Contacts of the helix formed by residues 55 - 66 (chain V) in PDB entry 2DYS
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 ASP 55 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53V ASN 3.5 5.4 + - - +
54V TYR* 1.3 77.5 - - - +
56V SER* 1.3 58.5 + - - +
57V MET* 3.4 12.0 + - - +
58V LYS* 3.1 43.6 + - + +
59V ASP* 3.0 26.0 + - - +
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Residues in contact with SER 56 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146O MET* 3.4 19.0 - - - +
147O GLU* 2.9 32.6 + - - -
187O SER 4.6 0.4 - - - -
189O PRO* 3.7 6.5 - - - +
54V TYR* 3.6 31.2 + - - -
55V ASP* 1.3 70.4 + - - +
57V MET* 1.3 61.5 + - - +
59V ASP* 3.3 1.4 + - - +
60V PHE* 2.8 30.1 + - - +
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Residues in contact with MET 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146O MET* 4.4 6.5 - - + -
215O PRO* 3.3 39.0 - - + -
218O TYR* 4.8 7.9 - - + -
55V ASP* 3.4 9.2 + - - +
56V SER* 1.3 76.2 + - - +
58V LYS* 1.3 56.5 + - - +
60V PHE* 3.3 7.2 + - + +
61V GLU* 2.7 62.1 + - - +
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Residues in contact with LYS 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55V ASP* 3.1 35.9 + - + +
56V SER 3.3 0.2 - - - -
57V MET* 1.3 77.9 - - - +
59V ASP* 1.3 61.4 + - - +
61V GLU* 3.3 7.3 + - + +
62V GLU* 2.9 54.0 + - + +
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Residues in contact with ASP 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188O ARG* 4.5 5.0 + - - +
189O PRO* 3.6 2.9 - - + +
127Q LYS* 2.8 41.9 + - - +
50V PHE* 5.7 0.5 - - - -
54V TYR* 2.6 39.6 + - + +
55V ASP 3.0 11.7 + - - +
56V SER 3.5 4.7 - - - +
57V MET 3.2 0.2 - - - -
58V LYS* 1.3 77.9 - - - +
60V PHE* 1.3 63.3 + - - +
62V GLU* 3.2 8.8 + - - +
63V MET* 3.0 46.5 + - - +
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Residues in contact with PHE 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146O MET* 4.7 0.4 - - - -
189O PRO* 3.6 19.9 - - + +
214O VAL* 3.8 11.4 - - + -
215O PRO* 3.3 38.1 - - + -
218O TYR* 3.7 30.1 - + - -
56V SER 2.8 17.9 + - - +
57V MET* 3.5 9.4 - - + +
59V ASP* 1.3 77.6 - - - +
61V GLU* 1.3 71.3 + - - +
63V MET* 3.1 6.5 + - - +
64V ARG* 2.8 34.2 + - + +
69V PHE* 3.2 34.8 - + - -
72V ALA* 3.5 25.1 - - + -
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Residues in contact with GLU 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O TYR* 3.3 13.6 + - - -
57V MET* 2.7 40.6 + - - +
58V LYS* 3.7 8.7 - - + +
60V PHE* 1.3 77.1 - - - +
62V GLU* 1.3 57.6 + - + +
64V ARG* 2.9 45.0 + - - +
65V LYS* 2.9 56.4 + - - +
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Residues in contact with GLU 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125Q ASP 5.3 0.4 - - - -
127Q LYS* 3.0 29.0 + - - +
140Q TYR* 6.1 0.5 - - - -
58V LYS* 2.9 51.9 + - + +
59V ASP* 3.5 7.1 - - - +
60V PHE 3.2 0.2 - - - -
61V GLU* 1.3 76.1 - - + +
63V MET* 1.3 62.4 + - - +
65V LYS* 3.5 13.6 + - + +
66V ALA* 3.1 22.7 + - - +
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Residues in contact with MET 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188O ARG* 6.1 0.7 - - - +
189O PRO* 3.1 25.8 - - + +
190O GLY* 3.7 17.5 - - - -
192O TYR* 5.2 0.7 - - - +
125Q ASP 3.5 22.7 - - - +
126Q MET 3.9 16.2 - - - +
127Q LYS* 4.3 10.1 - - + +
59V ASP* 3.0 45.1 + - - +
60V PHE 3.1 7.4 + - - +
62V GLU* 1.3 75.1 - - - +
64V ARG* 1.3 63.3 + - - +
66V ALA* 3.3 4.4 + - - +
67V GLY 3.2 13.9 + - - -
68V ILE* 3.3 42.2 + - + +
69V PHE* 3.5 9.6 - - + -
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Residues in contact with ARG 64 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O TYR* 3.8 18.8 + - - -
60V PHE* 2.8 20.4 + - + +
61V GLU* 2.9 42.4 + - - +
63V MET* 1.3 74.7 - - - +
65V LYS* 1.3 74.9 + - - +
67V GLY* 2.8 25.4 + - - +
68V ILE 5.1 0.2 - - - +
69V PHE* 4.0 8.3 - - + -
72V ALA* 3.3 38.1 - - + +
73V LYS* 2.9 38.3 + - - +
54X ARG* 4.3 0.9 + - - -
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Residues in contact with LYS 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61V GLU* 2.9 47.4 + - - +
62V GLU* 3.8 11.5 - - + +
64V ARG* 1.3 89.9 - - - +
66V ALA* 1.3 52.4 + - - +
73V LYS* 5.7 0.7 - - - -
54X ARG* 2.3 28.2 + - - -
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Residues in contact with ALA 66 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125Q ASP* 3.8 36.5 - - + +
62V GLU 3.1 14.3 + - - +
63V MET* 3.6 10.3 - - - +
64V ARG 3.1 1.0 - - - -
65V LYS* 1.3 75.9 - - - +
67V GLY* 1.3 60.9 + - - +
68V ILE* 3.6 1.1 - - + +
53X TRP* 3.5 15.8 - - - -
54X ARG* 3.2 17.8 + - - +
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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