Contacts of the strand formed by residues 38 - 55 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C VAL* 5.1 0.4 - - - -
38C LEU* 3.6 32.5 - - + +
35D GLU* 3.3 28.5 - - + +
37D VAL* 1.3 82.0 - - - +
39D TYR* 1.3 64.5 + - - +
40D VAL* 4.2 7.4 - - + -
35E GLU* 4.1 9.9 - - - +
37E VAL 3.2 6.3 + - - +
38E LEU* 3.6 27.3 - - + -
39E TYR 3.0 27.4 + - - +
40E VAL* 5.6 0.6 - - - +
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Residues in contact with TYR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU 3.0 8.5 + - - +
39C TYR* 3.4 53.2 - + + -
40C VAL 3.0 26.0 + - - +
42C SER* 3.9 7.5 + - - +
37D VAL* 3.5 24.7 - - + -
38D LEU* 1.3 77.1 - - - +
40D VAL* 1.3 63.9 - - - +
41D GLY 4.3 0.2 - - - -
42D SER* 4.0 15.3 - - - +
37E VAL* 4.0 5.5 - - - +
39E TYR* 3.4 51.3 - + + -
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Residues in contact with VAL 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 5.6 1.6 - - + +
40C VAL* 3.3 26.5 - - + +
38D LEU* 5.1 7.2 - - + -
39D TYR* 1.3 82.5 - - - +
41D GLY* 1.3 71.4 + - - +
42D SER* 4.3 0.6 + - - -
39E TYR 3.0 10.3 + - - +
40E VAL* 3.3 23.4 - - + +
41E GLY 3.2 14.7 + - - -
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Residues in contact with GLY 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL 3.2 3.4 + - - -
41C GLY* 2.9 22.2 + - - -
40D VAL* 1.3 72.6 - - - +
42D SER* 1.3 56.6 + - - +
43D LYS* 5.3 4.0 - - - -
41E GLY* 2.9 33.7 + - - -
42E SER 3.3 1.6 + - - +
43E LYS* 4.8 8.7 + - - -
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Residues in contact with SER 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLY 3.3 5.1 + - - -
42C SER* 3.4 13.0 + - - -
43C LYS 3.1 23.6 + - - +
39D TYR* 4.0 21.4 - - - -
40D VAL 4.0 2.3 + - - -
41D GLY* 1.3 78.4 + - - +
43D LYS* 1.3 66.4 + - - +
44D THR* 5.1 4.9 - - - -
39E TYR* 3.9 20.8 + - - +
42E SER* 3.4 16.9 + - - -
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Residues in contact with LYS 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLY 4.8 7.9 + - - -
43C LYS* 3.0 48.9 - - + +
41D GLY* 5.3 2.6 - - - -
42D SER* 1.3 82.6 + - - +
44D THR* 1.3 64.3 + - - +
45D LYS* 5.2 6.3 - - - -
42E SER 3.1 7.0 + - - +
43E LYS* 3.0 41.4 - - + +
44E THR* 2.9 29.3 + - - +
45E LYS* 4.8 14.1 - - - +
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Residues in contact with THR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LYS 2.9 17.0 + - - +
44C THR* 3.4 16.8 - - + -
45C LYS 3.1 23.2 + - - +
46C GLU* 5.7 2.2 - - + +
42D SER* 5.1 4.7 - - - -
43D LYS* 1.3 76.5 + - - +
45D LYS* 1.3 69.8 + - - +
46D GLU* 4.3 20.4 - - + +
44E THR* 3.4 18.6 - - + +
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Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LYS* 4.8 10.3 - - - +
45C LYS* 3.3 47.2 - - + +
43D LYS* 5.2 7.9 - - - -
44D THR* 1.3 80.9 + - - +
46D GLU* 1.3 67.1 + - - +
48D VAL* 4.5 16.6 - - + -
44E THR* 3.1 7.1 + - - +
45E LYS* 3.3 38.6 - - + +
46E GLU* 3.0 24.5 + - - +
48E VAL* 4.5 11.6 - - + +
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Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS 3.0 10.6 + - - +
46C GLU* 3.3 27.1 - - + +
47C GLY 3.1 14.9 + - - -
80C LYS* 2.8 41.8 + - + +
44D THR* 4.3 16.6 - - + +
45D LYS* 1.3 81.4 - - - +
47D GLY* 1.3 67.9 + - - +
48D VAL* 3.9 1.0 - - - +
80D LYS* 5.7 0.2 - - - -
44E THR* 5.7 2.4 - - + +
46E GLU* 3.3 32.9 - - + +
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Residues in contact with GLY 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLY* 3.0 33.5 + - - -
48C VAL 3.2 1.6 + - - -
78C ALA* 3.7 4.4 - - - +
79C GLN 3.9 23.3 - - - -
80C LYS* 5.4 4.2 - - - +
46D GLU* 1.3 69.6 - - - +
48D VAL* 1.3 58.6 + - - +
78D ALA* 3.9 6.1 - - - -
46E GLU 3.1 4.4 + - - -
47E GLY* 3.0 20.0 + - - -
48E VAL* 4.7 0.2 - - - +
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LYS* 4.5 15.0 - - + +
47C GLY 4.7 0.4 - - - +
48C VAL* 3.3 30.5 - - + +
78C ALA* 4.6 0.2 - - - -
45D LYS* 4.5 17.0 - - + -
46D GLU 4.2 16.4 - - - +
47D GLY* 1.3 82.7 - - - +
49D VAL* 1.3 69.2 + - - +
50D HIS* 5.8 2.9 - - + -
78D ALA* 3.5 5.5 - - - +
47E GLY 3.2 5.3 + - - -
48E VAL* 3.3 20.9 - - + +
49E VAL 3.1 23.1 + - - -
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Residues in contact with VAL 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C VAL 3.1 4.8 + - - +
49C VAL* 3.3 22.4 - - + -
50C HIS* 3.1 23.2 + - - +
76C ALA* 3.9 9.0 - - + -
77C VAL 3.2 33.7 - - - +
78C ALA* 3.9 2.0 - - + +
48D VAL* 1.3 78.6 - - - +
50D HIS* 1.3 67.3 + - - +
76D ALA* 3.3 41.1 - - + +
78D ALA* 4.3 0.7 - - + -
49E VAL* 3.3 18.2 - - + -
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Residues in contact with HIS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C HIS* 3.2 46.8 - + + +
52C VAL* 5.1 0.7 - - + -
48D VAL* 5.8 2.9 - - + -
49D VAL* 1.3 81.0 - - - +
51D GLY* 1.3 62.1 + - - +
52D VAL* 2.9 28.7 - - + +
76D ALA* 5.2 0.6 - - - +
49E VAL 3.1 6.0 + - - +
50E HIS* 3.2 40.6 + + + +
51E GLY 3.1 22.3 + - - +
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Residues in contact with GLY 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C HIS 3.1 7.6 + - - +
51C GLY* 3.3 7.2 - - - -
52C VAL 3.1 23.8 + - - +
74C VAL* 4.8 8.3 - - - +
76C ALA* 5.4 3.6 - - - +
49D VAL* 4.8 2.8 - - - +
50D HIS* 1.3 74.5 - - - +
52D VAL* 1.3 65.3 + - - +
74D VAL* 4.7 13.5 - - - -
76D ALA* 5.4 5.2 - - - -
51E GLY* 3.3 8.7 - - - -
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL* 3.5 22.4 - - + +
50D HIS* 2.9 34.8 - - + +
51D GLY* 1.3 74.8 - - - +
53D ALA* 1.3 63.3 + - - +
54D THR* 4.5 12.1 - - - +
74D VAL* 5.2 3.8 - - - +
50E HIS* 5.1 0.4 - - + -
51E GLY 3.1 9.2 + - - +
52E VAL* 3.5 19.8 - - + +
53E ALA* 2.9 27.7 + - - +
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Residues in contact with ALA 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL* 2.9 10.8 + - - +
53C ALA* 3.3 11.5 - - + +
54C THR* 3.1 24.1 + - - +
73C GLY 5.8 0.4 - - - +
74C VAL* 5.4 0.9 - - + -
52D VAL* 1.3 74.5 - - - +
54D THR* 1.3 64.1 + - - +
55D VAL* 4.3 6.5 - - + -
73D GLY* 6.0 1.3 - - - -
74D VAL* 3.8 26.4 - - + +
53E ALA* 3.3 10.8 - - + +
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C THR* 3.6 20.9 + - + +
52D VAL* 4.5 11.1 - - - +
53D ALA* 1.3 75.1 + - - +
55D VAL* 1.3 72.1 + - - +
56D ALA* 5.1 1.8 - - + +
53E ALA 3.1 11.8 + - - +
54E THR* 3.6 16.9 + - + -
55E VAL* 2.9 29.1 + - - +
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Residues in contact with VAL 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C THR* 2.9 18.3 + - - +
55C VAL* 4.5 17.7 - - + -
56C ALA* 3.1 23.6 + - - +
53D ALA* 5.2 5.4 - - + -
54D THR* 1.3 84.9 - - - +
56D ALA* 1.3 61.4 + - - +
57D GLU 3.6 18.4 - - - +
58D LYS 5.4 1.1 - - - -
59D THR* 4.8 18.4 - - + -
55E VAL* 3.4 23.8 - - + +
57E GLU 5.3 1.1 - - - +
59E 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
------------------------------------------------------------
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