Contacts of the strand formed by residues 38 - 55 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.4 28.7 - - + +
37A VAL* 1.3 81.8 - - - +
39A TYR* 1.3 67.3 + - - +
40A VAL* 4.2 8.1 - - + -
35B GLU* 4.1 9.4 - - - +
37B VAL 3.2 6.9 + - - -
38B LEU* 3.6 27.7 - - + -
39B TYR 3.0 27.4 + - - +
40B VAL* 5.6 0.4 - - - +
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Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 3.5 35.2 + - + -
38A LEU* 1.3 78.1 - - - +
40A VAL* 1.3 66.5 + - - +
41A GLY 4.3 0.4 - - - -
42A SER* 4.0 18.6 - - - +
37B VAL* 4.0 5.2 - - - +
39B TYR* 3.4 52.0 - + + -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 5.1 6.5 - - + -
39A TYR* 1.3 82.4 - - - +
41A GLY* 1.3 70.4 + - - +
42A SER* 3.7 0.8 + - - -
39B TYR 3.0 10.1 + - - +
40B VAL* 3.3 24.4 - - + +
41B GLY 3.2 14.4 + - - -
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR 4.3 0.4 - - - -
40A VAL* 1.3 74.4 - - - +
42A SER* 1.3 57.7 + - - +
43A LYS* 5.4 5.2 - - - -
41B GLY* 2.9 33.2 + - - -
42B SER 3.3 1.6 + - - +
43B LYS* 4.7 8.8 + - - -
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 4.0 23.8 - - - -
40A VAL 4.0 2.1 + - - -
41A GLY* 1.3 78.7 + - - +
43A LYS* 1.3 75.1 + - - +
44A THR* 4.2 5.4 + - - -
39B TYR* 3.9 22.4 + - - +
42B SER* 3.4 15.5 + - - -
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A GLY* 5.4 3.8 - - - -
42A SER* 1.3 83.3 + - - +
44A THR* 1.3 63.6 + - - +
45A LYS* 5.3 7.9 - - - +
42B SER 3.1 6.8 + - - +
43B LYS* 3.0 40.1 - - + +
44B THR* 2.9 29.3 + - - +
45B LYS* 4.8 13.5 - - - +
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Residues in contact with THR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A SER* 4.2 6.0 + - - -
43A LYS* 1.3 76.8 + - - +
45A LYS* 1.3 72.9 + - - +
46A GLU* 4.3 21.3 - - + +
44B THR* 3.3 18.9 - - + +
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 5.3 8.9 - - - +
44A THR* 1.3 83.6 + - - +
46A GLU* 1.3 66.5 + - - +
47A GLY 4.4 0.4 - - - -
48A VAL* 4.5 20.6 - - + -
44B THR* 3.1 7.1 + - - +
45B LYS* 3.3 38.6 - - + +
46B GLU 3.0 24.1 + - - -
48B VAL* 4.5 10.2 - - + +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR* 4.3 18.5 - - + +
45A LYS* 1.3 81.4 - - - +
47A GLY* 1.3 68.1 + - - +
48A VAL* 4.2 5.0 - - - +
80A LYS* 5.6 2.1 + - - -
44B THR* 5.8 2.2 - - + +
46B GLU* 3.3 32.6 - - + +
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS 4.4 0.4 - - - -
46A GLU* 1.3 75.0 - - - +
48A VAL* 1.3 63.8 + - - +
78A ALA* 3.9 17.0 - - - -
79A GLN* 6.0 1.3 - - - -
46B GLU 3.1 3.8 + - - -
47B GLY* 3.0 20.7 + - - -
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS* 4.5 17.7 - - + -
46A GLU 4.2 16.4 - - - +
47A GLY* 1.3 81.7 - - - +
49A VAL* 1.3 72.2 + - - +
50A HIS* 5.8 2.5 - - + -
78A ALA* 3.5 6.1 - - - +
47B GLY 3.2 4.0 + - - -
48B VAL* 3.3 20.5 - - + +
49B VAL 3.1 23.0 + - - -
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 1.3 81.1 - - - +
50A HIS* 1.3 69.4 + - - +
51A GLY 4.8 0.9 - - - +
76A ALA* 3.3 45.1 - - + +
77A VAL* 5.1 0.4 - - - -
78A ALA* 4.4 10.5 - - + +
49B VAL* 3.3 17.9 - - + +
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Residues in contact with HIS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 5.8 2.9 - - + -
49A VAL* 1.3 81.0 + - - +
51A GLY* 1.3 60.6 + - - +
52A VAL* 2.9 31.8 - - + +
76A ALA* 5.3 0.6 - - - +
49B VAL 3.1 6.8 + - - +
50B HIS* 3.2 38.7 + + + +
51B GLY 3.1 22.5 + - - +
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 4.8 2.6 - - - +
50A HIS* 1.3 77.3 + - - +
52A VAL* 1.3 65.7 + - - +
74A VAL* 4.7 16.6 - - - -
76A ALA* 5.4 5.8 - - - -
51B GLY 3.3 8.7 - - - -
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A HIS* 2.9 36.8 - - + +
51A GLY* 1.3 74.0 - - - +
53A ALA* 1.3 65.3 + - - +
54A THR* 4.5 12.1 - - - +
74A VAL* 5.2 4.2 - - - +
50B HIS* 5.1 0.4 - - + -
51B GLY 3.0 8.6 + - - +
52B VAL* 3.5 20.8 - - + +
53B ALA* 2.9 27.4 + - - +
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLY 4.3 0.6 - - - -
52A VAL* 1.3 76.4 - - - +
54A THR* 1.3 64.2 + - - +
55A VAL* 4.4 6.0 + - + -
73A GLY* 6.0 1.6 - - - -
74A VAL* 3.8 26.2 - - + -
53B ALA* 3.3 11.7 - - + +
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Residues in contact with THR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 4.5 11.3 - - - +
53A ALA* 1.3 74.3 + - - +
55A VAL* 1.3 71.8 + - - +
56A ALA* 5.1 1.8 - - + +
53B ALA 3.1 10.2 + - - +
54B THR* 3.6 17.0 + - + -
55B VAL* 2.9 29.8 + - - +
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Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA* 4.4 5.1 + - + -
54A THR* 1.3 87.5 - - - +
56A ALA* 1.3 65.1 + - - +
57A GLU 3.6 18.6 - - - +
58A LYS 5.4 0.7 - - - -
59A THR* 4.8 18.4 - - + -
55B VAL* 3.4 24.5 - - + +
57B GLU 5.2 1.1 - - - +
59B THR* 6.5 0.9 - - + -
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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