Contacts of the helix formed by residues 37 - 49 (chain F) in PDB entry 2XQL
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 TYR 37 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E PHE* 3.7 24.2 - + + -
26E PRO* 4.7 5.2 - - + -
29E ARG* 3.9 19.5 - - - -
30E VAL* 4.7 6.4 - - + +
33E LEU* 3.7 24.4 - - + +
55E LEU* 5.0 3.0 - - + +
36F SER* 1.3 87.1 - - - +
38F SER* 1.3 66.8 + - - +
39F ILE 3.0 3.1 - - - -
40F TYR* 2.7 31.8 + + - -
41F VAL* 2.9 19.2 + - + -
63F ASN* 2.7 22.1 + - - +
66F VAL* 3.4 39.3 - - + +
67F ASN* 3.4 28.1 + - - -
70F PHE* 4.6 9.5 - - - -
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Residues in contact with SER 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F SER 3.6 11.3 + - - -
37F TYR* 1.3 76.7 - - - +
39F ILE* 1.3 66.5 + - - +
41F VAL* 3.4 10.9 - - - +
42F TYR* 3.0 23.7 + - - +
59F MET* 3.5 19.2 - - - +
63F ASN* 3.1 19.8 + - - +
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Residues in contact with ILE 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ARG* 6.2 0.2 - - - +
36F SER 5.9 2.2 - - - +
37F TYR 2.8 4.0 + - - -
38F SER* 1.3 78.7 - - - +
40F TYR* 1.3 79.5 + - + +
42F TYR* 3.3 4.0 - - - +
43F LYS* 2.9 52.0 + - + +
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Residues in contact with TYR 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E GLN* 3.0 24.9 - - - +
25E PHE* 3.8 23.1 - - + -
26E PRO* 3.4 41.7 - - + +
29E ARG* 3.7 28.3 + - - -
36F SER 4.2 1.8 - - - -
37F TYR* 2.7 25.5 + + - +
39F ILE* 1.3 89.0 - - + +
41F VAL* 1.3 55.7 + - - +
43F LYS* 2.8 15.6 + - - +
44F VAL* 2.7 40.0 + - - +
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Residues in contact with VAL 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 4.2 5.5 - - + -
59E THR* 4.2 12.1 - - + -
63E LEU* 3.5 22.0 - - + +
37F TYR* 2.9 28.1 + - + +
38F SER* 3.4 7.6 - - - +
40F TYR* 1.3 71.5 - - - +
42F TYR* 1.3 56.0 + - - +
44F VAL* 3.4 7.5 + - - +
45F LEU* 2.9 25.7 + - + +
54F ILE* 5.1 0.9 - - + -
59F MET* 3.2 35.9 - - + -
62F MET* 4.0 27.1 - - + -
63F ASN* 4.8 1.8 - - - +
66F VAL* 5.7 2.0 - - + -
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Residues in contact with TYR 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F SER 3.0 21.0 + - - +
39F ILE* 3.3 5.2 - - - +
41F VAL* 1.3 74.2 - - - +
43F LYS* 1.3 68.5 - - + +
45F LEU* 3.0 23.3 + - + +
46F LYS* 3.0 24.6 + - + +
52F THR 5.9 0.4 - - - -
53F GLY* 5.0 8.3 - - - -
54F ILE* 4.2 31.0 - - + -
59F MET* 4.2 5.4 - - + -
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Residues in contact with LYS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E GLN* 3.8 35.4 + - + +
39F ILE* 2.9 44.0 + - + +
40F TYR* 2.8 19.5 + - - +
42F TYR* 1.3 79.1 - - + +
44F VAL* 1.3 60.4 + - - +
46F LYS* 3.1 32.0 - - + +
47F GLN* 3.3 8.5 + - - +
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Residues in contact with VAL 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E GLN* 4.1 13.5 - - + -
25E PHE* 3.5 31.0 - - + -
56E GLU* 4.1 10.8 - - + +
59E THR* 4.3 4.9 - - + -
60E ALA* 3.7 39.7 - - + +
63E LEU* 4.4 2.2 - - + -
40F TYR 2.7 23.9 + - - +
41F VAL* 3.7 6.1 - - - +
43F LYS* 1.3 68.8 - - - +
45F LEU* 1.3 66.6 + - - +
47F GLN* 3.1 18.2 + - - +
48F VAL* 3.1 20.5 + - + +
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Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LEU* 3.8 21.1 - - + +
78E ILE* 4.2 12.3 - - + -
41F VAL* 2.9 14.8 + - + +
42F TYR* 3.0 18.8 + - + +
44F VAL* 1.3 76.9 - - - +
46F LYS* 1.3 54.7 + - - +
48F VAL* 2.9 17.5 + - + +
49F HIS* 2.6 45.4 + - + +
52F THR 3.4 26.7 - - - +
53F GLY* 4.1 4.9 - - - +
54F ILE* 3.7 40.2 - - + -
59F MET* 6.0 0.2 - - + -
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Residues in contact with LYS 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F TYR* 3.0 23.3 + - + +
43F LYS* 3.1 28.5 - - + +
45F LEU* 1.3 76.4 - - - +
47F GLN* 1.3 67.4 + - + +
49F HIS 3.7 8.5 - - - -
50F PRO* 3.0 39.4 - - + +
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Residues in contact with GLN 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E GLN* 3.4 30.0 + - - +
56E GLU* 3.9 11.0 + - - +
60E ALA* 5.5 5.1 - - - +
43F LYS 3.3 8.7 + - - +
44F VAL* 3.2 21.5 + - - +
45F LEU 3.1 0.4 - - - -
46F LYS* 1.3 85.9 - - + +
48F VAL* 1.3 58.0 + - - +
50F PRO* 4.7 3.8 - - - +
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Residues in contact with VAL 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ALA* 4.3 12.6 - - + +
63E LEU* 4.5 5.6 - - + +
64E GLU* 3.5 54.4 - - + +
71E ARG* 5.2 0.2 + - - -
44F VAL 3.1 11.4 + - - +
45F LEU* 2.9 27.4 + - + +
47F GLN* 1.3 81.5 - - + +
49F HIS* 1.3 82.2 + - + +
50F PRO* 3.9 5.6 - - - +
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Residues in contact with HIS 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LEU 5.2 0.2 - - - -
64E GLU* 3.8 25.6 - - - -
67E GLY* 3.5 24.3 - - - -
68E ASN* 2.8 33.0 + - - -
71E ARG* 3.4 29.8 + - - +
45F LEU* 2.6 23.0 + - + +
46F LYS* 3.7 3.6 - - - -
48F VAL* 1.3 101.1 + - + +
50F PRO* 1.3 60.4 - - - +
51F ASP* 2.9 12.7 + - - -
52F THR* 3.4 29.6 + - - +
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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