Contacts of the helix formed by residues 28 - 41 (chain A) in PDB entry 6FP4
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 CYS 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LYS* 3.4 20.2 - - + +
26A THR 3.3 4.6 + - - -
27A THR* 1.3 75.5 - - - +
29A PRO* 1.3 76.7 - - - +
30A TYR* 3.7 6.3 - - - -
31A CYS* 2.0 60.3 - - + -
32A LYS* 3.3 26.0 + - + +
72A VAL* 4.1 10.3 - - - -
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Residues in contact with PRO 29 (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 THR 4.6 2.0 - - - +
28A CYS* 1.3 89.5 - - - +
30A TYR* 1.3 72.0 + - + +
32A LYS* 3.4 5.8 + - + +
33A LYS* 3.2 24.5 + - + +
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Residues in contact with TYR 30 (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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28A CYS* 3.7 3.5 - - - -
29A PRO* 1.3 87.1 - - + +
31A CYS* 1.3 65.7 + - - +
33A LYS* 3.2 36.0 + - + +
34A VAL* 3.4 5.0 + - - +
72A VAL 4.7 3.4 - - - +
73A PRO* 3.9 9.9 - - + -
85A SER* 3.3 40.2 + - - +
89A LEU* 6.2 1.1 - - + -
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Residues in contact with CYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 4.8 1.1 - - + +
24A SER* 2.9 31.6 - - - +
25A LYS 3.7 2.0 - - - +
28A CYS* 2.0 51.8 - - + -
30A TYR* 1.3 76.3 - - - +
32A LYS* 1.3 58.5 + - + +
34A VAL* 2.8 21.8 + - - +
35A LYS* 3.0 16.2 + - - +
72A VAL* 3.6 27.6 - - - -
73A PRO* 3.8 17.3 - - + -
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Residues in contact with LYS 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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25A LYS 5.7 0.2 - - - +
26A THR 3.4 25.4 + - - +
27A THR* 4.6 12.5 - - - +
28A CYS 3.3 20.3 + - - +
29A PRO* 3.8 5.2 - - + +
30A TYR 3.4 0.4 - - - -
31A CYS* 1.3 78.2 - - + +
33A LYS* 1.3 57.0 + - - +
35A LYS* 4.2 19.1 - - + +
36A ASP* 3.0 40.3 + - - +
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PRO 3.2 19.1 - - - +
30A TYR* 3.3 30.2 - - + +
31A CYS 3.1 0.2 - - - -
32A LYS* 1.3 79.1 - - + +
34A VAL* 1.3 60.7 + - + +
36A ASP* 3.8 5.8 + - - +
37A VAL* 3.2 26.5 + - - +
85A SER* 5.4 0.7 - - - +
89A LEU* 4.2 23.5 - - + +
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Residues in contact with VAL 34 (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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22A LEU* 4.0 18.8 - - + -
30A TYR 3.6 5.2 - - - +
31A CYS 2.8 7.9 + - - +
33A LYS* 1.3 76.1 - - - +
35A LYS* 1.3 65.3 + - - +
37A VAL* 3.1 7.0 + - - +
38A LEU* 3.0 21.8 + - + +
73A PRO* 3.4 31.4 - - + -
75A MET* 3.3 35.0 - - + -
84A ASP 5.2 0.7 - - - +
85A SER* 4.0 17.7 - - - +
88A VAL* 4.1 11.2 - - + -
89A LEU* 4.6 6.7 - - + -
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Residues in contact with LYS 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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22A LEU* 3.9 13.7 - - + -
24A SER* 3.2 20.5 + - - -
25A LYS 4.2 5.3 + - - -
26A THR* 5.1 3.4 + - - +
31A CYS* 3.0 16.7 + - - +
32A LYS* 3.4 22.9 + - + +
34A VAL* 1.3 76.6 - - - +
36A ASP* 1.3 61.2 + - - +
38A LEU* 3.1 10.3 + - - +
39A ALA* 2.8 32.4 + - - +
45A HIS* 4.8 9.7 - - + +
47A THR* 3.9 17.3 - - - -
49A GLU* 2.8 28.5 + - - -
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Residues in contact with ASP 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 LYS* 3.0 23.6 + - - +
33A LYS* 4.1 5.9 - - - +
34A VAL 3.3 0.2 - - - -
35A LYS* 1.3 78.2 - - - +
37A VAL* 1.3 62.7 + - + +
39A ALA* 3.7 5.5 - - - +
40A GLU* 3.1 37.6 + - - +
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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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33A LYS 3.2 17.0 + - - +
34A VAL* 3.1 10.1 + - - +
36A ASP* 1.3 75.2 - - + +
38A LEU* 1.3 65.9 + - + +
40A GLU* 3.3 10.3 + - - +
41A ALA* 3.0 22.0 + - - +
88A VAL* 5.0 6.5 - - + -
89A LEU* 4.2 19.5 - - + -
92A TYR* 3.5 49.2 - - + -
97A LEU* 4.1 11.9 - - + -
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Residues in contact with LEU 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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20A VAL* 5.6 0.2 - - + -
22A LEU* 4.0 14.6 - - + -
34A VAL* 3.0 18.9 + - + +
35A LYS* 3.7 4.9 - - - +
37A VAL* 1.3 75.2 - - - +
39A ALA* 1.3 58.8 + - - +
41A ALA* 3.3 3.4 + - - -
42A LYS 2.8 23.6 + - - -
43A ILE* 2.9 48.8 + - + +
45A HIS* 3.4 40.8 - - + +
75A MET* 3.7 39.3 - - + -
88A VAL* 5.1 0.7 - - + -
97A LEU* 4.4 11.2 - - + -
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Residues in contact with ALA 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 LYS 2.8 17.4 + - - +
36A ASP* 3.7 8.1 - - - +
38A LEU* 1.3 76.0 - - - +
40A GLU* 1.3 56.7 + - + +
42A LYS* 2.7 29.2 + - - +
43A ILE 5.5 0.2 - - - -
45A HIS* 5.2 2.3 - - - -
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Residues in contact with GLU 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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36A ASP* 3.1 28.2 + - - +
37A VAL* 3.3 8.7 + - - +
39A ALA* 1.3 80.3 - - + +
41A ALA* 1.3 58.6 + - - +
42A LYS* 3.2 15.4 + - - +
92A TYR* 3.7 23.0 + - - +
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Residues in contact with ALA 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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37A VAL 3.0 16.5 + - - +
38A LEU 4.0 0.9 - - - +
40A GLU* 1.3 74.3 - - - +
42A LYS* 1.3 71.6 + - - +
43A ILE* 3.2 27.9 + - + +
92A TYR* 4.0 24.0 + - + -
97A LEU* 5.3 0.4 - - + -
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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