Contacts of the strand formed by residues 38 - 55 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H VAL* 5.2 0.2 - - - -
38H LEU* 3.6 30.5 - - + +
35I GLU* 3.3 28.5 - - + +
37I VAL* 1.3 81.7 - - - +
39I TYR* 1.3 65.5 + - - +
40I VAL* 5.1 7.4 - - + -
35J GLU* 4.0 10.1 - - - +
37J VAL 3.2 6.3 + - - +
38J LEU* 3.6 28.6 - - + -
39J TYR 3.0 27.3 + - - +
40J VAL* 5.6 0.7 - - - +
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Residues in contact with TYR 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H LEU 3.0 8.2 + - - +
39H TYR* 3.4 53.1 - + + -
40H VAL 3.0 25.6 + - - +
42H SER* 3.9 7.8 + - - +
37I VAL* 3.5 25.5 - - + +
38I LEU* 1.3 77.4 - - - +
40I VAL* 1.3 63.2 + - - +
42I SER* 4.0 16.4 - - - +
37J VAL* 4.0 5.2 - - - +
39J TYR* 3.4 51.8 - + + -
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Residues in contact with VAL 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LYS 5.3 2.1 - - - +
11C ALA* 5.3 15.3 - - - +
38H LEU* 5.6 1.8 - - + +
40H VAL* 3.3 26.0 - - + +
38I LEU* 5.1 6.5 - - + -
39I TYR* 1.3 82.9 - - - +
41I GLY* 1.3 72.0 + - - +
42I SER* 3.7 0.8 + - - -
39J TYR 3.0 9.8 + - - +
40J VAL* 3.4 24.5 - - + +
41J GLY 3.2 14.9 + - - -
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Residues in contact with GLY 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C SER 6.1 0.2 - - - -
10C LYS* 4.7 16.2 - - - -
40H VAL 3.2 3.2 + - - -
41H GLY* 2.9 21.9 + - - -
40I VAL* 1.3 72.3 - - - +
42I SER* 1.3 58.4 + - - +
43I LYS* 5.3 4.3 - - - -
41J GLY* 2.9 32.5 + - - -
42J SER 3.3 1.4 + - - +
43J LYS* 4.8 8.3 + - - -
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Residues in contact with SER 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H GLY 3.3 5.1 + - - -
42H SER* 3.4 11.7 - - - -
43H LYS 3.1 25.3 + - - +
39I TYR* 4.0 21.1 - - - -
40I VAL 3.9 6.6 + - - -
41I GLY* 1.3 78.1 + - - +
43I LYS* 1.3 68.7 + - - +
44I THR* 5.1 4.7 - - - -
39J TYR* 3.9 16.2 + - - +
42J SER* 3.4 16.7 + - - -
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Residues in contact with LYS 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 6.1 4.3 - - - -
9C SER 5.2 10.0 + - - -
41H GLY 4.8 8.1 + - - -
43H LYS* 3.0 47.0 - - + +
41I GLY* 5.3 2.6 - - - -
42I SER* 1.3 81.9 + - - +
44I THR* 1.3 64.1 + - - +
45I LYS* 5.2 7.0 - - - -
42J SER 3.0 6.6 + - - +
43J LYS* 3.0 41.4 - - + +
44J THR* 2.9 28.9 + - - +
45J LYS* 4.9 13.2 - - - +
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Residues in contact with THR 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LYS 2.9 17.2 + - - +
44H THR* 4.5 16.2 - - + -
45H LYS 3.1 23.3 + - - +
46H GLU* 5.7 2.0 - - + +
42I SER* 5.1 4.7 - - - -
43I LYS* 1.3 77.6 + - - +
45I LYS* 1.3 69.9 + - - +
46I GLU* 4.3 20.2 - - + +
44J THR* 3.4 19.6 - - + +
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Residues in contact with LYS 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H LYS* 4.9 9.7 - - - +
45H LYS* 3.3 46.7 - - + +
43I LYS* 5.2 8.1 - - - -
44I THR* 1.3 82.2 + - - +
46I GLU* 1.3 67.1 + - - +
47I GLY 4.4 0.4 - - - -
48I VAL* 4.4 17.3 - - + -
44J THR* 3.1 8.7 + - - +
45J LYS* 3.3 37.6 - - + +
46J GLU 3.0 24.1 + - - -
48J VAL* 4.5 10.7 - - + +
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Residues in contact with GLU 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G LYS* 5.4 0.2 - - - -
45H LYS 3.0 9.4 + - - +
46H GLU* 3.3 26.9 - - + +
47H GLY 3.1 15.4 + - - -
80H LYS* 2.8 42.1 + - + +
44I THR* 4.3 17.3 - - + +
45I LYS* 1.3 82.5 - - - +
47I GLY* 1.3 68.5 + - - +
48I VAL* 4.2 1.2 - - - +
44J THR* 5.7 2.2 - - + +
46J GLU* 3.3 32.5 - - + +
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Residues in contact with GLY 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H GLY* 3.0 32.7 + - - -
48H VAL 3.2 1.4 + - - -
78H ALA* 3.7 4.1 - - - +
79H GLN 3.9 23.6 - - - -
80H LYS* 5.4 4.1 - - - +
46I GLU* 1.3 68.5 - - - +
48I VAL* 1.3 59.7 + - - +
78I ALA* 3.9 6.5 - - - -
79I GLN 6.2 0.2 - - - -
46J GLU 3.1 4.2 + - - -
47J GLY* 3.0 20.2 + - - -
48J VAL* 4.7 0.2 - - - +
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Residues in contact with VAL 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H LYS* 4.5 15.5 - - + +
47H GLY 4.7 0.4 - - - +
48H VAL* 3.3 31.0 - - + +
78H ALA* 4.6 0.2 - - - -
45I LYS* 4.4 17.3 - - + -
46I GLU 4.2 15.9 - - - +
47I GLY* 1.3 81.8 - - - +
49I VAL* 1.3 69.3 + - - +
50I HIS* 5.8 2.7 - - + -
78I ALA* 3.5 5.2 - - - +
47J GLY 3.2 4.9 + - - -
48J VAL* 3.3 21.1 - - + +
49J VAL 3.1 22.5 + - - -
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Residues in contact with VAL 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H VAL 3.1 5.5 + - - +
49H VAL* 3.3 22.0 - - + -
50H HIS* 3.1 23.1 + - - +
76H ALA* 3.9 9.6 - - + -
77H VAL 3.2 34.5 - - - +
78H ALA* 3.9 1.6 - - + +
48I VAL* 1.3 79.6 - - - +
50I HIS* 1.3 66.9 + - - +
76I ALA* 3.3 40.8 - - + +
78I ALA* 4.3 0.7 - - + -
49J VAL* 3.3 18.4 - - + +
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Residues in contact with HIS 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H HIS* 3.2 46.9 - + - +
52H VAL* 5.1 0.7 - - + -
48I VAL* 5.8 2.5 - - + -
49I VAL* 1.3 82.1 - - - +
51I GLY* 1.3 61.5 + - - +
52I VAL* 2.9 28.5 - - + +
76I ALA* 5.2 0.4 - - - +
49J VAL 3.1 6.2 + - - +
50J HIS* 3.2 39.6 + + - +
51J GLY 3.1 22.0 + - - -
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Residues in contact with GLY 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H HIS 3.1 7.5 + - - +
51H GLY* 3.3 6.8 - - - -
52H VAL 3.1 23.9 + - - +
74H VAL* 4.8 8.4 - - - +
76H ALA* 5.4 4.0 - - - +
49I VAL* 4.8 2.8 - - - +
50I HIS* 1.3 73.4 - - - +
52I VAL* 1.3 64.9 + - - +
53I ALA 4.3 0.4 - - - -
74I VAL* 4.7 13.5 - - - -
76I ALA* 5.4 4.7 - - - -
51J GLY 3.3 9.2 - - - -
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Residues in contact with VAL 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H VAL* 3.5 23.8 - - + +
50I HIS* 2.9 35.0 - - + +
51I GLY* 1.3 73.8 - - - +
53I ALA* 1.3 64.2 + - - +
54I THR* 4.5 12.6 - - - +
74I VAL* 5.2 3.6 - - - +
50J HIS* 5.1 0.7 - - + -
51J GLY 3.1 6.9 + - - +
52J VAL* 3.5 20.5 - - + +
53J ALA* 2.9 27.6 + - - +
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Residues in contact with ALA 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H VAL* 2.9 10.8 + - - +
53H ALA* 3.3 11.9 - - + +
54H THR 3.1 24.1 + - - +
73H GLY 5.7 0.4 - - - +
74H VAL* 5.3 0.9 - - + -
52I VAL* 1.3 74.8 - - - +
54I THR* 1.3 63.6 + - - +
55I VAL* 5.2 6.5 - - + -
73I GLY* 6.0 1.1 - - - -
74I VAL* 3.8 26.0 - - + +
53J ALA* 3.3 10.8 - - + +
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Residues in contact with THR 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H THR* 3.6 21.0 + - + +
52I VAL* 4.5 10.9 - - - +
53I ALA* 1.3 75.2 + - - +
55I VAL* 1.3 70.9 + - - +
56I ALA* 5.1 2.0 - - + +
53J ALA 3.1 10.2 + - - +
54J THR* 3.6 17.5 + - + -
55J VAL* 2.9 28.9 + - - +
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Residues in contact with VAL 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H THR* 2.9 17.7 + - - +
55H VAL* 4.5 18.2 - - + -
56H ALA* 3.0 24.6 + - - +
53I ALA* 5.2 5.6 - - + -
54I THR* 1.3 84.7 - - - +
56I ALA* 1.3 61.1 + - - +
57I GLU 3.6 18.8 - - - +
58I LYS 5.4 0.4 - - - -
59I THR* 4.8 18.6 - - + -
55J VAL* 3.4 23.6 - - + +
57J GLU 5.3 1.1 - - - +
59J 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