Contacts of the strand formed by residues 38 - 55 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G VAL* 5.2 0.2 - - - -
38G LEU* 3.6 31.4 - - + +
35H GLU* 3.3 27.6 - - + +
37H VAL* 1.3 81.4 - - - +
39H TYR* 1.3 66.1 + - - +
40H VAL* 4.2 7.4 - - + -
35I GLU* 4.0 10.1 - - - +
37I VAL 3.2 7.3 + - - +
38I LEU* 3.6 28.6 - - + -
39I TYR 3.0 27.1 + - - +
40I VAL* 5.6 1.0 - - - +
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Residues in contact with TYR 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G LEU 3.0 8.4 + - - +
39G TYR* 3.4 52.5 - + + -
40G VAL 3.0 26.2 + - - +
42G SER* 3.9 7.2 + - - +
37H VAL* 3.5 24.4 - - + +
38H LEU* 1.3 77.7 - - - +
40H VAL* 1.3 63.7 + - - +
41H GLY 4.3 0.2 - - - -
42H SER* 4.0 15.9 - - - +
37I VAL* 4.0 5.8 - - + +
39I TYR* 3.4 51.2 - + + -
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Residues in contact with VAL 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ALA 6.0 2.0 - - - +
12C LYS 6.0 1.8 - - - +
14C GLY* 5.9 7.0 - - - +
38G LEU* 5.6 1.3 - - + +
40G VAL* 3.3 26.0 - - + +
38H LEU* 5.1 6.7 - - + -
39H TYR* 1.3 82.2 - - - +
41H GLY* 1.3 72.9 + - - +
42H SER* 4.3 0.8 + - - -
39I TYR 3.0 10.4 + - - +
40I VAL* 3.3 24.1 - - + +
41I GLY 3.2 14.7 + - - -
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Residues in contact with GLY 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G VAL 3.2 3.8 + - - -
41G GLY* 2.9 20.9 + - - -
39H TYR 4.3 0.2 - - - -
40H VAL* 1.3 73.1 - - - +
42H SER* 1.3 57.6 + - - +
43H LYS* 5.3 3.8 - - - -
41I GLY* 2.9 33.0 + - - -
42I SER 3.3 1.4 + - - -
43I LYS* 4.8 8.3 + - - -
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Residues in contact with SER 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G GLY 3.3 5.3 + - - -
42G SER* 3.4 12.2 - - - -
43G LYS 3.1 24.9 + - - +
39H TYR* 4.0 21.1 - - - -
40H VAL 3.9 6.4 + - - -
41H GLY* 1.3 78.6 + - - +
43H LYS* 1.3 68.9 + - - +
44H THR* 5.1 4.7 - - - -
39I TYR* 3.9 16.2 + - - +
42I SER* 3.4 15.9 + - - -
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Residues in contact with LYS 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PHE* 6.0 2.8 - - - -
41G GLY 4.8 7.5 + - - -
43G LYS* 3.0 47.0 - - + +
41H GLY* 5.3 2.8 - - - -
42H SER* 1.3 82.9 + - - +
44H THR* 1.3 64.1 + - - +
45H LYS* 5.2 7.0 - - - -
42I SER 3.1 6.6 + - - +
43I LYS* 3.0 41.8 - - + +
44I THR* 2.9 29.1 + - - +
45I LYS* 4.9 13.0 - - - +
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Residues in contact with THR 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G LYS 2.9 17.8 + - - +
44G THR* 3.4 16.3 - - + -
45G LYS 3.1 23.1 + - - +
46G GLU* 5.7 1.8 - - + +
42H SER* 5.1 5.2 - - - -
43H LYS* 1.3 76.9 + - - +
45H LYS* 1.3 71.2 + - - +
46H GLU* 4.3 20.9 - - + +
44I THR* 3.4 19.4 - - + +
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Residues in contact with LYS 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G LYS* 4.9 9.7 - - - +
45G LYS* 3.3 46.5 - - + +
43H LYS* 5.2 8.3 - - - -
44H THR* 1.3 81.5 + - - +
46H GLU* 1.3 67.8 + - - +
48H VAL* 4.5 16.4 - - + -
44I THR* 3.1 9.1 + - - +
45I LYS* 3.3 37.2 - - + +
46I GLU 3.0 24.1 + - - -
48I VAL* 4.5 10.9 - - + +
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Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G LYS 3.0 9.6 + - - +
46G GLU* 3.3 26.2 - - + +
47G GLY 3.1 15.8 + - - -
80G LYS* 2.8 41.3 + - + +
44H THR* 4.3 17.3 - - + +
45H LYS* 1.3 80.5 - - - +
47H GLY* 1.3 67.9 + - - +
48H VAL* 4.3 1.2 - - - +
80H LYS* 5.7 0.2 - - - -
44I THR* 5.7 2.1 - - + +
46I GLU* 3.3 33.0 - - + +
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Residues in contact with GLY 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G GLY* 3.0 32.6 + - - -
48G VAL 3.2 1.2 + - - -
78G ALA* 3.7 4.1 - - - +
79G GLN 3.9 23.8 - - - -
80G LYS* 5.4 3.9 - - - +
46H GLU* 1.3 69.0 - - - +
48H VAL* 1.3 59.5 + - - +
78H ALA* 3.9 6.3 - - - -
79H GLN 6.2 0.4 - - - -
46I GLU 3.1 4.2 + - - -
47I GLY* 3.0 20.6 + - - -
48I VAL* 4.7 0.2 - - - +
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Residues in contact with VAL 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G LYS* 4.5 15.7 - - + +
47G GLY 4.7 0.4 - - - +
48G VAL* 3.3 30.7 - - + +
78G ALA* 4.6 0.2 - - - -
45H LYS* 4.5 16.6 - - + -
46H GLU 4.2 15.7 - - - +
47H GLY* 1.3 83.4 - - - +
49H VAL* 1.3 69.3 + - - +
50H HIS* 5.8 2.7 - - + -
78H ALA* 3.5 6.3 - - - +
47I GLY 3.2 5.1 + - - -
48I VAL* 3.3 20.7 - - + +
49I VAL 3.1 22.5 + - - -
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Residues in contact with VAL 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G VAL 3.1 5.7 + - - +
49G VAL* 3.3 21.7 - - + -
50G HIS* 3.1 22.9 + - - +
76G ALA* 3.9 9.6 - - + -
77G VAL 3.2 34.5 - - - +
78G ALA* 3.9 1.6 - - + +
48H VAL* 1.3 78.9 - - - +
50H HIS* 1.3 67.6 + - - +
76H ALA* 3.3 40.6 - - + +
78H ALA* 4.3 0.4 - - + -
49I VAL* 3.3 19.3 - - + -
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Residues in contact with HIS 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G HIS* 3.2 47.2 + + - +
52G VAL* 5.1 0.4 - - + -
48H VAL* 5.8 2.5 - - + -
49H VAL* 1.3 82.3 - - - +
51H GLY* 1.3 62.4 + - - +
52H VAL* 2.9 28.5 - - + +
76H ALA* 5.2 0.2 - - - +
49I VAL 3.1 6.0 + - - +
50I HIS* 3.2 40.1 + + + +
51I GLY 3.1 22.2 + - - +
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Residues in contact with GLY 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G HIS 3.1 7.8 + - - +
51G GLY* 3.3 7.2 - - - -
52G VAL 3.1 23.9 + - - +
74G VAL* 4.8 8.2 - - - +
76G ALA* 5.4 4.0 - - - +
49H VAL* 4.8 2.6 - - - +
50H HIS* 1.3 73.9 - - - +
52H VAL* 1.3 65.4 + - - +
74H VAL* 4.7 13.9 - - - -
76H ALA* 5.4 4.7 - - - -
51I GLY 3.3 8.7 - - - -
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Residues in contact with VAL 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G VAL* 3.5 23.1 - - + +
50H HIS* 2.9 35.4 - - + +
51H GLY* 1.3 73.5 - - - +
53H ALA* 1.3 65.3 + - - +
54H THR* 4.5 12.3 - - - +
74H VAL* 5.2 3.2 - - - +
50I HIS* 5.1 0.4 - - + -
51I GLY 3.1 7.1 + - - +
52I VAL* 3.5 21.3 - - + +
53I ALA* 2.9 27.5 + - - +
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Residues in contact with ALA 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G VAL* 2.9 10.9 + - - +
53G ALA* 3.3 11.9 - - + -
54G THR 3.1 23.4 + - - +
73G GLY 5.7 0.4 - - - +
74G VAL* 5.3 1.3 - - + -
51H GLY 4.3 0.2 - - - -
52H VAL* 1.3 75.3 - - - +
54H THR* 1.3 64.5 + - - +
55H VAL* 5.2 6.3 - - + -
73H GLY* 6.0 1.1 - - - -
74H VAL* 3.8 26.2 - - + -
53I ALA* 3.3 10.5 - - + +
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Residues in contact with THR 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G THR* 3.6 20.3 + - + +
52H VAL* 4.5 10.6 - - - +
53H ALA* 1.3 75.6 + - - +
55H VAL* 1.3 73.6 + - - +
56H ALA* 5.1 2.0 - - + +
53I ALA 3.1 10.4 + - - +
54I THR* 3.6 17.4 + - + -
55I VAL* 2.9 28.7 + - - +
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Residues in contact with VAL 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G THR* 2.9 17.9 + - - +
55G VAL* 4.5 17.9 - - + -
56G ALA* 3.1 24.6 + - - +
53H ALA* 5.2 5.8 - - + -
54H THR* 1.3 84.2 - - - +
56H ALA* 1.3 60.4 + - - +
57H GLU 3.6 18.6 - - - +
58H LYS 5.4 0.9 - - - -
59H THR* 4.8 18.4 - - + -
55I VAL* 3.4 23.6 - - + +
57I GLU 5.3 1.3 - - - +
59I 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