Contacts of the strand formed by residues 38 - 55 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E VAL 5.1 0.2 - - - -
38E LEU* 3.6 32.1 - - + +
35F GLU* 3.3 28.7 - - + +
37F VAL* 1.3 82.0 - - - +
39F TYR* 1.3 66.5 + - - +
40F VAL* 4.2 7.6 - - + -
35G GLU* 4.0 9.9 - - - +
37G VAL 3.2 5.7 + - - -
38G LEU* 3.6 28.5 - - + -
39G TYR 3.0 27.1 + - - +
40G VAL* 5.6 0.6 - - - +
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Residues in contact with TYR 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E LEU 3.0 8.8 + - - +
39E TYR* 3.4 53.2 - + + -
40E VAL 3.0 25.9 + - - +
42E SER* 3.9 8.0 + - - +
37F VAL* 3.5 24.7 - - + -
38F LEU* 1.3 78.3 - - - +
40F VAL* 1.3 63.4 + - - +
42F SER* 4.0 14.4 - - - +
37G VAL* 4.0 5.2 - - - +
39G TYR* 3.4 52.7 - + + -
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Residues in contact with VAL 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E LEU* 5.6 1.6 - - + +
40E VAL* 3.3 26.0 - - + +
38F LEU* 5.1 6.7 - - + -
39F TYR* 1.3 81.8 - - - +
41F GLY* 1.3 72.8 + - - +
42F SER* 3.7 0.8 + - - -
39G TYR 3.0 10.0 + - - +
40G VAL* 3.3 23.6 - - + +
41G GLY 3.2 14.2 + - - -
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Residues in contact with GLY 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E VAL 3.2 3.6 + - - -
41E GLY* 2.9 21.1 + - - -
39F TYR 4.3 0.2 - - - -
40F VAL* 1.3 72.9 - - - +
42F SER* 1.3 57.4 + - - +
43F LYS* 5.3 3.8 - - - -
41G GLY* 2.9 32.8 + - - -
42G SER 3.3 1.6 + - - +
43G LYS* 4.8 8.1 + - - -
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Residues in contact with SER 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E GLY 3.3 4.9 + - - -
42E SER* 3.4 13.4 - - - -
43E LYS 3.1 24.1 + - - +
39F TYR* 4.0 21.2 - - - -
40F VAL 3.9 2.1 + - - -
41F GLY* 1.3 80.0 + - - +
43F LYS* 1.3 69.1 + - - +
44F THR* 4.2 4.3 - - - -
39G TYR* 3.9 20.4 + - - +
42G SER* 3.4 15.5 + - - -
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Residues in contact with LYS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E GLY* 4.8 8.3 + - - -
43E LYS* 3.0 47.2 - - + +
41F GLY* 5.3 2.4 - - - -
42F SER* 1.3 83.4 + - - +
44F THR* 1.3 64.2 + - - +
45F LYS* 5.2 6.3 - - - -
42G SER 3.1 7.1 + - - +
43G LYS* 3.0 42.0 - - + +
44G THR* 2.9 29.5 + - - +
45G LYS* 4.8 13.6 - - - +
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Residues in contact with THR 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LYS* 2.9 17.2 + - - +
44E THR* 4.5 16.2 - - + -
45E LYS 3.1 23.8 + - - +
46E GLU* 5.7 2.2 - - + +
42F SER* 4.2 4.9 - - - -
43F LYS* 1.3 77.6 + - - +
45F LYS* 1.3 68.6 + - - +
46F GLU* 4.3 20.9 - - + +
44G THR* 3.4 18.4 - - + +
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Residues in contact with LYS 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 6.1 2.9 - - - -
43E LYS* 4.8 9.7 - - - +
45E LYS* 3.3 46.6 - - + +
43F LYS* 5.2 8.5 - - - -
44F THR* 1.3 82.1 + - - +
46F GLU* 1.3 65.9 + - - +
47F GLY 4.4 0.4 - - - -
48F VAL* 4.4 17.5 - - + -
44G THR 3.1 8.0 + - - +
45G LYS* 3.3 37.5 - - + +
46G GLU 3.0 24.5 + - - -
48G VAL* 4.5 10.5 - - + +
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Residues in contact with GLU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E LYS 3.0 10.4 + - - +
46E GLU* 3.3 27.4 - - + +
47E GLY 3.1 15.4 + - - -
80E LYS* 2.8 42.2 + - + +
44F THR* 4.3 16.8 - - + +
45F LYS* 1.3 81.2 - - - +
47F GLY* 1.3 68.4 + - - +
48F VAL* 4.3 0.8 - - - +
80F LYS* 5.7 0.2 - - - -
44G THR* 5.7 2.6 - - + +
46G GLU* 3.3 33.1 - - + +
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Residues in contact with GLY 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E GLY* 3.0 33.5 + - - -
48E VAL 3.2 1.2 + - - -
78E ALA* 3.7 3.9 - - - +
79E GLN 3.9 24.0 - - - -
80E LYS* 5.4 3.9 - - - +
45F LYS 4.4 0.6 - - - -
46F GLU* 1.3 68.8 - - - +
48F VAL* 1.3 60.1 + - - +
78F ALA* 3.9 5.4 - - - -
79F GLN 6.2 0.2 - - - -
46G GLU 3.1 3.8 + - - -
47G GLY* 3.0 20.6 + - - -
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Residues in contact with VAL 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E LYS* 4.5 15.3 - - + +
47E GLY 4.7 0.7 - - - +
48E VAL* 3.3 30.3 - - + +
78E ALA* 4.6 0.2 - - - -
45F LYS* 4.4 16.8 - - + -
46F GLU 4.2 16.4 - - - +
47F GLY* 1.3 81.6 - - - +
49F VAL* 1.3 71.7 + - - +
50F HIS* 5.8 2.0 - - + -
78F ALA* 3.5 5.9 - - - +
47G GLY 3.2 5.5 + - - -
48G VAL* 3.3 20.6 - - + +
49G VAL 3.1 22.7 + - - -
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Residues in contact with VAL 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E VAL 3.1 5.1 + - - +
49E VAL* 3.3 22.6 - - + -
50E HIS* 3.1 22.3 + - - +
76E ALA* 3.9 9.4 - - + -
77E VAL 3.2 33.7 - - - +
78E ALA* 3.9 1.6 - - + +
48F VAL* 1.3 79.2 - - - +
50F HIS* 1.3 67.4 + - - +
76F ALA* 3.3 40.6 - - + +
78F ALA* 4.3 0.9 - - + -
49G VAL* 3.3 18.2 - - + -
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Residues in contact with HIS 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E HIS* 3.2 47.2 + + - +
52E VAL* 5.1 0.7 - - + -
48F VAL* 5.8 2.9 - - + -
49F VAL* 1.3 82.5 - - - +
51F GLY* 1.3 61.7 + - - +
52F VAL* 2.9 28.3 - - + +
76F ALA* 5.2 0.4 - - - +
49G VAL 3.1 6.0 + - - +
50G HIS* 3.2 40.5 + + + +
51G GLY 3.1 22.0 + - - -
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Residues in contact with GLY 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E HIS 3.1 8.0 + - - +
51E GLY* 3.3 7.2 - - - -
52E VAL 3.1 23.4 + - - +
74E VAL* 4.8 8.7 - - - +
76E ALA* 5.4 3.7 - - - +
49F VAL* 4.8 2.4 - - - +
50F HIS* 1.3 74.1 + - - +
52F VAL* 1.3 65.6 + - - +
74F VAL* 4.7 13.9 - - - -
76F ALA* 5.4 5.2 - - - -
51G GLY 3.3 8.5 - - - -
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Residues in contact with VAL 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E VAL* 3.5 22.9 - - + +
50F HIS* 2.9 35.2 - - + +
51F GLY* 1.3 75.4 - - - +
53F ALA* 1.3 63.9 + - - +
54F THR* 4.5 11.9 - - - +
74F VAL* 5.2 4.4 - - - +
50G HIS* 5.1 0.4 - - + -
51G GLY 3.1 6.9 + - - +
52G VAL* 3.5 20.4 - - + +
53G ALA* 2.9 27.4 + - - +
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Residues in contact with ALA 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E VAL* 2.9 11.0 + - - +
53E ALA* 3.3 11.9 - - + +
54E THR* 3.1 23.8 + - - +
73E GLY 5.8 0.7 - - - +
74E VAL* 5.3 0.7 - - + -
51F GLY 4.3 0.2 - - - -
52F VAL* 1.3 74.9 - - - +
54F THR* 1.3 64.0 + - - +
55F VAL* 5.2 5.4 - - + -
73F GLY* 6.0 1.1 - - - -
74F VAL* 3.8 27.1 - - + +
53G ALA* 3.3 10.5 - - + +
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Residues in contact with THR 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E THR* 3.6 20.9 + - + +
52F VAL* 4.5 10.7 - - - +
53F ALA* 1.3 75.0 + - - +
55F VAL* 1.3 73.2 + - - +
56F ALA* 5.1 1.3 - - + +
53G ALA 3.1 9.7 + - - +
54G THR* 3.6 17.0 + - + -
55G VAL* 2.9 29.2 + - - +
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Residues in contact with VAL 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E THR* 2.9 18.3 + - - +
55E VAL* 3.4 18.1 - - + -
56E ALA* 3.1 23.9 + - - +
53F ALA* 5.2 5.8 - - + -
54F THR* 1.3 85.5 - - - +
56F ALA* 1.3 61.6 + - - +
57F GLU 3.6 18.8 - - - +
58F LYS 5.4 0.9 - - - -
59F THR* 4.8 18.6 - - + -
55G VAL* 3.4 23.8 - - + +
57G GLU 5.3 1.3 - - - +
59G 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