Contacts of the helix formed by residues 26 - 37 (chain I) in PDB entry 6FF7
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 GLU 26 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7I ILE* 5.6 3.5 + - - +
8I SER* 5.2 6.9 - - - -
12I PRO* 5.8 4.0 - - - -
14I HIS 4.3 2.5 - - - +
16I CYS* 4.8 0.7 - - - +
25I TYR* 1.3 77.7 - - - +
27I ARG* 1.3 65.2 + - - +
28I ARG* 3.4 3.1 - - + +
29I LEU* 4.1 22.0 - - + +
30I ILE* 3.1 24.3 + - - +
76J LYS* 5.5 6.3 - - + +
80J ASP* 4.6 11.9 - - + -
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Residues in contact with ARG 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I HIS* 4.0 25.5 + - + +
16I CYS* 5.7 2.9 - - - -
25I TYR 3.9 0.6 + - - -
26I GLU* 1.3 74.2 - - - +
28I ARG* 1.3 54.1 + - - +
30I ILE* 5.4 0.7 - - - -
31I GLU* 2.6 42.6 + - + +
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Residues in contact with ARG 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I GLU* 3.4 3.6 - - + +
27I ARG* 1.3 77.2 - - - +
29I LEU* 1.3 60.3 + - - +
31I GLU* 4.6 1.8 - - - -
32I LYS* 2.8 37.8 + - + +
80J ASP* 6.2 1.6 - - + -
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Residues in contact with LEU 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ILE* 6.0 5.8 - - + +
25I TYR* 5.6 1.8 - - + -
26I GLU* 3.6 17.3 + - + +
27I ARG 3.4 0.4 - - - -
28I ARG* 1.3 79.5 - - - +
30I ILE* 1.3 54.2 + - - +
32I LYS* 5.1 0.2 - - - -
33I TYR* 2.6 41.1 + - + +
41I PRO* 5.5 5.1 - - + +
80J ASP* 3.9 31.8 - - + +
84J ALA* 5.9 2.7 - - + -
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Residues in contact with ILE 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I CYS* 4.5 13.9 - - + +
25I TYR* 4.0 19.3 - - + +
26I GLU 3.1 16.2 + - - +
27I ARG* 4.8 0.7 - - - +
29I LEU* 1.3 76.2 - - - +
31I GLU* 1.3 61.4 + - - +
33I TYR* 4.6 1.1 - - - -
34I ILE* 2.8 37.2 + - + +
41I PRO* 5.7 5.6 - - + -
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Residues in contact with GLU 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I ARG* 2.6 25.5 + - + +
28I ARG* 4.6 1.3 - - - -
30I ILE* 1.3 79.4 - - - +
32I LYS* 1.3 50.0 + - - +
34I ILE* 4.9 0.4 - - - -
35I ALA* 2.6 39.2 + - - +
49I GLU* 5.9 3.9 - - - +
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Residues in contact with LYS 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I ARG* 2.8 24.9 + - + +
31I GLU* 1.3 75.5 - - - +
33I TYR* 1.3 60.2 + - - +
35I ALA* 3.5 4.7 - - - +
36I GLU* 2.9 31.7 + - - +
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Residues in contact with TYR 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I LEU* 2.6 24.5 + - - +
30I ILE* 4.6 1.3 - - - +
32I LYS* 1.3 79.2 - - - +
34I ILE* 1.3 57.1 + - - +
36I GLU* 3.6 2.7 + - - +
37I ASN* 2.8 27.3 + - - +
39I THR 5.6 0.2 - - - -
41I PRO* 5.2 12.8 - - + -
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Residues in contact with ILE 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ILE* 2.8 24.4 + - + +
31I GLU 4.6 0.4 - - - +
33I TYR* 1.3 75.8 - - - +
35I ALA* 1.3 62.9 + - - +
37I ASN 3.6 8.3 - - - -
38I GLY* 3.5 19.4 + - - -
39I THR 4.2 19.2 + - - +
48I SER 5.1 2.9 - - - +
49I GLU* 4.7 28.8 + - + +
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Residues in contact with ALA 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I GLU 2.6 25.4 + - - +
32I LYS* 3.5 7.2 - - - +
33I TYR 3.2 0.2 - - - -
34I ILE* 1.3 79.2 - - - +
36I GLU* 1.3 66.9 + - - +
38I GLY 5.1 0.2 + - - -
49I GLU* 5.7 3.1 - - - -
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Residues in contact with GLU 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I LYS 2.9 17.3 + - - +
33I TYR* 4.1 4.3 - - - +
35I ALA* 1.3 79.5 - - - +
37I ASN* 1.3 61.3 + - + +
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Residues in contact with ASN 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I TYR 2.8 20.5 + - - +
34I ILE* 3.6 3.8 - - - -
36I GLU* 1.3 82.3 - - + +
38I GLY* 1.3 66.1 + - - +
39I THR* 3.2 8.9 + - - +
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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