Contacts of the strand formed by residues 42 - 50 (chain A) in PDB entry 1EE8
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 ARG 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A THR* 4.3 2.0 - - - -
22A LEU* 2.7 37.6 + - - +
38A LEU 2.7 24.4 + - - -
39A ALA 3.6 13.9 - - - +
40A GLU 3.9 2.5 - - - +
41A GLY* 1.3 85.1 - - - +
43A ARG* 1.3 59.4 + - - +
58A LEU* 3.9 21.3 - - + +
59A GLU* 3.1 31.0 + - - +
60A GLY* 3.7 6.5 + - - -
62A VAL* 3.5 20.4 - - - +
37B ALA 4.3 4.6 + - - -
38B LEU 3.7 5.3 + - - -
40B GLU 2.7 23.2 + - - -
41B GLY 3.3 21.4 + - - -
42B ARG* 3.4 28.1 - - - +
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Residues in contact with ARG 43 (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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19A GLY* 3.2 26.4 + - - +
20A GLN 3.3 5.8 - - - +
21A THR* 3.1 30.6 + - + +
42A ARG* 1.3 72.8 - - - +
44A ILE* 1.3 63.0 + - - +
45A LEU* 3.4 10.0 + - + +
58A LEU* 3.4 4.7 - - - -
59A GLU* 3.0 54.1 + - + +
89A GLU* 3.2 15.6 + - - -
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Residues in contact with ILE 44 (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 VAL* 3.7 44.9 - - + +
18A LEU* 4.8 1.1 - - - -
19A GLY* 2.7 33.3 + - - -
20A GLN 2.7 17.1 + - - +
22A LEU* 4.2 12.8 - - + -
43A ARG* 1.3 71.7 - - - +
45A LEU* 1.3 61.2 + - - +
46A GLU* 3.8 20.0 - - - +
47A VAL* 4.3 1.8 - - + -
56A PHE* 4.3 20.9 - - + -
57A ALA 3.6 5.6 - - - +
58A LEU* 3.6 16.6 - - + -
86A LEU* 6.1 1.6 - - + -
88A LEU* 4.2 25.6 - - + -
93A LEU* 5.8 0.4 - - + -
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Residues in contact with LEU 45 (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 LEU* 3.3 17.6 - - - +
19A GLY* 5.0 3.4 - - - +
43A ARG* 4.1 13.0 - - + +
44A ILE* 1.3 78.2 - - - +
46A GLU* 1.3 70.8 + - + +
57A ALA* 2.7 19.0 + - + +
58A LEU 4.3 2.5 - - - +
59A GLU* 3.6 48.7 - - + +
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Residues in contact with GLU 46 (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 ARG* 5.3 0.7 - - - -
14A ARG* 3.0 38.4 + - - -
18A LEU* 4.0 11.9 - - + +
44A ILE* 3.6 4.3 - - - +
45A LEU* 1.3 86.0 - - + +
47A VAL* 1.3 80.9 + - - +
48A ASP* 4.0 17.8 - - - +
56A PHE* 3.5 3.5 - - - -
57A ALA* 2.7 41.4 + - + +
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Residues in contact with VAL 47 (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 ARG* 2.9 35.7 + - - +
13A LEU* 5.2 4.0 - - + -
14A ARG* 3.7 20.2 - - + +
17A VAL* 3.7 30.5 - - + -
18A LEU* 4.5 1.8 - - + -
44A ILE* 4.3 1.3 - - + -
46A GLU* 1.3 90.5 + - - +
48A ASP* 1.3 60.5 + - - +
54A LEU* 4.0 31.2 - - + -
55A LEU 3.2 6.7 - - - +
56A PHE* 3.9 22.7 - - + -
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Residues in contact with ASP 48 (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 ARG* 4.0 10.1 + - - +
46A GLU* 4.1 24.0 - - - +
47A VAL* 1.3 80.3 - - - +
49A ARG* 1.3 60.8 + - - +
54A LEU* 3.5 7.3 - - - +
55A LEU* 2.7 50.9 + - + +
57A ALA* 4.6 9.2 - - - +
63A GLU* 5.3 3.3 - - - +
109A ARG* 4.7 10.4 + - - -
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Residues in contact with ARG 49 (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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3A LEU* 3.6 30.0 - - - +
6A VAL* 3.7 12.6 - - + -
7A GLU* 2.6 53.2 + - - +
10A ARG* 4.0 16.9 - - - +
48A ASP* 1.3 79.8 - - - +
50A ARG* 1.3 64.0 + - - +
51A GLY 2.9 31.2 + - - +
53A PHE 3.2 12.6 - - - +
54A LEU* 4.7 1.6 - - + -
55A LEU* 4.3 1.1 - - - -
124A GLU* 2.9 53.0 + - - +
126A LEU* 5.7 6.1 - - - +
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Residues in contact with ARG 50 (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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49A ARG* 1.3 74.8 - - - +
51A GLY* 1.3 60.2 + - - +
52A LYS 3.1 0.2 + - - -
53A PHE* 2.8 34.4 + - - +
55A LEU* 3.9 11.3 - - + +
118A LEU* 3.6 26.4 + - + +
121A LEU* 3.0 40.5 + - + +
122A GLY 2.9 26.7 + - - -
123A PRO* 4.6 2.6 - - - +
124A GLU* 2.4 42.5 + - - +
157A ALA* 4.0 2.0 - - - +
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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