Contacts of the helix formed by residues 19 - 30 (chain F) in PDB entry 5MS0
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 19 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F ALA* 5.5 3.4 - - + -
17F GLY 3.8 2.9 - - - +
18F PHE* 1.3 78.0 - - - +
20F GLY* 1.3 61.8 + - - +
21F ARG 3.4 1.8 - - - -
22F VAL* 3.1 8.1 + - - +
23F ALA* 3.0 25.1 + - - +
46F THR* 4.7 15.9 - - - -
67F GLY* 4.1 29.2 - - - +
68F TYR 5.3 0.7 - - - +
69F VAL* 6.2 4.5 - - + -
13I A 3.5 2.6 + - - -
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Residues in contact with GLY 20 (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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19F GLU* 1.3 80.1 - - - +
21F ARG* 1.3 58.1 + - - +
23F ALA* 3.2 10.4 + - - +
24F THR* 2.9 23.3 + - - -
44F VAL* 5.3 10.3 - - - -
46F THR* 5.6 4.9 - - - -
47F GLU 6.2 1.1 - - - -
48F GLU* 5.3 15.3 - - - +
13I A 3.9 1.2 + - - -
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Residues in contact with ARG 21 (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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20F GLY* 1.3 72.5 - - - +
22F VAL* 1.3 60.5 + - - +
24F THR* 3.6 13.4 - - - -
25F SER* 2.8 27.5 + - - -
48F GLU* 5.8 1.8 - - - +
12I T 4.1 4.3 - - - +
13I A 3.2 39.2 + - - +
30J T 5.2 15.5 - - - +
31J A 6.0 0.2 - - - +
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Residues in contact with VAL 22 (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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14F ALA* 5.8 3.6 - - + -
18F PHE 3.9 15.7 - - - +
19F GLU* 3.1 14.3 + - - +
21F ARG* 1.3 78.4 - - - +
23F ALA* 1.3 56.6 - - - +
25F SER* 3.3 6.4 + - - -
26F LEU* 2.9 25.5 + - - +
86F VAL* 4.6 8.5 - - + +
87F PRO 4.5 16.2 - - - +
88F ARG 4.9 3.8 - - - +
89F VAL* 6.4 1.1 - - + -
13I A 4.0 10.5 - - - -
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Residues in contact with ALA 23 (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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19F GLU 3.0 11.5 + - - +
20F GLY* 3.2 11.6 + - - +
22F VAL* 1.3 75.4 - - - +
24F THR* 1.3 63.8 + - - +
26F LEU* 3.1 19.1 + - - +
27F ARG* 3.1 11.4 + - - +
42F VAL* 5.3 13.2 - - + -
43F MET 6.0 1.6 - - - +
44F VAL* 5.1 13.5 - - + -
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Residues in contact with THR 24 (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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20F GLY 2.9 16.2 + - - -
21F ARG* 3.7 13.5 - - - -
22F VAL 3.3 0.2 - - - -
23F ALA* 1.3 74.8 - - - +
25F SER* 1.3 56.7 + - - +
27F ARG* 3.2 12.0 + - - +
28F GLU* 2.9 22.9 + - - +
30J T 5.4 6.7 - - - -
31J A 4.3 17.0 - - - -
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Residues in contact with SER 25 (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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21F ARG 2.8 19.7 + - - -
22F VAL* 3.6 6.1 - - - -
23F ALA 3.2 0.2 - - - -
24F THR* 1.3 73.9 - - - +
26F LEU* 1.3 61.6 + - - +
27F ARG 3.3 0.2 - - - -
28F GLU* 3.5 12.7 - - - +
29F HIS* 2.9 30.7 + - - +
86F VAL* 4.5 11.5 - - - +
87F PRO 6.0 0.4 - - - -
13I A 3.7 19.5 - - - -
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Residues in contact with LEU 26 (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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22F VAL 2.9 14.1 + - - +
23F ALA* 3.1 14.8 + - - +
25F SER* 1.3 76.6 - - - +
27F ARG* 1.3 56.3 + - - +
29F HIS* 5.2 0.7 - - - -
30F ILE* 3.0 38.7 + - + +
82F LEU 6.0 2.0 - - - +
83F VAL* 6.2 4.5 - - + -
86F VAL* 4.7 9.2 - - + +
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Residues in contact with ARG 27 (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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23F ALA 3.1 10.9 + - - +
24F THR* 3.2 15.2 + - - +
26F LEU* 1.3 76.5 - - - +
28F GLU* 1.3 59.9 + - - +
30F ILE 5.3 0.9 - - - -
31F LYS* 3.3 22.6 + - - +
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Residues in contact with GLU 28 (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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24F THR 2.9 14.3 + - - +
25F SER* 3.6 15.0 - - - +
26F LEU 3.2 0.6 - - - -
27F ARG* 1.3 74.6 - - - +
29F HIS* 1.3 64.2 + - - +
31F LYS* 3.3 17.5 - - - +
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Residues in contact with HIS 29 (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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25F SER 2.9 18.7 + - - +
26F LEU* 4.8 0.9 - - - +
28F GLU* 1.3 76.4 - - + +
30F ILE* 1.3 57.8 + - + +
31F LYS* 3.2 6.7 + - - +
85F SER 6.4 0.2 - - - -
86F VAL* 5.4 10.1 - - + -
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Residues in contact with ILE 30 (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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26F LEU* 3.0 23.2 + - + +
27F ARG* 4.2 1.1 - - - -
29F HIS* 1.3 77.1 - - + +
31F LYS* 1.3 62.6 + - - +
33F HIS* 5.2 4.7 + - - +
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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