Contacts of the strand formed by residues 38 - 55 (chain E) in PDB entry 2N0A
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 38 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D VAL* 5.1 0.4 - - - -
38D LEU* 3.6 32.3 - - + +
35E GLU* 3.3 28.7 - - + +
37E VAL* 1.3 81.5 - - - +
39E TYR* 1.3 65.2 + - - +
40E VAL* 4.2 7.2 - - + -
35F GLU* 4.1 9.6 - - - +
37F VAL 3.2 6.1 + - - -
38F LEU* 3.6 27.4 - - + -
39F TYR 3.0 27.5 + - - +
40F VAL* 5.6 0.6 - - - +
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Residues in contact with TYR 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU 3.0 8.8 + - - +
39D TYR* 3.4 52.8 - + + -
40D VAL 3.0 25.6 + - - +
42D SER* 3.9 8.2 + - - +
37E VAL* 3.5 24.5 - - + -
38E LEU* 1.3 76.7 - - - +
40E VAL* 1.3 64.0 - - - +
42E SER* 4.0 14.1 - - - +
37F VAL* 4.0 5.2 - - - +
39F TYR* 3.4 51.6 - + + -
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Residues in contact with VAL 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU* 5.6 1.6 - - + +
40D VAL* 3.3 26.5 - - + +
38E LEU* 5.1 7.0 - - + -
39E TYR* 1.3 83.3 - - - +
41E GLY* 1.3 72.0 + - - +
42E SER* 4.3 0.6 + - - -
39F TYR 3.0 10.0 + - - +
40F VAL* 3.3 23.7 - - + +
41F GLY 3.2 14.2 + - - -
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Residues in contact with GLY 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D VAL 3.2 3.4 + - - -
41D GLY* 2.9 21.6 + - - -
39E TYR 4.3 0.2 - - - -
40E VAL* 1.3 72.2 - - - +
42E SER* 1.3 56.5 + - - +
43E LYS* 5.3 3.8 - - - -
41F GLY* 2.9 33.0 + - - -
42F SER 3.3 1.7 + - - +
43F LYS* 4.8 7.7 + - - -
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Residues in contact with SER 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLY 3.3 5.3 + - - -
42D SER* 3.4 13.7 + - - -
43D LYS 3.1 23.7 + - - +
39E TYR* 4.0 21.1 - - - -
40E VAL 3.9 2.3 + - - -
41E GLY* 1.3 79.0 + - - +
43E LYS* 1.3 67.9 + - - +
44E THR* 4.2 4.7 - - - -
39F TYR* 3.9 20.6 + - - +
42F SER* 3.4 16.6 + - - -
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Residues in contact with LYS 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLY 4.8 7.9 + - - -
43D LYS* 3.0 48.5 - - + +
41E GLY* 5.3 2.4 - - - -
42E SER* 1.3 83.1 + - - +
44E THR* 1.3 64.4 + - - +
45E LYS* 5.2 6.3 - - - -
42F SER 3.1 7.2 + - - +
43F LYS* 3.0 41.6 - - + +
44F THR* 2.9 29.1 + - - +
45F LYS* 4.8 13.6 - - - +
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Residues in contact with THR 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LYS 2.9 17.4 + - - +
44D THR* 4.5 16.2 - - + -
45D LYS 3.1 23.7 + - - +
46D GLU* 5.7 2.5 - - + +
42E SER* 4.2 4.9 - - - -
43E LYS* 1.3 76.7 + - - +
45E LYS* 1.3 69.0 + - - +
46E GLU* 4.3 20.4 - - + +
44F THR* 3.4 18.4 - - + +
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Residues in contact with LYS 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LYS* 4.8 10.9 - - - +
45D LYS* 3.3 47.0 - - + +
43E LYS* 5.2 8.3 - - - -
44E THR* 1.3 80.9 + - - +
46E GLU* 1.3 66.5 + - - +
47E GLY 4.3 0.4 - - - -
48E VAL* 4.4 17.0 - - + -
44F THR 3.1 6.9 + - - +
45F LYS* 3.3 38.8 - - + +
46F GLU* 3.0 24.5 + - - +
48F VAL* 4.5 10.7 - - + +
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Residues in contact with GLU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LYS 3.0 10.2 + - - +
46D GLU* 3.3 27.0 - - + +
47D GLY 3.1 15.1 + - - -
80D LYS* 2.8 40.8 + - + +
44E THR* 4.3 18.1 - - + +
45E LYS* 1.3 80.9 - - - +
47E GLY* 1.3 68.2 + - - +
48E VAL* 4.3 1.0 - - - +
80E LYS* 5.7 0.2 - - - -
44F THR* 5.7 2.4 - - + +
46F GLU* 3.3 33.1 - - + +
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Residues in contact with GLY 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLY* 3.0 33.5 + - - -
48D VAL 3.2 1.6 + - - -
78D ALA* 3.7 4.1 - - - +
79D GLN 3.9 23.6 - - - -
80D LYS* 5.4 4.1 - - - +
46E GLU* 1.3 70.0 - - - +
48E VAL* 1.3 59.4 + - - +
78E ALA* 3.9 6.1 - - - -
46F GLU 3.1 4.0 + - - -
47F GLY* 3.0 19.6 + - - -
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Residues in contact with VAL 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LYS* 4.5 15.3 - - + +
47D GLY 4.7 0.7 - - - +
48D VAL* 3.3 29.8 - - + +
78D ALA* 4.6 0.2 - - - -
45E LYS* 4.4 17.0 - - + -
46E GLU 4.2 16.6 - - - +
47E GLY* 1.3 81.0 - - - +
49E VAL* 1.3 70.9 + - - +
50E HIS* 5.8 2.0 - - + -
78E ALA* 3.5 5.3 - - - +
47F GLY 3.2 5.7 + - - -
48F VAL* 3.3 20.4 - - + +
49F VAL 3.1 23.2 + - - -
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Residues in contact with VAL 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D VAL 3.1 5.0 + - - +
49D VAL* 3.3 22.1 - - + -
50D HIS* 3.1 22.5 + - - +
76D ALA* 3.9 9.2 - - + -
77D VAL 3.2 34.8 - - - +
78D ALA* 3.9 2.0 - - + +
48E VAL* 1.3 78.7 - - - +
50E HIS* 1.3 67.0 + - - +
76E ALA* 3.3 41.5 - - + +
78E ALA* 4.3 0.7 - - + -
49F VAL* 3.3 18.6 - - + -
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Residues in contact with HIS 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D HIS* 3.2 47.6 + + + +
52D VAL* 5.1 0.7 - - + -
48E VAL* 5.8 3.1 - - + -
49E VAL* 1.3 82.1 - - - +
51E GLY* 1.3 61.9 + - - +
52E VAL* 2.9 28.7 - - + +
76E ALA* 5.2 0.4 - - - +
49F VAL 3.1 5.8 + - - +
50F HIS* 3.2 40.5 + + + +
51F GLY 3.1 22.3 + - - +
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Residues in contact with GLY 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D HIS 3.1 8.2 + - - +
51D GLY* 3.3 7.0 - - - -
52D VAL 3.1 23.4 + - - +
74D VAL* 4.8 9.0 - - - +
76D ALA* 5.4 3.8 - - - +
49E VAL* 4.4 2.6 - - - +
50E HIS* 1.3 73.0 - - - +
52E VAL* 1.3 65.1 + - - +
74E VAL* 4.7 14.1 - - - -
76E ALA* 5.4 5.2 - - - -
51F GLY 3.3 9.4 - - - -
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Residues in contact with VAL 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL* 3.5 22.9 - - + +
50E HIS* 2.9 34.8 - - + +
51E GLY* 1.3 75.0 - - - +
53E ALA* 1.3 63.1 + - - +
54E THR* 4.5 11.9 - - - +
74E VAL* 5.2 4.1 - - - +
50F HIS* 5.1 0.7 - - + -
51F GLY 3.1 6.5 + - - +
52F VAL* 3.5 21.1 - - + +
53F ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL 2.9 10.8 + - - +
53D ALA* 3.3 11.7 - - + +
54D THR* 3.1 24.1 + - - +
73D GLY 5.8 0.4 - - - +
74D VAL* 5.4 0.4 - - + -
52E VAL* 1.3 74.5 - - - +
54E THR* 1.3 63.9 + - - +
55E VAL* 4.3 6.5 - - + -
73E GLY* 6.0 1.8 - - - -
74E VAL* 3.8 26.9 - - + +
53F ALA* 3.3 10.5 - - + +
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Residues in contact with THR 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D THR* 3.6 20.9 + - + +
52E VAL* 4.5 10.9 - - - +
53E ALA* 1.3 75.2 + - - +
55E VAL* 1.3 72.4 + - - +
56E ALA* 5.1 1.6 - - + +
53F ALA 3.1 11.4 + - - +
54F THR* 3.6 17.0 + - + -
55F VAL* 2.9 29.1 + - - +
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Residues in contact with VAL 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D THR* 2.9 17.7 + - - +
55D VAL* 3.4 17.9 - - + -
56D ALA* 3.1 23.9 + - - +
53E ALA* 5.2 5.6 - - + -
54E THR* 1.3 85.5 - - - +
56E ALA* 1.3 61.9 + - - +
57E GLU 3.6 18.8 - - - +
58E LYS 5.4 0.9 - - - -
59E THR* 4.8 18.8 - - + -
55F VAL* 3.4 24.0 - - + +
57F GLU 5.3 1.1 - - - +
59F THR* 6.5 0.4 - - + -
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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
------------------------------------------------------------
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