 12.0 + - - +
508W MET 3.2 10.0 + - - +
509W THR* 3.2 21.3 + - - +
511W VAL* 1.3 77.3 - - - +
513W ASP* 1.3 57.1 + - - +
515W LEU* 3.4 7.1 + - - +
516W GLU* 2.9 26.3 + - - +
528W ARG* 3.5 40.2 - - + +
529W LEU 4.0 7.6 - - - +
530W ASP* 4.2 10.1 - - + -
556W MET* 4.0 18.0 - - + +
557W LEU* 3.6 40.8 - - - +
558W SER* 3.8 6.1 - - - +
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Residues in contact with ASP 513 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B HIS* 3.3 21.6 - - - +
19B ARG* 3.6 19.8 + - - +
509W THR 2.9 13.0 + - - +
510W ARG* 3.2 16.9 + - - +
512W LEU* 1.3 81.0 - - + +
514W ILE* 1.3 59.5 + - - +
516W GLU* 3.1 25.3 + - - +
517W ASP* 3.0 44.7 + - - +
528W ARG* 5.0 12.0 + - - +
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Residues in contact with ILE 514 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ARG* 3.7 33.7 - - + +
459W HIS* 4.6 9.4 - - + +
461W TYR* 5.2 10.5 - - + +
462W LEU* 4.5 13.7 - - + -
478W LEU* 3.8 26.5 - - + +
485W MET* 3.7 24.0 - - + -
510W ARG* 2.9 21.0 + - + +
511W VAL* 3.2 7.2 + - - +
513W ASP* 1.3 76.8 - - - +
515W LEU* 1.3 58.8 + - - +
517W ASP* 3.2 18.7 + - - +
518W TYR* 2.9 26.0 + - - +
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Residues in contact with LEU 515 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485W MET* 3.7 23.3 - - + -
488W LEU* 4.0 24.9 - - + -
492W LEU* 6.0 0.9 - - + -
504W ILE* 4.8 16.8 - - + -
506W SER* 5.5 1.8 - - - +
511W VAL* 2.9 37.8 + - + +
512W LEU* 3.7 6.7 - - - +
514W ILE* 1.3 73.6 - - - +
516W GLU* 1.3 60.5 + - - +
518W TYR* 3.8 26.1 - - + +
519W CYS* 2.9 33.2 + - + +
556W MET* 3.8 13.4 - - + +
577W TYR* 4.6 11.4 - - + -
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Residues in contact with GLU 516 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 4.4 9.5 + - - -
18B HIS* 4.4 1.9 - - - +
512W LEU 2.9 15.1 + - - +
513W ASP* 3.1 25.4 + - - +
515W LEU* 1.3 76.2 - - - +
517W ASP* 1.3 77.9 + - - +
519W CYS* 3.2 5.7 - - - -
520W MET* 3.0 43.5 + - - +
526W TYR* 3.8 31.8 + - + -
528W ARG* 5.0 13.5 + - - -
556W MET* 3.6 18.8 - - + -
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Residues in contact with ASP 517 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B HIS* 2.7 54.9 + - + +
474W THR* 4.1 14.4 + - + -
478W LEU* 5.5 4.5 - - + -
513W ASP* 3.0 18.2 + - - +
514W ILE* 3.5 16.1 - - + +
516W GLU* 1.3 96.0 - - - +
518W TYR* 1.3 57.8 + - - +
520W MET* 3.5 13.4 + - + +
521W TRP* 2.9 27.2 + - - +
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Residues in contact with TYR 518 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474W THR* 5.4 1.3 - - - -
475W ASP 6.2 0.7 - - - -
476W MET* 5.1 1.8 - - + -
478W LEU* 4.5 14.4 - - + -
479W VAL* 3.8 28.7 - - + -
485W MET* 5.2 3.1 - - - -
488W LEU* 3.6 12.8 - - + -
489W ASP* 3.3 33.0 + - + +
492W LEU* 3.5 31.4 - - + +
493W PRO* 5.6 0.3 - - - +
514W ILE 2.9 17.1 + - - +
515W LEU* 3.8 23.1 - - + +
516W GLU 3.2 0.2 - - - -
517W ASP* 1.3 78.4 - - - +
519W CYS* 1.3 63.4 + - + +
521W TRP* 3.0 12.2 + + - +
522W ARG* 2.8 56.6 + - + +
524W TYR* 4.9 1.0 + - - -
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Residues in contact with CYS 519 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515W LEU* 2.9 25.2 + - + +
516W GLU* 3.2 16.8 - - - -
518W TYR* 1.3 80.4 - - + +
520W MET* 1.3 56.1 + - - +
522W ARG* 4.2 1.3 - - - +
523W ASN 2.7 25.7 + - - -
524W TYR* 3.0 30.6 + - + +
526W TYR* 3.5 35.4 - - - -
554W VAL* 4.2 18.2 - - + -
556W MET* 3.9 5.4 - - - -
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Residues in contact with MET 520 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 4.5 24.9 - - - +
18B HIS* 4.8 6.3 - - + +
474W THR* 5.6 3.4 - - + -
516W GLU* 3.0 35.3 + - - +
517W ASP* 3.6 17.0 - - + +
519W CYS* 1.3 78.7 - - - +
521W TRP* 1.3 51.8 + - - +
523W ASN* 2.5 34.3 + - - +
524W TYR 5.2 0.9 - - - -
526W TYR* 4.7 19.3 - - + -
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Residues in contact with TRP 521 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473W THR* 4.5 14.8 - - - -
474W THR* 3.1 48.4 + - - +
475W ASP* 4.9 6.5 - - - -
476W MET* 4.0 14.6 - - + +
517W ASP 2.9 11.1 + - - +
518W TYR* 3.0 15.7 + + - +
520W MET* 1.3 78.4 - - - +
522W ARG* 1.3 99.2 + - + +
523W ASN* 3.5 12.0 + - - +
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Residues in contact with ARG 522 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476W MET* 2.7 47.4 - - - +
518W TYR* 2.8 40.4 + - + +
519W CYS 4.4 0.2 - - - +
521W TRP* 1.3 101.7 + - + +
523W ASN* 1.3 72.6 + - - +
524W TYR* 3.2 42.9 + - + +
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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