Contacts of the helix formed by residues 31 - 46 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A THR* 5.7 4.4 - - - +
27A PHE* 2.9 46.3 + - + +
30A ASP* 1.3 87.7 - - + +
32A HIS* 1.3 60.1 + - + +
35A GLY* 2.9 27.5 + - - -
173B ASN* 3.6 44.9 - - + +
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Residues in contact with HIS 32 (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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27A PHE 3.3 14.6 + - - -
28A HIS* 3.4 12.8 - - + +
31A LYS* 1.3 71.7 - - - +
33A HIS* 1.3 66.3 + - - +
35A GLY* 3.3 1.9 + - - -
36A TYR* 3.0 39.3 + - + -
165A HIS* 3.4 50.6 + + + +
164B GLU* 3.7 10.3 + - - -
167B TYR* 6.1 0.7 - + - -
168B TYR* 2.6 30.8 + + - -
173B ASN* 3.5 28.8 - - + +
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Residues in contact with HIS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.5 29.7 - - + +
28A HIS 2.8 16.2 + - - +
29A TYR* 3.4 17.9 - + - +
32A HIS* 1.3 72.2 - - - +
34A MET* 1.3 63.8 + - - +
36A TYR* 3.2 20.4 + + - +
37A VAL* 3.6 8.8 + - - +
72A GLN 4.5 0.4 - - - -
73A ILE* 3.3 21.7 + - - -
76A HIS* 3.4 31.6 - + + +
77A ASN* 2.9 33.1 + - - -
80A TRP* 3.1 27.0 + + - +
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Residues in contact with MET 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER* 6.0 0.2 - - - -
5A ILE* 3.7 31.6 - - + -
29A TYR* 2.9 27.6 + - + +
30A ASP* 3.4 22.7 - - - +
31A LYS 4.2 0.2 + - - -
33A HIS* 1.3 70.2 - - - +
35A GLY* 1.3 64.6 + - - +
37A VAL* 3.2 24.6 + - + -
38A THR* 3.0 36.3 + - - +
41A ASN* 5.9 0.2 - - - +
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Residues in contact with GLY 35 (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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30A ASP 4.4 0.6 + - - -
31A LYS 2.9 23.7 + - - -
32A HIS 3.6 1.8 - - - -
33A HIS 3.2 0.4 - - - -
34A MET* 1.3 76.7 - - - +
36A TYR* 1.3 56.7 + - - +
38A THR* 3.4 7.9 + - - -
39A LYS* 3.0 39.2 + - - +
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Residues in contact with TYR 36 (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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32A HIS* 3.0 32.0 + - + +
33A HIS* 3.2 13.5 + + - +
35A GLY* 1.3 73.0 - - - +
37A VAL* 1.3 61.2 + - - +
39A LYS* 3.3 7.0 + - + +
40A LEU* 2.8 31.0 + - - +
69A LEU* 3.9 28.2 - - + +
72A GLN* 2.9 52.5 + - + +
73A ILE* 3.7 17.8 - - + +
76A HIS* 3.6 18.4 - + - -
163A TRP* 3.9 17.2 - - - -
165A HIS* 4.2 6.9 - - - -
121B PHE* 4.1 15.5 - + - -
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Residues in contact with VAL 37 (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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3A PHE* 3.5 33.7 - - + +
4A SER* 4.2 5.2 - - - -
5A ILE* 3.5 31.9 - - + -
33A HIS 3.7 13.0 - - - +
34A MET* 3.2 30.5 + - + +
36A TYR* 1.3 72.2 - - - +
38A THR* 1.3 58.3 + - - +
40A LEU* 3.2 1.8 + - - +
41A ASN* 2.8 41.7 + - - +
73A ILE* 4.0 15.7 - - + -
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Residues in contact with THR 38 (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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34A MET* 3.0 23.9 + - - +
35A GLY* 3.5 12.6 - - - +
37A VAL* 1.3 76.5 - - - +
39A LYS* 1.3 65.5 + - + +
41A ASN* 3.4 6.9 + - - +
42A ALA* 3.1 22.6 + - + +
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Residues in contact with LYS 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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35A GLY* 3.0 24.5 + - - +
36A TYR* 3.8 7.5 - - - +
38A THR* 1.3 79.0 - - + +
40A LEU* 1.3 61.7 + - - +
42A ALA* 3.4 8.1 + - - +
43A ALA* 3.1 20.8 + - - +
69A LEU* 3.8 27.4 - - + +
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Residues in contact with LEU 40 (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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3A PHE* 3.7 42.8 - - + -
36A TYR 2.8 18.2 + - - +
37A VAL* 3.8 4.0 - - - +
39A LYS* 1.3 73.4 - - - +
41A ASN* 1.3 60.3 + - - +
43A ALA* 3.2 5.4 + - + +
44A ALA* 2.9 29.3 + - - +
50A LEU* 4.4 7.4 - - + -
55A VAL* 4.6 1.6 - - + -
58A ILE* 4.2 15.0 - - + -
66A ILE* 3.9 29.6 - - + +
69A LEU* 3.6 16.9 - - + +
70A ALA* 4.5 8.1 - - + -
73A ILE* 3.7 22.4 - - + -
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Residues in contact with ASN 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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1A MET* 4.0 31.4 - - + +
2A ALA* 3.2 11.4 + - - +
3A PHE* 2.8 51.6 + - - +
37A VAL* 2.8 30.7 + - - +
38A THR* 3.7 7.6 - - - +
40A LEU* 1.3 72.9 - - - +
42A ALA* 1.3 56.5 + - - +
44A ALA* 3.3 4.7 + - - +
45A ASN* 2.9 29.5 + - - +
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Residues in contact with ALA 42 (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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38A THR* 3.1 14.4 + - + +
39A LYS* 3.6 11.9 - - - +
40A LEU 3.3 0.2 - - - -
41A ASN* 1.3 76.6 - - - +
43A ALA* 1.3 60.8 - - - +
44A ALA 3.5 0.2 + - - -
45A ASN* 3.5 17.6 + - - +
46A SER* 4.2 4.9 + - - -
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Residues in contact with ALA 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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39A LYS 3.1 12.4 + - - +
40A LEU* 3.2 9.1 + - - +
42A ALA* 1.3 77.0 - - - +
44A ALA* 1.3 61.4 + - - +
45A ASN 3.5 0.3 + - - -
46A SER* 3.7 10.0 + - - -
47A ASN* 3.7 17.5 + - - +
50A LEU* 3.9 11.9 - - + +
66A ILE* 3.6 31.9 - - + -
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Residues in contact with ALA 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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2A ALA* 4.0 7.6 - - + -
3A PHE* 3.7 24.9 - - + -
40A LEU 2.9 16.9 + - - +
41A ASN* 3.6 5.8 - - - +
42A ALA 3.3 0.2 - - - -
43A ALA* 1.3 76.0 - - - +
45A ASN* 1.3 62.0 - - - +
46A SER 3.2 0.9 - - - -
47A ASN 3.0 25.8 + - - +
48A PRO* 4.1 0.9 - - - +
50A LEU* 4.2 6.5 - - + -
51A ALA* 3.8 23.1 - - + +
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Residues in contact with ASN 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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1A MET* 6.1 3.7 - - + +
41A ASN 2.9 16.1 + - - +
42A ALA* 3.5 12.8 + - - +
43A ALA 3.3 0.4 - - - -
44A ALA* 1.3 75.4 - - - +
46A SER* 1.3 60.6 + - - +
47A ASN 3.9 0.2 + - - -
48A PRO* 5.5 1.9 - - - +
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Residues in contact with SER 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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42A ALA 4.2 3.9 + - - -
43A ALA* 3.7 9.5 + - - -
44A ALA 3.2 0.4 - - - -
45A ASN* 1.3 80.9 - - - +
47A ASN* 1.3 58.6 + - - +
48A PRO* 3.8 8.6 - - - +
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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