Contacts of the strand formed by residues 38 - 55 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F VAL* 5.1 0.4 - - - -
38F LEU* 3.6 31.2 - - + +
35G GLU* 3.3 28.0 - - + +
37G VAL* 1.3 82.0 - - - +
39G TYR* 1.3 66.7 + - - +
40G VAL* 4.2 7.6 - - + -
35H GLU* 4.0 9.6 - - - +
37H VAL 3.2 6.7 + - - +
38H LEU* 3.6 28.9 - - + -
39H TYR 3.0 27.1 + - - +
40H VAL* 5.6 0.6 - - - +
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Residues in contact with TYR 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F LEU 3.0 9.0 + - - +
39F TYR* 3.4 52.0 - + + -
40F VAL 3.0 26.0 + - - +
42F SER* 3.9 7.5 + - - +
37G VAL* 3.5 25.4 - - + -
38G LEU* 1.3 77.3 - - - +
40G VAL* 1.3 63.0 + - - +
41G GLY 4.3 0.2 - - - -
42G SER* 4.0 15.7 - - - +
37H VAL* 4.0 5.6 - - + +
39H TYR* 3.4 51.5 - + + -
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Residues in contact with VAL 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F LEU* 5.6 1.6 - - + +
40F VAL* 3.3 26.2 - - + +
38G LEU* 5.1 6.3 - - + -
39G TYR* 1.3 81.6 - - - +
41G GLY* 1.3 73.0 + - - +
42G SER* 4.3 0.6 + - - -
39H TYR 3.0 10.6 + - - +
40H VAL* 3.3 23.2 - - + +
41H GLY 3.2 14.0 + - - -
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Residues in contact with GLY 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F VAL 3.2 3.4 + - - -
41F GLY* 2.9 20.9 + - - -
39G TYR 4.3 0.2 - - - -
40G VAL* 1.3 73.3 - - - +
42G SER* 1.3 58.0 + - - +
43G LYS* 5.3 3.6 - - - -
41H GLY* 2.9 33.0 + - - -
42H SER 3.3 1.6 + - - -
43H LYS* 4.8 8.1 + - - -
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Residues in contact with SER 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F GLY 3.3 4.8 + - - -
42F SER* 3.4 12.8 - - - -
43F LYS 3.1 23.9 + - - +
39G TYR* 4.0 21.2 - - - -
40G VAL 3.9 1.7 + - - -
41G GLY* 1.3 79.0 + - - +
43G LYS* 1.3 69.5 + - - +
44G THR* 5.1 4.5 - - - -
39H TYR* 3.9 20.4 + - - +
42H SER* 3.4 15.7 + - - -
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Residues in contact with LYS 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PHE* 5.9 8.3 - - - -
41F GLY* 4.8 8.1 + - - -
43F LYS* 3.0 47.2 - - + +
41G GLY* 5.3 2.2 - - - -
42G SER* 1.3 82.3 + - - +
44G THR* 1.3 64.6 + - - +
45G LYS* 5.2 6.1 - - - -
42H SER 3.1 6.9 + - - +
43H LYS* 3.0 41.6 - - + +
44H THR* 2.9 29.4 + - - +
45H LYS* 4.9 13.5 - - - +
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Residues in contact with THR 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F LYS 2.9 18.2 + - - +
44F THR* 3.4 16.6 - - + -
45F LYS 3.1 23.7 + - - +
46F GLU* 5.7 2.0 - - + +
42G SER* 5.1 5.4 - - - -
43G LYS* 1.3 77.7 + - - +
45G LYS* 1.3 70.0 + - - +
46G GLU* 4.3 20.6 - - + +
44H THR* 3.4 19.2 - - + +
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Residues in contact with LYS 45 (chain G).
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* 4.8 20.1 - - - +
43F LYS* 4.8 9.7 - - - +
45F LYS* 3.3 45.5 - - + +
43G LYS* 5.2 8.5 - - - -
44G THR* 1.3 81.9 + - - +
46G GLU* 1.3 66.7 + - - +
48G VAL* 4.4 18.2 - - + -
44H THR 3.1 8.0 + - - +
45H LYS* 3.3 37.2 - - + +
46H GLU 3.0 24.1 + - - -
48H VAL* 4.5 11.6 - - + +
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Residues in contact with GLU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LYS 3.0 9.9 + - - +
46F GLU* 3.3 26.9 - - + +
47F GLY 3.1 15.8 + - - -
80F LYS* 2.8 42.1 + - + +
44G THR* 4.3 16.7 - - + +
45G LYS* 1.3 81.2 - - - +
47G GLY* 1.3 67.8 + - - +
48G VAL* 4.3 1.0 - - - +
80G LYS* 5.7 0.2 - - - -
44H THR* 5.7 2.4 - - + +
46H GLU* 3.3 33.2 - - + +
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Residues in contact with GLY 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F GLY* 3.0 32.9 + - - -
48F VAL 3.2 1.2 + - - -
78F ALA* 3.7 3.9 - - - +
79F GLN 3.9 23.6 - - - -
80F LYS* 5.4 3.7 - - - +
45G LYS 4.3 0.4 - - - -
46G GLU* 1.3 69.1 - - - +
48G VAL* 1.3 60.0 + - - +
78G ALA* 3.9 5.8 - - - -
79G GLN* 6.0 0.4 - - - -
46H GLU 3.1 4.2 + - - -
47H GLY* 3.0 20.6 + - - -
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Residues in contact with VAL 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LYS* 4.5 15.5 - - + +
47F GLY 4.7 0.7 - - - +
48F VAL* 3.3 29.8 - - + +
78F ALA* 4.6 0.2 - - - -
45G LYS* 4.4 15.9 - - + -
46G GLU 4.2 16.4 - - - +
47G GLY* 1.3 81.8 - - - +
49G VAL* 1.3 70.8 + - - +
50G HIS* 5.8 2.2 - - + -
78G ALA* 3.5 6.5 - - - +
47H GLY 3.2 5.7 + - - -
48H VAL* 3.3 20.8 - - + +
49H VAL 3.1 22.2 + - - -
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Residues in contact with VAL 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F VAL 3.1 5.9 + - - +
49F VAL* 3.3 21.5 - - + -
50F HIS* 3.1 22.9 + - - +
76F ALA* 3.9 9.6 - - + -
77F VAL 3.2 34.1 - - - +
78F ALA* 3.9 1.3 - - + +
48G VAL* 1.3 78.8 - - - +
50G HIS* 1.3 67.2 + - - +
76G ALA* 3.3 40.2 - - + +
78G ALA* 4.3 0.7 - - + -
49H VAL* 3.3 18.6 - - + -
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Residues in contact with HIS 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F HIS* 3.2 46.5 + + - +
52F VAL* 5.1 0.2 - - + -
48G VAL* 5.8 2.7 - - + -
49G VAL* 1.3 83.1 - - - +
51G GLY* 1.3 61.1 + - - +
52G VAL* 2.9 28.3 - - + +
76G ALA* 5.4 0.2 - - - -
49H VAL 3.1 6.0 + - - +
50H HIS* 3.2 40.2 + + + +
51H GLY 3.1 22.5 + - - +
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Residues in contact with GLY 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F HIS 3.1 8.0 + - - +
51F GLY* 3.3 6.6 - - - -
52F VAL 3.1 23.9 + - - +
74F VAL* 4.8 8.7 - - - +
76F ALA* 5.4 4.0 - - - +
49G VAL* 4.8 2.2 - - - +
50G HIS* 1.3 73.7 + - - +
52G VAL* 1.3 65.3 + - - +
74G VAL* 4.7 13.7 - - - -
76G ALA* 5.4 5.2 - - - -
51H GLY 3.3 8.5 - - - -
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Residues in contact with VAL 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F VAL* 3.5 22.4 - - + +
50G HIS* 2.9 35.2 - - + +
51G GLY* 1.3 74.8 - - - +
53G ALA* 1.3 65.2 + - - +
54G THR* 4.5 12.1 - - - +
74G VAL* 5.2 4.0 - - - +
50H HIS* 5.1 0.4 - - + -
51H GLY 3.1 7.1 + - - +
52H VAL* 3.5 21.0 - - + +
53H ALA* 2.9 27.1 + - - +
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Residues in contact with ALA 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F VAL* 2.9 10.9 + - - +
53F ALA* 3.3 11.7 - - + -
54F THR* 3.1 23.4 + - - +
73F GLY 5.7 0.9 - - - +
74F VAL* 5.3 1.1 - - + -
51G GLY 4.3 0.2 - - - -
52G VAL* 1.3 75.1 - - - +
54G THR* 1.3 64.9 + - - +
55G VAL* 5.2 6.1 - - + -
73G GLY* 6.0 1.1 - - - -
74G VAL* 3.8 26.5 - - + -
53H ALA* 3.3 10.5 - - + +
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Residues in contact with THR 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F THR* 3.6 20.5 + - + +
52G VAL* 4.5 11.3 - - - +
53G ALA* 1.3 75.2 + - - +
55G VAL* 1.3 73.3 + - - +
56G ALA* 5.1 1.6 - - + +
53H ALA 3.1 10.6 + - - +
54H THR* 3.6 17.6 + - + -
55H VAL* 2.9 29.0 + - - +
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Residues in contact with VAL 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F THR* 2.9 17.7 + - - +
55F VAL* 4.5 17.9 - - + -
56F ALA* 3.1 24.3 + - - +
53G ALA* 5.2 5.6 - - + -
54G THR* 1.3 85.9 - - - +
56G ALA* 1.3 61.0 + - - +
57G GLU 3.6 18.6 - - - +
58G LYS 5.4 0.9 - - - -
59G THR* 4.8 18.6 - - + -
55H VAL* 3.4 23.6 - - + +
57H GLU 5.3 1.3 - - - +
59H 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
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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