Contacts of the helix formed by residues 59 - 67 (chain A) in PDB entry 2STW
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A PHE* 6.4 0.9 - - + -
57A ASP* 2.6 29.8 + - + +
58A PRO* 1.3 75.9 - - - +
60A GLU* 1.3 65.5 + - + +
62A ALA* 4.4 1.2 - - - +
63A ARG* 3.5 23.0 + - - +
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Residues in contact with GLU 60 (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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10A VAL* 6.0 1.6 - - - +
11A ILE* 5.9 2.8 - - - +
43A PHE* 4.1 33.0 - - + +
57A ASP 4.6 0.8 + - - -
59A ASP* 1.3 79.9 - - + +
61A VAL* 1.3 70.2 + - + +
63A ARG* 3.5 9.2 + - - +
64A ARG* 2.9 38.6 + - + +
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Residues in contact with VAL 61 (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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30A PHE* 6.0 0.9 - - + -
31A LEU* 5.3 6.7 - - + -
34A LEU* 4.4 27.1 - - + -
43A PHE* 5.8 7.4 - - + +
44A ILE* 5.2 12.6 - - + -
55A LEU* 6.1 3.4 - - + -
58A PRO* 3.8 21.7 + - + -
60A GLU* 1.3 80.1 - - + +
62A ALA* 1.3 64.4 + - - +
64A ARG* 3.1 7.7 + - - +
65A TRP* 2.9 41.3 + - + +
79A LEU* 5.5 5.8 - - + -
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Residues in contact with ALA 62 (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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58A PRO* 2.8 33.1 + - + +
59A ASP* 4.4 2.2 - - - +
61A VAL* 1.3 77.3 - - - +
63A ARG* 1.3 60.4 + - - +
65A TRP* 3.5 17.4 + - - +
66A GLY* 3.5 5.4 + - - -
74A MET* 4.1 23.5 - - - +
75A ASN 5.5 0.2 - - - +
76A TYR* 4.7 18.4 - - + +
79A LEU* 5.0 7.2 - - + -
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Residues in contact with ARG 63 (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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59A ASP 3.5 15.7 + - - +
60A GLU* 3.5 10.8 + - - +
61A VAL 3.2 0.4 - - - -
62A ALA* 1.3 76.4 - - - +
64A ARG* 1.3 67.0 + - - +
66A GLY* 3.4 1.8 + - - +
67A LYS* 2.9 26.0 + - + +
72A PRO 3.6 24.4 + - - +
73A LYS* 4.2 23.0 - - + +
74A MET 4.9 3.8 - - - +
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Residues in contact with ARG 64 (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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11A ILE* 3.2 44.9 - - - +
13A ALA* 5.1 5.6 - - - +
14A ALA* 5.1 10.7 - - - +
30A PHE* 5.6 14.9 - - + -
34A LEU* 6.0 5.4 - - - -
60A GLU* 2.9 31.3 + - + +
61A VAL* 3.6 7.4 - - + +
63A ARG* 1.3 76.7 - - - +
65A TRP* 1.3 64.2 + - + +
67A LYS* 3.0 24.3 + - + +
68A ARG* 3.1 23.0 + - + +
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Residues in contact with TRP 65 (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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27A LEU* 3.5 41.7 - - + -
30A PHE* 3.8 31.9 - + - -
31A LEU* 4.2 28.7 - - + -
61A VAL* 2.9 23.5 + - + +
62A ALA* 3.5 14.8 - - - +
64A ARG* 1.3 80.1 - - - +
66A GLY* 1.3 61.1 + - - +
68A ARG* 3.8 15.3 + - - +
69A LYS* 4.0 13.5 + - + +
74A MET* 5.9 1.3 - - + -
78A LYS* 4.8 17.0 - - + -
79A LEU* 3.4 41.7 - - + +
83A LEU* 5.8 1.1 - - + -
24C T 3.6 18.8 + - - -
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Residues in contact with GLY 66 (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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62A ALA 3.5 5.0 + - - -
63A ARG 3.4 5.0 + - - -
65A TRP* 1.3 79.0 - - - +
67A LYS* 1.3 63.0 + - - +
68A ARG 3.3 0.2 - - - -
69A LYS* 3.2 10.0 + - - +
71A LYS* 2.8 35.2 + - - +
72A PRO 5.7 0.4 - - - -
74A MET* 3.9 30.7 - - - +
78A LYS* 5.1 0.9 - - - -
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Residues in contact with LYS 67 (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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63A ARG* 2.9 19.7 + - + +
64A ARG* 3.0 18.0 + - + +
66A GLY* 1.3 74.0 - - - +
68A ARG* 1.3 55.0 + - + +
69A LYS 2.8 4.9 - - - -
70A ASN* 2.6 31.7 + - - +
71A LYS 3.6 8.7 + - - +
72A PRO* 5.5 3.4 - - + +
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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