Contacts of the helix formed by residues 508 - 519 (chain A) in PDB entry 5N4D
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 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423A PHE 5.0 1.8 + - - -
506A PHE* 3.8 7.1 + - - -
507A PHE* 1.3 79.1 - - - +
509A PRO* 1.3 67.2 - - - +
510A ILE* 3.5 7.6 + - - +
511A ILE* 3.1 41.0 + - - +
512A LEU* 3.1 24.1 + - - +
13C HIS 4.7 3.3 + - - -
14C VAL* 3.7 19.5 - - - +
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Residues in contact with PRO 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 3.2 30.5 - - - +
79A ARG* 3.8 23.1 - - - +
81A TYR* 3.8 15.7 - - + +
453A LEU* 3.5 22.0 - - + +
507A PHE* 3.6 26.4 - - + +
508A SER* 1.3 84.5 - - - +
510A ILE* 1.3 58.3 + - - +
512A LEU* 4.6 0.2 - - + -
513A THR* 2.7 34.0 + - - -
802A GOL 6.1 0.2 - - - +
14C VAL* 5.6 2.5 - - + -
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Residues in contact with ILE 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PHE* 3.6 32.8 - - + -
78A SER* 3.7 14.8 - - - +
79A ARG* 4.0 36.6 - - + +
508A SER* 3.1 6.1 + - - +
509A PRO* 1.3 76.1 - - + +
511A ILE* 1.3 66.0 + - + +
513A THR* 3.3 2.9 + - - -
514A PHE* 3.0 19.2 + - - +
707A ASN 5.4 0.2 - - - +
708A VAL* 5.1 7.4 - - + -
711A ALA* 3.9 20.6 - - + -
715A TRP* 3.6 34.1 - - + +
13C HIS 5.6 3.1 - - - +
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Residues in contact with ILE 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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494A TYR* 6.1 1.3 - - + -
506A PHE* 4.0 11.9 - - + -
508A SER* 3.1 29.5 + - - +
510A ILE* 1.3 75.9 - - + +
512A LEU* 1.3 68.1 + - + +
514A PHE* 3.1 9.6 + - + +
515A LEU* 2.9 31.2 + - + +
522A PHE* 3.7 60.1 - - + -
715A TRP* 4.1 27.4 - - + +
13C HIS* 6.2 3.1 - - + -
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Residues in contact with LEU 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A PHE* 3.5 19.1 - - + +
424A ASN* 4.8 3.1 - - - -
453A LEU* 4.2 9.0 - - + -
455A PRO* 5.3 3.1 - - + -
458A PHE* 3.3 55.4 - - + -
478A VAL* 4.0 19.7 - - + -
507A PHE* 3.4 36.8 - - + -
508A SER 3.1 14.4 + - - +
509A PRO 4.0 3.4 - - - +
511A ILE* 1.3 79.0 - - + +
513A THR* 1.3 58.7 + - - +
515A LEU* 3.2 7.1 + - + -
516A GLN* 2.9 25.5 + - - +
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Residues in contact with THR 513 (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 LYS* 3.8 32.5 - - + +
75A PHE* 3.9 16.6 - - + -
78A SER* 3.2 16.7 - - - -
453A LEU* 3.8 16.1 - - + +
509A PRO 2.7 22.5 + - - -
510A ILE 3.6 4.7 - - - -
512A LEU* 1.3 78.1 - - - +
514A PHE* 1.3 54.0 + - - +
516A GLN* 3.4 3.4 + - - +
517A THR* 2.7 43.9 + - - +
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Residues in contact with PHE 514 (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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71A LEU* 4.8 0.9 - - + -
75A PHE* 4.2 14.1 - + + -
492A ILE* 3.3 34.8 - - + -
510A ILE 3.0 13.3 + - - +
511A ILE* 3.4 11.0 - - - +
513A THR* 1.3 75.1 - - - +
515A LEU* 1.3 69.8 + - + +
517A THR* 3.2 4.2 + - - -
518A TYR* 3.0 55.1 + + - +
520A ALA* 3.7 19.5 - - + -
715A TRP* 3.4 50.3 - + + -
718A ILE* 4.5 2.2 - - + -
719A ALA* 4.0 11.4 - - + -
724A LEU* 4.3 8.5 - - + -
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Residues in contact with LEU 515 (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 PHE* 4.3 6.3 - - + -
478A VAL* 3.5 42.2 - - + +
479A ARG* 4.2 4.9 - - - -
480A HIS* 4.4 7.3 - - - +
492A ILE* 5.8 2.2 - - + -
511A ILE* 2.9 24.0 + - + +
512A LEU* 3.2 16.1 + - + +
514A PHE* 1.3 83.2 - - + +
516A GLN* 1.3 55.9 + - - +
519A GLY* 2.8 32.1 + - - -
520A ALA* 3.3 29.9 + - + +
521A ILE 3.5 19.1 - - - +
522A PHE* 3.7 14.8 - - + +
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Residues in contact with GLN 516 (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 LEU* 3.9 14.3 - - - +
454A ASP 5.4 0.3 + - - -
457A ASP* 4.6 8.5 + - - +
458A PHE* 3.6 22.5 - - + -
480A HIS* 3.6 34.4 + - + +
512A LEU 2.9 16.1 + - - +
513A THR* 3.9 4.7 - - - +
515A LEU* 1.3 76.2 - - - +
517A THR* 1.3 67.0 + - - +
518A TYR 3.4 0.2 + - - -
519A GLY* 3.9 4.6 + - - -
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Residues in contact with THR 517 (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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71A LEU* 4.4 2.7 - - + -
74A LYS* 3.7 29.0 + - + +
513A THR* 2.7 28.5 + - - +
514A PHE* 3.7 5.2 - - - -
516A GLN* 1.3 77.5 - - - +
518A TYR* 1.3 76.3 + - + +
725A GLU 5.0 0.7 - - - +
726A LEU* 3.5 31.9 - - + -
727A LYS* 4.9 16.3 + - - +
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Residues in contact with TYR 518 (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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67A ASP* 4.4 8.5 + - - +
71A LEU* 3.7 21.9 - - + +
490A ALA 5.8 0.7 + - - -
514A PHE* 3.0 52.0 + + - +
517A THR* 1.3 88.8 - - + +
519A GLY* 1.3 65.1 + - - +
520A ALA* 4.3 6.1 - - + +
716A GLY* 5.3 0.3 - - - -
719A ALA* 3.5 15.3 - - + +
724A LEU* 3.5 51.3 + - + +
725A GLU 3.8 20.9 - - - -
726A LEU* 3.7 30.1 - - + +
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Residues in contact with GLY 519 (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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480A HIS* 5.8 0.4 - - - -
483A THR* 3.3 25.7 - - - +
489A ALA* 3.3 23.0 - - - +
490A ALA 5.2 0.2 - - - -
515A LEU 2.8 13.9 + - - -
516A GLN 3.9 3.9 + - - -
517A THR 3.7 1.8 - - - -
518A TYR* 1.3 78.7 - - - +
520A ALA* 1.3 57.9 + - - -
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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