Contacts of the strand formed by residues 38 - 55 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 3.6 31.4 - - + +
35C GLU* 3.3 27.6 - - + +
37C VAL* 1.3 82.2 - - - +
39C TYR* 1.3 65.9 + - - +
40C VAL* 4.2 7.4 - - + -
35D GLU* 4.1 10.3 - - - +
37D VAL 3.2 6.5 + - - +
38D LEU* 3.6 27.5 - - + -
39D TYR 3.0 27.8 + - - +
40D VAL* 5.6 0.6 - - - +
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Residues in contact with TYR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU 3.0 8.7 + - - +
39B TYR* 3.4 52.5 - + + -
40B VAL 3.0 26.0 + - - +
42B SER* 3.9 7.5 + - - +
37C VAL* 3.5 24.7 - - + -
38C LEU* 1.3 77.3 - - - +
40C VAL* 1.3 62.8 - - - +
41C GLY 4.3 0.2 - - - -
42C SER* 4.0 16.8 - - - +
37D VAL* 4.0 5.4 - - - +
39D TYR* 3.4 52.3 - + + -
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 5.6 1.6 - - + +
40B VAL* 3.3 27.4 - - + +
38C LEU* 5.1 7.2 - - + -
39C TYR* 1.3 80.1 - - - +
41C GLY* 1.3 70.9 + - - +
42C SER* 3.7 1.0 + - - -
39D TYR 3.0 10.9 + - - +
40D VAL* 3.3 23.2 - - + +
41D GLY 3.2 14.7 + - - -
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Residues in contact with GLY 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL 3.2 3.4 + - - -
41B GLY* 2.9 21.1 + - - -
39C TYR 4.3 0.2 - - - -
40C VAL* 1.3 73.7 - - - +
42C SER* 1.3 57.6 + - - +
43C LYS* 5.3 3.8 - - - -
41D GLY* 2.9 33.3 + - - -
42D SER 3.3 1.4 + - - -
43D LYS* 4.8 8.3 + - - -
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Residues in contact with SER 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY 3.3 5.1 + - - -
42B SER* 3.4 13.3 + - - -
43B LYS 3.1 24.1 + - - +
39C TYR* 4.0 21.8 - - - -
40C VAL 4.0 2.3 + - - -
41C GLY* 1.3 79.0 + - - +
43C LYS* 1.3 66.6 + - - +
44C THR* 5.1 4.7 - - - -
39D TYR* 3.9 20.8 + - - +
42D SER* 3.4 17.1 + - - -
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Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLY 4.7 7.9 + - - -
43B LYS* 3.0 48.7 - - + +
41C GLY* 5.3 2.6 - - - -
42C SER* 1.3 82.4 + - - +
44C THR* 1.3 64.5 + - - +
45C LYS* 5.2 6.5 - - - -
42D SER 3.1 6.6 + - - +
43D LYS* 3.0 42.1 - - + +
44D THR* 2.9 29.3 + - - +
45D LYS* 4.8 13.7 - - - +
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Residues in contact with THR 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS 2.9 17.1 + - - +
44B THR* 4.5 15.9 - - + -
45B LYS 3.1 23.1 + - - +
46B GLU* 5.8 2.2 - - + +
42C SER* 5.1 5.2 - - - -
43C LYS* 1.3 76.5 + - - +
45C LYS* 1.3 70.2 + - - +
46C GLU* 4.3 20.6 - - + +
44D THR* 3.4 18.1 - - + +
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Residues in contact with LYS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 4.8 10.5 - - - +
45B LYS* 3.3 47.4 - - + +
43C LYS* 5.2 8.3 - - - -
44C THR* 1.3 82.5 + - - +
46C GLU* 1.3 66.4 + - - +
47C GLY 4.4 0.2 - - - -
48C VAL* 4.5 17.3 - - + -
44D THR* 3.1 7.3 + - - +
45D LYS* 3.3 38.0 - - + +
46D GLU* 3.0 24.5 + - - +
48D VAL* 4.5 11.6 - - + +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LYS 3.0 10.7 + - - +
46B GLU* 3.3 27.0 - - + +
47B GLY 3.1 14.9 + - - -
80B LYS* 2.8 40.7 + - + +
44C THR* 4.3 17.2 - - + +
45C LYS* 1.3 82.0 - - - +
47C GLY* 1.3 68.7 + - - +
48C VAL* 4.3 1.0 - - - +
80C LYS* 5.6 0.2 - - - -
44D THR* 5.7 2.4 - - + +
46D GLU* 3.3 32.7 - - + +
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Residues in contact with GLY 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY* 3.0 33.1 + - - -
48B VAL 3.2 1.6 + - - -
78B ALA* 3.7 4.0 - - - +
79B GLN 3.9 24.0 - - - -
80B LYS* 5.4 3.5 - - - +
46C GLU* 1.3 69.9 - - - +
48C VAL* 1.3 58.7 + - - +
78C ALA* 3.9 6.7 - - - -
46D GLU 3.1 4.0 + - - -
47D GLY* 3.0 20.2 + - - -
48D VAL* 4.7 0.2 - - - +
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LYS* 4.5 15.5 - - + +
47B GLY 4.7 0.7 - - - +
48B VAL* 3.3 31.2 - - + +
78B ALA* 4.6 0.2 - - - -
45C LYS* 4.5 16.6 - - + -
46C GLU 4.2 16.4 - - - +
47C GLY* 1.3 82.7 - - - +
49C VAL* 1.3 69.8 + - - +
50C HIS* 5.8 2.5 - - + -
78C ALA* 3.5 6.7 - - - +
47D GLY 3.2 4.8 + - - -
48D VAL* 3.3 20.7 - - + +
49D VAL 3.1 22.9 + - - -
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Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B VAL 3.1 5.5 + - - +
49B VAL* 3.3 21.8 - - + -
50B HIS* 3.1 23.8 + - - +
76B ALA* 3.9 9.0 - - + -
77B VAL 3.2 33.2 - - - +
78B ALA* 3.9 2.0 - - + +
48C VAL* 1.3 79.2 - - - +
50C HIS* 1.3 67.9 + - - +
76C ALA* 3.3 40.8 - - + +
78C ALA* 4.3 0.7 - - + -
49D VAL* 3.3 17.5 - - + -
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Residues in contact with HIS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 3.2 47.4 - + + +
52B VAL* 5.1 0.7 - - + -
48C VAL* 5.8 2.9 - - + -
49C VAL* 1.3 80.8 - - - +
51C GLY* 1.3 62.0 + - - +
52C VAL* 2.9 28.9 - - + +
76C ALA* 5.2 0.4 - - - +
49D VAL 3.1 7.0 + - - +
50D HIS* 3.2 39.5 + + + +
51D GLY 3.1 22.7 + - - +
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Residues in contact with GLY 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B HIS 3.1 7.6 + - - +
51B GLY* 3.3 7.2 - - - -
52B VAL 3.1 23.6 + - - +
74B VAL* 4.8 7.4 - - - +
76B ALA* 5.4 3.8 - - - +
49C VAL* 4.8 3.0 - - - +
50C HIS* 1.3 73.1 - - - +
52C VAL* 1.3 65.3 + - - +
53C ALA 4.3 0.4 - - - -
74C VAL* 4.7 14.6 - - - -
76C ALA* 5.4 5.6 - - - -
51D GLY* 3.3 8.7 - - - -
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 3.5 22.2 - - + +
50C HIS* 2.9 35.2 - - + +
51C GLY* 1.3 74.6 - - - +
53C ALA* 1.3 64.7 + - - +
54C THR* 4.5 12.3 - - - +
74C VAL* 5.2 2.7 - - - +
50D HIS* 5.1 0.2 - - + -
51D GLY 3.1 9.2 + - - +
52D VAL* 3.5 20.5 - - + +
53D ALA* 2.9 26.9 + - - +
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Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B VAL* 2.9 11.0 + - - +
53B ALA* 3.3 11.7 - - + +
54B THR* 3.1 23.7 + - - +
73B GLY 5.8 0.7 - - - +
74B VAL* 5.4 0.9 - - + -
51C GLY 4.3 0.2 - - - -
52C VAL* 1.3 74.9 - - - +
54C THR* 1.3 64.3 + - - +
55C VAL* 5.2 6.3 - - + -
73C GLY* 6.0 0.9 - - - -
74C VAL* 3.8 26.7 - - + -
53D ALA* 3.3 10.8 - - + +
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Residues in contact with THR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B THR* 3.6 20.5 + - + +
52C VAL* 4.5 10.9 - - - +
53C ALA* 1.3 74.9 + - - +
55C VAL* 1.3 72.3 + - - +
56C ALA* 5.1 2.2 - - + +
53D ALA 3.1 11.4 + - - +
54D THR* 3.6 16.9 + - + -
55D VAL* 2.9 29.1 + - - +
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Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B THR* 2.9 18.4 + - - +
55B VAL* 4.5 17.0 - - + -
56B ALA* 3.1 23.4 + - - +
53C ALA* 5.2 5.2 - - + -
54C THR* 1.3 85.2 - - - +
56C ALA* 1.3 60.9 + - - +
57C GLU 3.6 19.1 - - - +
58C LYS 5.4 0.9 - - - -
59C THR* 4.8 18.2 - - + -
55D VAL* 3.4 24.2 - - + +
57D GLU 5.3 0.9 - - - +
59D THR* 6.5 0.7 - - + -
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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