Contacts of the helix formed by residues 31 - 46 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASN* 3.5 45.0 - - + +
26B THR* 6.5 0.2 - - + -
27B PHE* 3.0 37.7 + - + +
30B ASP* 1.3 88.0 - - + +
32B HIS* 1.3 61.3 + - - +
35B GLY* 2.9 28.1 + - - -
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLU* 3.8 10.7 + - - -
167A TYR* 5.8 1.3 - - - -
168A TYR* 2.6 31.1 + + - -
173A ASN* 3.4 29.7 - - + +
27B PHE 3.2 15.0 + - - -
28B HIS* 3.3 11.9 - - + +
31B LYS* 1.3 75.0 - - - +
33B HIS* 1.3 65.5 + - - +
35B GLY* 3.7 0.5 - - - -
36B TYR* 3.0 37.6 + - + -
76B HIS* 5.0 0.2 - - - +
165B HIS* 3.4 49.6 + + + +
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Residues in contact with HIS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.6 29.5 - - + +
6B PRO 5.5 0.7 - - - -
28B HIS 2.8 16.3 + - - +
29B TYR* 3.5 17.2 - + - +
32B HIS* 1.3 71.5 - - - +
34B MET* 1.3 62.7 + - - +
36B TYR* 3.2 24.5 + + - +
37B VAL* 3.5 5.4 + - - +
72B GLN 4.5 0.2 - - - -
73B ILE* 3.3 21.9 + - + -
76B HIS* 3.4 31.1 - + + +
77B ASN* 2.9 33.2 + - - -
80B TRP* 3.0 26.8 + + - +
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Residues in contact with MET 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B SER* 6.0 0.4 - - - -
5B ILE* 3.9 29.1 - - + +
29B TYR* 3.0 27.9 + - + +
30B ASP* 3.5 22.4 - - - +
33B HIS* 1.3 72.5 - - - +
35B GLY* 1.3 60.7 + - - +
37B VAL* 3.1 25.0 + - - +
38B THR* 2.9 36.9 + - - +
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Residues in contact with GLY 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ASP 4.4 0.6 + - - -
31B LYS 2.9 23.6 + - - -
32B HIS 3.7 1.6 - - - -
33B HIS 3.3 0.4 - - - -
34B MET* 1.3 76.9 - - - +
36B TYR* 1.3 60.4 + - - +
38B THR* 3.4 8.2 + - - -
39B LYS* 3.1 31.1 + - - +
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PHE* 4.1 14.4 - + - -
32B HIS* 3.0 31.3 + - + +
33B HIS* 3.2 13.7 + - - +
35B GLY* 1.3 75.3 - - - +
37B VAL* 1.3 57.0 + - - +
39B LYS* 3.3 4.8 + - + +
40B LEU* 2.9 30.0 + - - +
69B LEU* 3.8 29.2 - - + +
72B GLN* 3.1 53.4 + - + -
73B ILE* 3.7 16.6 - - + +
76B HIS* 3.6 19.7 - + - -
163B TRP* 4.0 16.1 - - - -
165B HIS* 4.2 8.5 - - - -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.7 18.3 - - + +
4B SER* 4.4 4.7 - - - +
5B ILE* 3.4 33.9 - - + +
33B HIS 3.7 11.2 - - - +
34B MET* 3.1 28.9 + - - +
36B TYR* 1.3 73.2 - - - +
38B THR* 1.3 61.2 + - - +
40B LEU* 3.3 2.4 + - - +
41B ASN* 2.8 47.0 + - - +
73B ILE* 3.8 18.2 - - + -
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B MET* 2.9 20.6 + - - +
35B GLY* 3.7 11.3 - - - -
37B VAL* 1.3 79.0 - - - +
39B LYS* 1.3 59.3 + - + +
41B ASN* 3.4 8.2 + - - +
42B ALA* 3.1 26.7 + - + +
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Residues in contact with LYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLY 3.1 20.1 + - - +
36B TYR* 3.7 6.1 - - + +
38B THR* 1.3 75.1 - - + +
40B LEU* 1.3 64.9 + - - +
42B ALA* 3.5 8.1 + - - +
43B ALA* 3.2 19.1 + - - +
69B LEU* 3.6 32.4 - - + +
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.8 40.4 - - + -
36B TYR 2.9 17.2 + - - +
37B VAL 3.8 3.4 - - - +
39B LYS* 1.3 77.0 - - - +
41B ASN* 1.3 57.7 + - - +
43B ALA* 3.3 3.7 + - - +
44B ALA* 2.8 26.7 + - - +
50B LEU* 4.4 11.9 - - + -
55B VAL* 4.5 1.3 - - + -
58B ILE* 4.4 8.7 - - + -
66B ILE* 4.3 25.6 - - + +
69B LEU* 3.6 21.5 - - + +
70B ALA* 4.4 13.5 - - + -
73B ILE* 3.7 22.4 - - + -
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Residues in contact with ASN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.6 17.1 - - + +
2B ALA* 3.3 13.1 + - - +
3B PHE* 2.8 51.5 + - - +
37B VAL* 2.8 29.0 + - - +
38B THR* 3.6 8.3 - - - +
40B LEU* 1.3 73.9 - - - +
42B ALA* 1.3 57.9 + - - +
44B ALA* 3.3 4.9 + - - +
45B ASN* 2.9 28.6 + - - +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B THR* 3.1 14.1 + - + +
39B LYS* 3.6 12.3 - - - +
40B LEU 3.3 0.2 - - - -
41B ASN* 1.3 72.5 - - - +
43B ALA* 1.3 64.7 - - - +
45B ASN* 3.4 19.1 - - - +
46B SER* 4.2 5.2 + - - -
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS 3.2 10.3 + - - +
40B LEU 3.6 8.1 - - - +
42B ALA* 1.3 78.5 - - - +
44B ALA* 1.3 62.7 + - - +
46B SER* 3.4 16.2 + - - -
47B ASN* 3.6 12.8 + - - +
50B LEU* 4.1 10.0 - - + +
66B ILE* 3.5 32.8 - - + -
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ALA* 4.1 8.1 - - + -
3B PHE* 3.8 23.8 - - + -
40B LEU 2.8 17.5 + - - +
41B ASN* 3.8 5.2 - - - +
42B ALA 3.3 0.2 - - - -
43B ALA* 1.3 76.6 - - - +
45B ASN* 1.3 63.5 + - - +
47B ASN 3.1 25.7 + - - +
48B PRO* 4.1 0.7 - - - +
50B LEU* 4.3 6.5 - - + -
51B ALA* 3.9 24.0 - - + +
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Residues in contact with ASN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.9 23.6 - - - +
41B ASN 2.9 13.4 + - - +
42B ALA* 3.4 17.7 - - - +
43B ALA 3.3 0.4 - - - -
44B ALA* 1.3 76.6 - - - +
46B SER* 1.3 58.3 + - - +
47B ASN 3.9 0.3 + - - -
48B PRO* 5.4 2.3 - - - +
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA 4.2 4.9 + - - -
43B ALA* 3.4 13.5 + - - -
45B ASN* 1.3 76.9 - - - +
47B ASN* 1.3 58.4 + - - +
48B PRO* 3.7 9.9 - - - +
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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