Contacts of the strand formed by residues 42 - 50 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ALA 3.9 0.6 + - - -
38A LEU 3.4 20.6 + - - -
40A GLU 2.7 29.8 + - - -
41A GLY 3.5 12.7 + - - -
42A ARG* 3.4 14.2 - - + +
21B THR* 4.1 3.6 - - - +
22B LEU* 2.8 34.1 + - - +
38B LEU* 2.7 37.4 + - - +
39B ALA 3.5 13.9 + - - +
40B GLU 3.3 3.3 - - - +
41B GLY* 1.3 82.1 - - - +
43B ARG* 1.3 63.0 + - - +
58B LEU* 3.9 21.7 - - + +
59B GLU* 3.1 31.7 + - - +
60B GLY* 4.0 3.8 + - - -
62B VAL* 3.7 15.2 - - - +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLY* 2.8 48.4 + - - +
20B GLN 3.5 4.3 - - - -
21B THR* 3.3 26.9 + - - +
42B ARG* 1.3 73.8 - - - +
44B ILE* 1.3 65.8 + - - +
45B LEU* 3.4 12.3 + - + +
58B LEU* 3.5 2.4 - - - -
59B GLU* 2.9 56.3 + - + +
89B GLU* 3.8 8.9 + - - -
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Residues in contact with ILE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.7 46.9 - - + +
18B LEU* 3.8 1.7 - - + -
19B GLY* 2.8 31.5 + - - -
20B GLN 2.8 21.1 + - - +
22B LEU* 4.3 13.0 - - + -
43B ARG* 1.3 71.2 - - - +
45B LEU* 1.3 63.0 + - - +
46B GLU 3.8 21.3 - - - +
56B PHE* 4.5 17.0 - - + -
57B ALA 3.7 5.4 - - - +
58B LEU* 3.7 18.2 - - + -
86B LEU* 6.5 0.9 - - + -
88B LEU* 4.2 23.6 - - + -
93B LEU* 6.3 0.4 - - + -
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.3 11.8 - - - +
19B GLY* 5.1 0.4 - - - +
43B ARG* 3.8 28.9 - - + +
44B ILE* 1.3 78.7 - - - +
46B GLU* 1.3 68.7 + - + +
57B ALA* 2.8 18.3 + - + +
58B LEU 4.3 2.7 - - - +
59B GLU* 3.8 34.8 - - + +
60B GLY 5.2 0.7 - - - +
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 4.7 3.7 + - - -
14B ARG* 2.8 43.6 + - - -
18B LEU* 3.4 10.6 - - - +
44B ILE* 3.7 3.4 - - - +
45B LEU* 1.3 86.6 - - + +
47B VAL* 1.3 85.4 + - - +
48B ASP* 4.1 14.6 - - - +
56B PHE* 3.6 2.4 - - - -
57B ALA* 2.8 39.9 + - + +
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 2.8 46.3 + - + +
13B LEU* 4.9 4.5 - - + -
14B ARG* 3.9 20.9 - - + +
17B VAL* 3.7 30.3 - - + -
18B LEU* 4.8 0.9 - - + -
44B ILE* 4.6 0.9 - - + -
46B GLU* 1.3 92.5 + - - +
48B ASP* 1.3 69.1 + - - +
54B LEU* 4.3 14.1 - - + -
55B LEU 3.6 4.7 - - - +
56B PHE* 3.9 21.8 - - + -
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Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 3.8 11.8 + - - +
46B GLU* 4.6 17.7 - - - +
47B VAL* 1.3 82.8 - - - +
49B ARG* 1.3 65.8 + - - +
54B LEU* 3.7 8.7 - - - +
55B LEU* 2.8 44.8 + - + +
57B ALA* 4.6 8.1 - - - +
63B GLU* 4.9 4.6 - - - +
109B ARG* 4.7 13.3 + - - -
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Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 3.6 27.2 - - - +
6B VAL* 3.7 11.9 - - + -
7B GLU* 2.7 53.8 + - - +
10B ARG* 3.9 15.4 - - - +
48B ASP* 1.3 80.6 - - - +
50B ARG* 1.3 66.4 + - - +
51B GLY 2.9 36.3 + - - +
53B PHE 3.3 14.4 - - - +
54B LEU* 4.5 3.4 - - + -
55B LEU* 4.0 2.5 - - - -
124B GLU* 2.9 36.8 + - - +
126B LEU* 5.9 4.0 - - - +
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Residues in contact with ARG 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ARG* 1.3 76.7 - - - +
51B GLY* 1.3 60.3 + - - +
52B LYS 3.1 0.2 + - - -
53B PHE* 2.8 33.9 + - - +
55B LEU* 3.6 16.7 - - + +
112B TYR* 6.1 2.0 - - + -
118B LEU* 3.5 27.2 + - + +
121B LEU* 3.2 23.6 + - + +
122B GLY 2.8 30.9 + - - -
123B PRO* 4.4 2.8 - - - +
124B GLU* 2.8 35.2 + - - +
157B ALA* 3.6 11.5 - - - +
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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