Contacts of the helix formed by residues 31 - 46 (chain D) in PDB entry 3ESF
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 LYS 31 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B GLU* 4.8 20.7 + - - +
152B ALA* 5.7 2.2 - - - +
153B ASP* 4.6 17.8 + - - -
173C ASN* 3.7 41.5 - - + +
27D PHE* 3.0 38.1 + - + +
30D ASP* 1.3 89.4 + - + +
32D HIS* 1.3 61.7 + - - +
35D GLY* 2.9 27.4 + - - -
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Residues in contact with HIS 32 (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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164C GLU* 3.8 9.6 + - - -
167C TYR* 6.0 0.7 - - - -
168C TYR* 2.7 30.0 + + - -
173C ASN* 3.4 28.3 - - + +
27D PHE 3.2 15.0 + - - -
28D HIS* 3.3 13.0 - - + +
31D LYS* 1.3 72.9 - - - +
33D HIS* 1.3 67.0 + - - +
35D GLY* 3.2 8.8 + - - -
36D TYR* 3.0 30.8 + - + -
76D HIS* 5.0 0.4 - - - +
165D HIS* 3.4 50.0 + + + +
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Residues in contact with HIS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ILE* 3.5 29.8 - - + +
6D PRO 5.5 0.4 - - - -
28D HIS* 2.8 16.5 + - - +
29D TYR* 3.4 16.7 - + - +
32D HIS* 1.3 72.6 - - - +
34D MET* 1.3 61.9 + - - +
36D TYR* 3.3 19.8 + + - +
37D VAL* 3.6 9.0 + - - +
72D GLN 4.4 0.2 - - - -
73D ILE* 3.2 24.8 + - + -
76D HIS* 3.4 32.5 - + + -
77D ASN* 2.9 32.9 + - - -
80D TRP* 3.0 25.4 + + - +
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Residues in contact with MET 34 (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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4D SER* 6.1 0.4 - - - -
5D ILE* 3.6 35.2 - - + +
29D TYR* 2.8 33.7 + - + +
30D ASP* 3.4 22.9 - - - +
31D LYS 4.2 0.2 + - - -
32D HIS 3.4 0.2 - - - -
33D HIS* 1.3 70.7 - - - +
35D GLY* 1.3 64.7 + - - +
37D VAL* 3.2 17.7 + - - +
38D THR* 3.0 32.0 + - - +
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Residues in contact with GLY 35 (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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30D ASP 4.4 0.8 + - - -
31D LYS 2.9 23.3 + - - -
32D HIS 3.2 1.7 + - - -
34D MET* 1.3 77.6 - - - +
36D TYR* 1.3 61.2 + - - +
38D THR* 3.5 8.4 + - - -
39D LYS* 3.0 32.2 + - - +
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Residues in contact with TYR 36 (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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121C PHE* 4.1 14.1 - + - -
32D HIS* 3.0 33.4 + - + +
33D HIS* 3.6 11.7 - - - +
34D MET 3.3 0.8 - - - -
35D GLY* 1.3 76.2 - - - +
37D VAL* 1.3 58.3 + - - +
39D LYS* 3.3 5.0 + - + +
40D LEU* 2.8 29.8 + - - +
69D LEU* 3.7 31.8 - - + +
72D GLN* 3.2 51.8 + - + +
73D ILE* 3.8 16.1 - - + +
76D HIS* 3.6 18.2 - + - -
163D TRP* 4.0 16.6 - - - -
165D HIS* 4.1 8.1 - - - -
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Residues in contact with VAL 37 (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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3D PHE* 3.6 23.1 - - + +
4D SER* 4.1 7.2 - - - +
5D ILE* 3.4 37.7 - - + -
33D HIS 3.6 12.1 - - - +
34D MET* 3.2 18.3 + - - +
36D TYR* 1.3 73.1 - - - +
38D THR* 1.3 59.8 + - - +
40D LEU* 3.2 2.1 + - - +
41D ASN* 2.8 48.3 + - - +
73D ILE* 3.6 17.5 - - + -
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Residues in contact with THR 38 (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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34D MET* 3.0 20.5 + - - +
35D GLY* 3.6 11.1 - - - -
37D VAL* 1.3 77.2 - - - +
39D LYS* 1.3 58.8 + - + +
41D ASN* 3.4 7.0 + - - +
42D ALA* 3.1 27.8 + - + +
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Residues in contact with LYS 39 (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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35D GLY* 3.0 21.1 + - - +
36D TYR* 5.5 2.1 - - + -
38D THR* 1.3 74.8 - - + +
40D LEU* 1.3 65.4 + - - +
42D ALA* 3.5 7.8 + - - +
43D ALA* 3.2 20.8 + - - +
69D LEU* 3.6 35.5 - - + +
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Residues in contact with LEU 40 (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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3D PHE* 3.7 42.8 - - + -
36D TYR 2.8 17.0 + - - +
37D VAL* 3.7 4.3 - - - +
39D LYS* 1.3 76.9 - - - +
41D ASN* 1.3 57.5 + - - +
43D ALA* 3.1 4.3 + - + +
44D ALA* 2.9 25.6 + - - +
50D LEU* 4.2 12.3 - - + -
55D VAL* 4.5 2.5 - - + -
58D ILE* 4.3 11.2 - - + -
66D ILE* 4.1 26.7 - - + +
69D LEU* 3.8 14.5 - - + +
70D ALA* 4.5 11.9 - - - +
73D ILE* 3.8 20.4 - - + -
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Residues in contact with ASN 41 (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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1D MET* 4.4 13.4 + - + +
2D ALA* 2.9 13.7 + - + +
3D PHE* 2.7 54.7 + - - +
37D VAL* 2.8 31.2 + - - +
38D THR* 3.8 7.2 - - - +
40D LEU* 1.3 73.0 - - - +
42D ALA* 1.3 54.6 + - - +
44D ALA* 3.4 3.9 + - - +
45D ASN* 2.9 28.6 + - - +
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Residues in contact with ALA 42 (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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38D THR* 3.1 15.1 + - + +
39D LYS* 3.6 11.2 - - - +
40D LEU 3.3 0.2 - - - -
41D ASN* 1.3 74.9 - - - +
43D ALA* 1.3 60.7 + - - +
45D ASN* 3.3 19.5 - - - +
46D SER* 3.9 7.3 + - - -
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Residues in contact with ALA 43 (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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39D LYS 3.2 11.1 + - - +
40D LEU* 3.1 10.9 + - - +
42D ALA* 1.3 77.2 - - - +
44D ALA* 1.3 62.3 + - - +
45D ASN 3.5 0.2 + - - -
46D SER* 3.7 9.3 + - - -
47D ASN* 3.5 18.7 + - - +
50D LEU* 4.0 11.8 - - + +
66D ILE* 3.5 32.1 - - + -
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Residues in contact with ALA 44 (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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2D ALA* 3.9 9.4 - - + -
3D PHE* 3.8 25.6 - - + -
40D LEU 2.9 16.4 + - - +
41D ASN* 3.8 4.7 - - - +
42D ALA 3.3 0.2 - - - -
43D ALA* 1.3 74.5 - - - +
45D ASN* 1.3 65.1 + - - +
46D SER 3.2 0.2 - - - -
47D ASN 3.1 25.1 + - - +
48D PRO* 4.1 0.5 - - - +
50D LEU* 4.1 6.7 - - + +
51D ALA* 3.9 22.3 - - + +
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Residues in contact with ASN 45 (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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1D MET* 4.7 23.4 - - + +
41D ASN 2.9 13.7 + - - +
42D ALA* 3.3 17.9 - - - +
44D ALA* 1.3 77.6 - - - +
46D SER* 1.3 59.8 + - - +
48D PRO* 5.5 1.9 - - - +
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Residues in contact with SER 46 (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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42D ALA 3.9 8.3 + - - -
43D ALA* 3.7 9.6 + - - -
44D ALA 3.2 0.4 - - - -
45D ASN* 1.3 78.0 + - - +
47D ASN* 1.3 58.1 + - - +
48D PRO* 3.7 9.6 - - - +
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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