Contacts of the strand formed by residues 37 - 44 (chain A) in PDB entry 2EE3
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 LEU 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A VAL* 2.7 19.6 - - - +
36A ARG* 1.3 97.8 - - + +
38A VAL* 1.3 75.9 + - - +
39A ARG* 5.6 4.5 - - + +
54A GLU* 3.3 32.3 - - + +
55A ALA 3.3 27.1 - - - +
56A PRO* 4.6 2.7 - - + -
57A GLY 4.1 1.3 - - - +
80A LEU* 3.0 23.9 + - + +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TRP* 4.5 9.6 - - + +
35A VAL* 4.2 9.4 - - + -
37A LEU* 1.3 84.8 - - - +
39A ARG* 1.3 63.2 + - - +
40A VAL* 3.9 9.4 + - + +
53A THR 3.8 0.7 - - - +
54A GLU* 3.4 3.8 - - - +
55A ALA* 2.7 50.2 + - + +
56A PRO 3.8 4.0 - - - +
57A GLY* 3.7 24.7 - - - +
59A ALA 4.9 4.9 - - - +
77A VAL* 3.5 32.8 - - + -
78A THR 3.4 7.9 - - - +
79A CYS* 4.1 9.0 - - - -
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Residues in contact with ARG 39 (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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37A LEU* 5.7 3.9 - - + +
38A VAL* 1.3 71.6 - - - +
40A VAL* 1.3 63.2 + - - +
41A THR* 3.8 3.5 + - + +
52A GLN* 2.7 52.7 + - + +
53A THR 3.3 6.5 - - - +
54A GLU* 3.8 32.5 + - + +
78A THR* 2.7 39.7 + - - +
80A LEU* 4.3 17.8 - - + +
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Residues in contact with VAL 40 (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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26A VAL* 4.7 1.3 - - + -
28A TRP* 4.6 9.2 - - + -
38A VAL* 4.2 8.5 - - + +
39A ARG* 1.3 73.5 - - - +
41A THR* 1.3 63.7 + - - +
42A TYR* 4.3 1.7 + - - -
52A GLN* 3.1 4.5 - - - -
53A THR* 2.8 54.7 + - + +
55A ALA* 5.6 1.8 - - + -
62A ALA* 4.8 6.3 - - + -
64A LEU* 4.0 15.0 - - + -
75A VAL* 3.7 29.8 - - + -
76A ARG 3.7 5.6 - - - +
77A VAL* 3.7 35.4 - - + +
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Residues in contact with THR 41 (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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39A ARG* 4.4 5.6 - - + +
40A VAL* 1.3 80.5 - - - +
42A TYR* 1.3 61.2 + - - +
43A VAL* 5.8 0.2 - - - +
51A GLY 3.6 6.5 - - - +
52A GLN* 3.8 31.9 - - + +
74A THR 3.5 3.3 - - - +
76A ARG* 2.9 50.7 + - - +
78A THR* 4.1 6.9 + - - +
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Residues in contact with TYR 42 (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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40A VAL 4.5 1.1 - - - -
41A THR* 1.3 77.9 - - - +
43A VAL* 1.3 60.7 + - - +
49A HIS* 3.8 17.5 + + - -
50A SER* 3.1 4.2 - - - -
51A GLY* 2.8 50.7 + - - +
52A GLN* 3.7 18.4 + - - -
53A THR* 4.4 9.3 - - - -
64A LEU* 3.4 34.3 - - + -
65A GLY 3.3 25.5 + - - -
67A LEU* 3.6 28.7 - - + -
73A TYR* 4.4 8.7 - + + -
74A THR 3.4 7.4 - - - +
75A VAL* 4.2 18.8 - - + -
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Residues in contact with VAL 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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41A THR 5.8 0.2 - - - +
42A TYR* 1.3 76.4 - - - +
44A SER* 1.3 74.0 + - - +
45A SER 3.7 0.3 + - - -
47A GLY* 5.2 3.1 - - - -
48A GLY 4.1 9.6 - - - +
49A HIS 3.3 5.4 - - - +
50A SER* 3.6 20.4 - - - -
73A TYR* 3.4 5.5 - - - -
74A THR* 2.7 54.6 + - + +
76A ARG* 6.2 3.1 - - - +
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Residues in contact with SER 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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43A VAL* 1.3 78.9 - - - +
45A SER* 1.3 73.4 + - - +
47A GLY* 3.3 3.3 + - - -
48A GLY* 3.0 18.1 + - - -
49A HIS 2.7 32.3 + - - -
71A THR* 3.0 28.6 - - - +
72A THR 3.6 5.6 - - - -
73A TYR* 3.7 17.7 + - - -
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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