Contacts of the helix formed by residues 64 - 70 (chain A) in PDB entry 2BOO
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 PHE 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PRO* 4.1 29.4 - - + -
23A LEU* 4.0 13.5 - - + -
35A PHE* 4.3 4.9 - + - -
40A PHE* 3.8 23.6 - + - -
60A ALA 5.4 2.7 - - - -
62A ASP 3.1 0.6 - - - -
63A VAL* 1.3 92.0 - - + +
65A ASN* 1.3 62.1 + - - +
66A ALA* 3.1 3.8 - - - -
67A LEU* 3.0 35.9 + - + +
68A ARG* 3.2 29.2 + - - +
145A LEU* 4.2 6.3 - - + -
160A TRP* 3.8 19.3 - + - -
163A PHE* 3.6 29.8 - + - -
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Residues in contact with ASN 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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61A PRO 3.7 2.6 - - - +
62A ASP* 3.0 40.0 + - - +
63A VAL 3.5 1.0 + - - -
64A PHE* 1.3 76.6 - - - +
66A ALA* 1.3 64.0 + - - +
68A ARG* 3.1 27.6 + - - -
69A TYR* 3.1 59.6 + - + -
92A HIS* 2.8 27.6 + - - +
93A GLY 3.9 4.4 + - - +
94A LEU* 4.0 2.0 - - + -
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Residues in contact with ALA 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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64A PHE* 3.1 2.0 + - - +
65A ASN* 1.3 77.8 - - - +
67A LEU* 1.3 64.3 + - + +
69A TYR* 3.7 1.0 + - - +
70A THR* 3.3 29.0 + - - -
93A GLY 3.2 13.3 + - - +
94A LEU* 3.6 11.9 - - + -
134A ALA* 6.0 0.2 - - - -
139A LEU* 3.5 13.9 - - + +
140A LEU 3.4 31.4 - - - +
141A LEU* 4.6 9.4 - - + -
145A LEU* 6.3 2.0 - - + -
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Residues in contact with LEU 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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23A LEU* 4.5 13.7 - - + -
24A PRO* 3.4 7.4 - - - +
27A TRP* 3.3 64.8 + - + +
31A LEU* 4.1 20.9 - - + -
64A PHE* 3.0 36.7 + - + +
66A ALA* 1.3 77.2 - - + +
68A ARG* 1.3 67.4 + - - +
70A THR 3.4 4.3 - - - +
139A LEU* 4.2 7.6 - - + -
141A LEU* 4.9 7.2 - - + -
145A LEU* 6.0 0.7 - - + -
163A PHE* 4.2 8.5 - - + -
167A VAL* 4.1 17.3 - - + -
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Residues in contact with ARG 68 (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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20A PRO* 4.2 11.9 - - - +
21A ALA* 4.0 25.7 - - - +
22A ASN* 3.1 48.2 + - - +
23A LEU* 4.1 8.6 - - + +
24A PRO* 3.8 17.6 - - - +
61A PRO* 3.1 28.9 + - - +
64A PHE* 3.5 38.2 - - - +
65A ASN* 3.1 23.3 + - - +
67A LEU* 1.3 81.3 - - - +
69A TYR* 1.3 72.8 + - + +
70A THR 3.3 0.3 + - - -
71A PRO* 4.1 3.1 - - - +
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Residues in contact with TYR 69 (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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65A ASN* 3.1 48.6 + - + +
66A ALA 4.5 0.9 - - - +
68A ARG* 1.3 87.9 - - + +
70A THR* 1.3 59.1 + - - +
71A PRO* 3.6 8.0 - - - +
74A GLU* 4.4 3.6 - - - +
92A HIS* 5.0 6.4 + - - -
94A LEU* 3.9 22.0 - - + -
129A TYR* 5.1 0.7 + - - -
131A ARG* 3.3 64.3 + - + -
134A ALA* 3.2 33.4 - - + +
135A GLU* 3.9 15.4 - - + +
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Residues in contact with THR 70 (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 TRP* 2.8 21.8 + - - -
66A ALA 3.3 16.3 + - - +
67A LEU 3.4 4.4 - - - +
68A ARG 3.2 0.4 - - - -
69A TYR* 1.3 78.3 - - - +
71A PRO* 1.3 64.6 - - - +
74A GLU* 4.4 2.5 - - + -
75A VAL* 3.7 25.1 - - + +
134A ALA* 2.8 22.2 + - - +
137A GLY* 3.8 31.6 - - - +
138A VAL 3.3 11.1 + - - -
139A LEU* 4.1 11.3 - - - +
140A LEU 5.1 0.2 + - - -
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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