Contacts of the helix formed by residues 559 - 569 (chain B) in PDB entry 5SY1
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 VAL 559 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B TYR* 4.1 14.6 - - + -
229B VAL* 4.6 8.3 - - + -
232B ILE* 4.3 15.7 - - + -
557B HIS* 2.9 25.0 + - + +
558B PRO* 1.3 81.4 - - - +
560B MET* 1.3 61.9 + - - +
561B LYS 3.2 0.9 - - - -
562B ALA* 3.2 5.5 + - - +
563B PHE* 2.7 26.7 + - - +
12D GLU* 4.8 4.5 - - + +
13D PHE* 3.7 31.0 - - + -
16D ALA* 3.7 14.6 - - + -
69D PHE* 4.9 8.5 - - + -
73D MET* 4.8 5.6 - - + +
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Residues in contact with MET 560 (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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554B SER 4.7 2.9 - - - +
555B GLN* 3.5 33.9 - - - +
556B SER* 4.7 0.7 - - - -
557B HIS* 3.3 16.5 + - + +
559B VAL* 1.3 78.9 - - - +
561B LYS* 1.3 61.5 + - + +
562B ALA 3.3 0.2 - - - -
563B PHE* 3.6 9.5 - - - +
564B CYS* 3.3 32.2 + - - -
16D ALA* 4.1 12.0 - - + +
19D LEU* 3.6 36.3 - - + +
20D PHE* 3.7 24.5 - - + -
36D VAL* 4.6 21.5 - - + -
39D SER* 5.9 2.0 - - - +
40D LEU* 4.8 8.3 - - + +
69D PHE* 5.7 0.2 - - - -
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Residues in contact with LYS 561 (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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79B ASN* 5.9 0.4 - - - +
81B LEU 3.5 20.4 + - - -
82B ASP* 3.3 24.2 + - - +
83B HIS* 4.4 1.5 - - + +
218B GLU* 3.7 24.5 + - - +
219B ASP* 4.4 11.8 - - + +
225B TYR* 3.2 42.1 + - + +
556B SER* 4.7 17.5 - - - +
557B HIS 3.1 18.4 + - - +
558B PRO* 4.6 2.2 - - + -
560B MET* 1.3 79.8 - - + +
562B ALA* 1.3 60.0 + - - +
564B CYS* 4.2 2.6 + - - +
565B GLY* 4.0 10.7 + - - -
40D LEU* 4.1 36.5 - - + +
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Residues in contact with ALA 562 (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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225B TYR* 3.4 41.6 - - + +
226B ARG* 5.2 0.9 - - - -
229B VAL* 3.7 16.2 - - + -
558B PRO 3.8 8.2 + - - +
559B VAL 3.2 8.5 + - - +
561B LYS* 1.3 78.3 - - - +
563B PHE* 1.3 62.2 + - - +
564B CYS 3.4 0.2 - - - -
565B GLY* 3.4 9.8 + - - +
566B LEU* 3.7 10.4 + - - +
73D MET* 4.1 8.6 - - + +
77D MET* 5.1 3.5 - - + +
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Residues in contact with PHE 563 (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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559B VAL 2.7 20.2 + - - +
560B MET* 3.7 8.7 - - - +
561B LYS 3.4 0.6 - - - -
562B ALA* 1.3 71.8 - - - +
564B CYS* 1.3 68.5 + - - +
565B GLY 3.1 1.3 - - - -
566B LEU* 3.2 13.1 + - + +
567B LEU* 3.4 46.3 + - + +
20D PHE* 3.4 31.2 - + - -
28D ILE* 5.7 4.0 - - + -
33D LEU* 5.1 7.2 - - + -
56D VAL* 4.8 9.4 - - + -
64D ILE* 5.5 6.3 - - + -
69D PHE* 3.4 38.8 - + + -
72D MET* 4.4 18.4 - - + -
73D MET* 3.7 24.2 - - + -
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Residues in contact with CYS 564 (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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219B ASP* 4.5 7.9 - - - +
560B MET 3.3 16.4 + - - +
561B LYS 4.2 2.4 + - - +
562B ALA 3.4 0.4 - - - -
563B PHE* 1.3 81.1 - - - +
565B GLY* 1.3 57.7 + - - +
567B LEU* 3.6 2.7 - - - +
568B LEU* 2.8 32.3 + - - +
20D PHE* 4.4 11.7 - - - -
33D LEU* 5.7 0.2 - - - -
36D VAL* 4.4 21.5 - - - -
37D MET* 3.6 39.3 - - + +
40D LEU* 4.4 17.0 - - + -
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Residues in contact with GLY 565 (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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219B ASP* 4.8 8.9 + - - +
221B SER* 4.6 20.1 - - - -
561B LYS 4.0 6.0 + - - -
562B ALA* 3.4 12.1 + - - -
563B PHE 3.1 1.0 - - - -
564B CYS* 1.3 79.5 - - - +
566B LEU* 1.3 59.1 + - - +
568B LEU* 4.5 3.6 - - - -
569B GLN* 3.2 34.1 + - - +
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Residues in contact with LEU 566 (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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562B ALA 3.7 6.1 + - - +
563B PHE* 3.2 8.9 + - + +
565B GLY* 1.3 78.8 - - - +
567B LEU* 1.3 59.1 + - + +
570B SER* 2.6 34.3 + - - +
55D GLU* 5.0 1.6 - - - +
72D MET* 4.0 24.3 - - + +
73D MET* 3.7 26.9 - - - -
76D LYS* 4.1 30.7 + - + +
77D MET* 3.8 31.0 - - + -
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Residues in contact with LEU 567 (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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563B PHE* 3.4 49.9 + - + +
564B CYS 3.2 3.6 + - - +
566B LEU* 1.3 83.2 - - + +
568B LEU* 1.3 59.6 + - - +
570B SER* 4.0 2.8 + - - -
571B SER* 3.2 19.9 + - - -
33D LEU* 4.6 13.5 - - + -
37D MET* 3.9 18.2 - - + -
52D MET* 3.3 56.5 - - + +
53D ILE* 5.8 0.2 - - - -
55D GLU* 5.7 4.3 - - - +
56D VAL* 4.4 13.9 - - + -
64D ILE* 5.9 1.8 - - + -
72D MET* 4.9 7.0 - - + -
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Residues in contact with LEU 568 (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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217B SER* 4.3 2.7 - - - +
219B ASP* 3.5 26.2 - - - +
564B CYS 2.8 16.7 + - - +
565B GLY* 4.4 2.7 - - - +
567B LEU* 1.3 77.6 - - - +
569B GLN* 1.3 66.1 + - + +
570B SER 3.1 3.8 - - - -
571B SER* 2.6 31.7 + - - +
572B GLY* 3.2 6.6 + - - -
37D MET* 5.6 7.6 - - - -
42D GLN* 3.6 35.4 - - + +
44D PRO* 5.5 8.5 - - + -
48D GLU* 5.6 2.0 - - - +
52D MET* 5.0 5.6 - - + -
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Residues in contact with GLN 569 (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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219B ASP 5.0 1.0 + - - -
220B LEU* 3.9 17.6 - - - +
221B SER* 3.3 47.1 + - - +
565B GLY* 3.2 13.9 + - - +
568B LEU* 1.3 85.4 - - + +
570B SER* 1.3 58.2 + - - +
572B GLY* 4.5 3.1 - - - +
573B GLN* 3.6 34.3 - - - +
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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