Contacts of the helix formed by residues 20 - 31 (chain M) 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 20 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M VAL* 4.5 4.3 - - + +
19M GLU* 1.3 81.0 - - + +
21M ASP* 1.3 55.4 + - - +
22M LEU 3.2 3.5 + - - -
23M PRO* 3.2 18.3 - - + -
24M TYR* 2.7 32.4 + - - +
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Residues in contact with ASP 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M GLU 3.7 1.3 - - - -
20M GLU* 1.3 74.4 - - - +
22M LEU* 1.3 57.6 + - - +
24M TYR* 3.2 9.6 + - - +
25M GLU* 2.9 26.2 + - - +
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Residues in contact with LEU 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M GLU 3.2 0.8 - - - -
21M ASP* 1.3 75.1 - - - +
23M PRO* 1.3 60.5 - - - +
25M GLU* 2.9 23.6 + - - +
26M GLU* 2.9 11.1 + - - +
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Residues in contact with PRO 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M VAL* 4.4 18.2 - - + +
20M GLU* 3.2 21.5 - - + +
22M LEU* 1.3 76.2 - - - +
24M TYR* 1.3 56.9 + - - +
26M GLU* 3.2 12.9 + - + +
27M GLU* 2.9 25.3 + - - +
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Residues in contact with TYR 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M VAL 4.6 9.3 + - - +
17M PHE* 5.5 4.3 - - - -
19M GLU 4.4 6.1 - - - +
20M GLU 2.7 18.7 + - - +
21M ASP* 3.3 15.0 - - - +
23M PRO* 1.3 73.1 - - - +
25M GLU* 1.3 58.2 + - - +
27M GLU* 3.2 10.1 + - - +
28M ILE* 2.9 24.1 + - - +
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Residues in contact with GLU 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M ASP 2.9 12.8 + - - +
22M LEU* 2.9 11.8 + - - +
24M TYR* 1.3 73.0 - - - +
26M GLU* 1.3 60.3 + - - +
28M ILE* 3.1 11.1 + - + +
29M MET* 2.9 24.9 + - - +
45M LYS* 5.6 4.7 - - + -
51M PRO* 5.1 15.9 - - + -
55M GLN* 6.0 1.7 - - - +
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Residues in contact with GLU 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M LEU 2.9 7.3 + - - +
23M PRO* 3.3 18.2 - - + +
25M GLU* 1.3 77.0 - - - +
27M GLU* 1.3 56.8 + - - +
29M MET* 3.1 11.6 + - - +
30M ARG* 2.9 25.5 + - - +
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Residues in contact with GLU 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M PRO* 4.6 23.2 - - + +
16M VAL* 5.1 8.1 - - + -
23M PRO 2.9 12.8 + - - +
24M TYR* 3.2 13.2 + - - +
26M GLU* 1.3 73.4 - - - +
28M ILE* 1.3 56.1 + - - +
30M ARG* 3.2 8.8 + - - +
31M ASN* 2.7 36.4 + - - +
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Residues in contact with ILE 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M TYR 2.9 14.1 + - - +
25M GLU* 3.1 15.0 + - + +
27M GLU* 1.3 76.1 - - - +
29M MET* 1.3 57.6 + - - +
31M ASN* 3.5 2.6 - - - +
32M GLN* 2.8 28.6 + - - +
41M TYR* 3.7 38.1 - - + +
55M GLN* 5.7 10.1 - - + -
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Residues in contact with MET 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLU 2.9 12.5 + - - +
26M GLU* 3.1 12.5 + - - +
28M ILE* 1.3 77.3 - - - +
30M ARG* 1.3 60.4 + - - +
32M GLN* 3.5 18.2 - - - +
33M PHE 4.9 0.5 + - - -
55M GLN* 6.1 4.9 - - + +
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Residues in contact with ARG 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M LEU 5.9 3.1 - - - +
8M SER 4.2 19.1 - - - +
9M ARG 5.7 3.4 - - - +
26M GLU 2.9 12.7 + - - +
27M GLU* 3.2 11.2 + - - +
29M MET* 1.3 77.4 - - - +
31M ASN* 1.3 59.3 + - - +
32M GLN 3.3 1.4 + - - -
33M PHE* 4.7 4.9 + - - +
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Residues in contact with ASN 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M PRO* 6.1 5.4 - - + -
27M GLU 2.7 20.5 + - - +
28M ILE* 3.5 6.3 - - - +
30M ARG* 1.3 72.2 - - - +
32M GLN* 1.3 66.4 + - - +
33M PHE 3.6 5.7 - - - +
34M SER 4.5 0.9 - - - +
37M CYS* 3.6 37.9 - - + +
38M TRP 3.9 3.3 + - - -
41M TYR* 5.1 1.8 - - + -
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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