Contacts of the strand formed by residues 70 - 75 (chain A) in PDB entry 3EYF
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A SER* 4.6 9.2 - - - -
23A CYS 3.8 4.8 - - - +
24A ARG* 4.9 6.2 - - + +
66A GLY* 3.4 4.5 - - - -
67A SER 3.3 26.1 + - - +
69A THR* 1.3 85.8 + - - +
71A PHE* 1.3 75.4 + - - +
72A THR* 4.9 4.0 + - - -
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Residues in contact with PHE 71 (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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22A SER* 3.2 8.3 - - - -
23A CYS* 2.9 44.5 + - + +
25A ALA* 4.8 4.5 - - + -
29A VAL* 3.6 17.5 - - + -
30A GLY 3.6 15.7 - - - -
31A GLY* 4.9 1.3 - - - -
33A LEU* 3.8 41.3 - - + -
35A TRP* 4.3 5.1 - - + +
51A ALA* 4.1 12.3 - - + -
65A SER 3.5 4.5 - - - +
66A GLY* 3.6 17.5 - - - -
67A SER* 3.5 20.9 - - - -
68A GLY 3.3 27.8 - - - -
69A THR* 3.7 10.8 - - - -
70A ASP* 1.3 77.9 + - - +
72A THR* 1.3 67.3 + - - +
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Residues in contact with THR 72 (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 THR* 4.5 15.5 - - + +
21A LEU 3.2 7.0 + - - +
22A SER* 4.6 6.1 - - - -
35A TRP* 4.0 6.9 + - - -
63A SER 3.8 0.3 - - - +
64A GLY* 3.4 4.0 - - - -
65A SER* 2.6 54.6 + - - +
70A ASP* 4.9 4.7 + - - -
71A PHE* 1.3 80.0 + - - +
73A LEU* 1.3 63.6 + - - +
74A THR* 3.4 22.0 - - - +
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Residues in contact with LEU 73 (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 THR* 3.5 1.4 - - - -
21A LEU* 2.6 51.3 + - + +
35A TRP* 3.6 51.3 - - + -
47A LEU* 4.4 7.2 - - + -
48A ILE* 3.7 30.1 - - + -
62A PHE* 5.1 2.5 - - + -
63A SER 3.5 7.4 - - - +
64A GLY* 4.6 0.2 - - - -
72A THR* 1.3 73.6 - - - +
74A THR* 1.3 67.0 + - - +
75A ILE* 4.7 9.0 - - + -
86A TYR* 3.7 35.9 - - + -
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Residues in contact with THR 74 (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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18A ARG* 3.8 36.4 + - + +
19A ALA 3.3 11.3 + - - +
20A THR* 4.6 5.0 + - - +
61A ARG 3.5 0.6 - - - +
62A PHE* 3.5 0.5 - - - -
63A SER* 2.7 51.0 + - - +
72A THR* 3.4 22.9 - - - +
73A LEU* 1.3 74.9 + - - +
75A ILE* 1.3 75.7 + - - +
76A THR* 4.4 5.4 - - + -
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Residues in contact with ILE 75 (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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17A GLU 3.9 1.4 - - - +
18A ARG* 3.3 0.7 - - - -
19A ALA* 2.8 40.7 + - + +
21A LEU* 4.8 3.1 - - + -
61A ARG* 3.2 23.6 - - + +
62A PHE* 3.7 30.5 - - + -
73A LEU* 4.7 11.0 - - + -
74A THR* 1.3 80.7 - - - +
76A THR* 1.3 65.4 + - - +
78A LEU* 3.6 23.5 - - + +
82A ASP* 3.8 15.3 - - + +
86A TYR* 4.1 13.2 - - + +
105A LEU* 4.0 26.9 - - + -
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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