Contacts of the helix formed by residues 508 - 519 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423B PHE 5.0 1.8 + - - -
506B PHE* 3.8 6.9 + - - -
507B PHE* 1.3 78.9 - - - +
509B PRO* 1.3 66.1 - - - +
510B ILE* 3.5 8.7 + - - +
511B ILE* 3.1 43.6 + - - +
512B LEU* 3.1 25.3 + - - +
13D HIS 4.8 2.8 + - - -
14D VAL* 3.7 19.8 - - - +
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Residues in contact with PRO 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B SER* 3.2 34.3 - - - +
79B ARG* 4.2 18.2 - - + +
81B TYR* 3.8 16.2 - - + +
453B LEU* 3.6 21.9 - - + +
507B PHE* 3.8 25.3 - - + +
508B SER* 1.3 84.7 - - - +
510B ILE* 1.4 57.1 + - + +
512B LEU 4.5 0.2 - - - +
513B THR* 2.7 37.4 + - - -
14D VAL* 5.4 3.4 - - + -
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Residues in contact with ILE 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 3.5 33.1 - - + -
78B SER* 3.7 15.9 - - - +
79B ARG* 3.6 38.1 - - + +
508B SER* 3.2 7.2 + - - +
509B PRO* 1.4 75.9 - - + +
511B ILE* 1.4 66.3 + - + +
513B THR* 3.3 3.1 + - - -
514B PHE* 3.0 19.1 + - - +
707B ASN 5.5 0.7 - - - +
708B VAL* 5.1 3.8 - - + -
711B ALA* 3.9 21.1 - - + -
715B TRP* 3.7 33.4 - - + +
13D HIS 5.6 4.7 - - - +
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Residues in contact with ILE 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ILE* 6.4 0.2 - - + -
494B TYR* 6.2 1.3 - - + -
506B PHE* 3.9 11.9 - - + -
508B SER* 3.1 29.6 + - - +
510B ILE* 1.4 75.8 - - + +
512B LEU* 1.3 68.9 + - + +
514B PHE* 3.0 8.8 + - + +
515B LEU* 2.9 33.9 + - + +
522B PHE* 3.8 61.0 - - + -
715B TRP* 4.4 25.6 - - + +
13D HIS* 6.3 2.7 - - + -
14D VAL* 5.8 0.2 - - + -
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 3.6 18.6 - - + +
424B ASN* 4.8 2.2 - - - -
453B LEU* 4.1 9.0 - - + -
455B PRO* 5.2 3.6 - - + -
458B PHE* 3.3 56.1 - - + -
478B VAL* 4.0 20.2 - - + -
507B PHE* 3.5 35.2 - - + -
508B SER 3.1 17.9 + - - +
509B PRO 4.0 3.1 - - - +
511B ILE* 1.3 77.7 - - + +
513B THR* 1.3 64.0 + - - +
515B LEU* 3.1 7.6 + - + -
516B GLN* 2.9 20.1 + - - +
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Residues in contact with THR 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LYS* 3.8 26.0 - - + +
75B PHE* 3.8 23.6 - - + -
78B SER* 3.2 16.6 - - - -
453B LEU* 3.9 15.5 - - - +
509B PRO 2.7 21.8 + - - -
510B ILE 3.5 4.7 - - - -
511B ILE 3.2 0.2 - - - -
512B LEU* 1.3 78.1 - - - +
514B PHE* 1.3 57.4 + - - +
516B GLN* 3.4 3.5 + - - +
517B THR* 2.8 41.2 + - - +
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Residues in contact with PHE 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 4.9 0.9 - - + -
75B PHE* 4.2 13.2 - + + -
492B ILE* 3.4 34.1 - - + -
510B ILE 3.0 11.5 + - - +
511B ILE* 3.0 13.0 + - + +
513B THR* 1.3 74.6 - - - +
515B LEU* 1.3 70.0 + - + +
517B THR* 3.2 4.4 + - - -
518B TYR* 3.1 53.6 + + + +
520B ALA* 3.7 18.8 - - + -
715B TRP* 3.5 50.3 - + + -
718B ILE* 4.5 7.0 - - + -
719B ALA* 4.1 8.1 - - + -
724B LEU* 4.4 7.9 - - + -
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Residues in contact with LEU 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B PHE* 4.2 6.3 - - + -
478B VAL* 3.6 41.5 - - + +
479B ARG* 4.3 3.6 - - - -
480B HIS* 4.4 7.9 - - - +
492B ILE* 5.6 2.0 - - + -
511B ILE* 2.9 25.0 + - + +
512B LEU* 3.5 17.5 - - + +
514B PHE* 1.3 81.4 - - + +
516B GLN* 1.3 53.7 - - - +
519B GLY* 2.8 35.2 + - - -
520B ALA* 3.2 29.5 + - + +
521B ILE 3.6 20.0 - - - +
522B PHE* 3.7 14.6 - - + +
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Residues in contact with GLN 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B LEU* 3.9 14.4 - - - +
454B ASP 5.4 0.2 + - - -
457B ASP* 4.6 9.1 + - - +
458B PHE* 3.5 22.2 - - + -
480B HIS* 3.7 34.4 + - + +
512B LEU 2.9 15.4 + - - +
513B THR* 3.9 4.3 - - - +
515B LEU* 1.3 75.5 - - - +
517B THR* 1.3 67.7 + - - +
518B TYR 3.4 0.5 + - - -
519B GLY* 3.8 4.5 + - - -
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Residues in contact with THR 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 4.4 2.9 - - + +
74B LYS* 3.7 30.2 + - + +
513B THR* 2.8 28.4 + - - +
514B PHE* 3.2 5.1 + - - -
516B GLN* 1.3 79.5 - - - +
518B TYR* 1.3 74.1 + - + +
725B GLU 5.0 1.0 - - - +
726B LEU* 3.5 32.1 - - + -
727B LYS* 4.9 13.9 + - - +
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Residues in contact with TYR 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP* 4.3 9.4 + - - +
71B LEU* 3.8 26.7 - - + +
490B ALA* 5.8 0.9 + - - +
514B PHE* 3.1 52.5 + + - +
517B THR* 1.3 81.6 - - + +
519B GLY* 1.3 64.8 + - - +
520B ALA* 4.3 7.1 - - + +
716B GLY* 5.3 0.2 - - - -
719B ALA* 3.5 16.7 - - + +
724B LEU* 3.5 47.0 + - + +
725B GLU 3.8 29.6 - - - -
726B LEU* 3.6 24.5 - - + +
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Residues in contact with GLY 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B HIS* 5.8 0.7 - - - -
483B THR* 3.4 23.8 - - - +
489B ALA* 3.4 23.6 - - - +
490B ALA 5.2 0.2 - - - -
515B LEU 2.8 13.8 + - - -
516B GLN 3.8 4.5 + - - -
517B THR 3.7 1.8 - - - -
518B TYR* 1.3 78.6 - - - +
520B ALA* 1.3 57.6 + - - -
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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