Contacts of the helix formed by residues 30 - 38 (chain F) in PDB entry 2R6C
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 ALA 30 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F ALA 3.2 35.0 - - - +
24F VAL* 3.8 6.3 - - + -
27F ASP* 3.6 13.2 - - + +
28F PRO 2.6 1.8 - - - -
29F ALA* 1.3 78.7 - - - +
31F LEU* 1.3 60.6 + - - +
32F VAL 3.3 0.2 - - - -
33F PRO* 3.2 13.0 - - - +
34F ALA* 3.4 10.0 + - - +
99F ALA* 4.5 0.4 - - + -
102F VAL* 3.4 33.3 - - + +
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Residues in contact with LEU 31 (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 VAL* 3.6 13.8 - - + +
28F PRO 2.9 13.5 + - - +
30F ALA* 1.3 79.2 - - - +
32F VAL* 1.3 65.8 + - + +
34F ALA* 4.3 0.7 - - + -
35F SER* 3.0 23.8 + - - +
52F PHE* 4.2 18.2 - - + -
55F MET* 3.9 38.8 - - + +
56F LEU* 4.5 17.0 - - + -
59F ALA* 3.9 17.9 - - + -
65F VAL* 3.8 31.4 - - + -
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Residues in contact with VAL 32 (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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302E ARG* 3.5 18.2 - - - +
344E ARG* 5.7 2.0 - - + +
345E SER* 3.3 30.3 - - - +
348E ALA* 3.8 21.8 - - + -
28F PRO 5.4 0.4 - - - +
29F ALA* 3.8 18.4 - - + +
31F LEU* 1.3 77.6 - - + +
33F PRO* 1.4 67.6 - - + +
35F SER* 3.1 18.5 + - - +
36F GLU* 3.2 26.1 - - - +
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Residues in contact with PRO 33 (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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302E ARG* 5.3 3.6 - - - +
306E ARG* 4.8 15.5 - - - +
29F ALA 3.3 14.8 - - - +
30F ALA* 3.2 17.3 - - - +
32F VAL* 1.4 90.7 - - + +
34F ALA* 1.3 62.8 + - - +
35F SER 3.2 0.7 - - - -
36F GLU* 3.2 26.1 + - - +
37F ILE* 3.4 19.3 + - - +
102F VAL* 5.3 4.5 - - + -
103F GLU* 3.9 33.2 - - + +
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Residues in contact with ALA 34 (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 VAL* 3.6 31.6 - - + -
24F VAL* 4.7 1.6 - - + -
30F ALA 3.4 18.1 + - - +
31F LEU* 3.9 7.2 - - - +
32F VAL 3.4 0.2 - - - -
33F PRO* 1.3 78.7 - - - +
35F SER* 1.3 56.7 + - - +
37F ILE* 3.4 0.7 + - - +
38F LEU* 2.8 34.5 + - - +
52F PHE* 3.8 12.6 - - + -
102F VAL* 4.0 5.5 - - + +
106F ALA* 4.5 10.8 - - + -
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Residues in contact with SER 35 (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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31F LEU* 3.0 14.6 + - - +
32F VAL* 3.1 15.9 + - - +
34F ALA* 1.3 74.0 - - - +
36F GLU* 1.3 58.2 + - - +
37F ILE 3.1 5.6 - - - -
38F LEU 3.2 19.9 + - - +
39F ILE* 5.3 2.6 - - - +
52F PHE* 4.0 7.4 - - - -
56F LEU* 3.8 29.8 - - - +
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Residues in contact with GLU 36 (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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297E ARG* 6.0 0.9 - - - -
298E VAL* 5.6 1.1 - - + -
299E SER* 3.3 50.9 + - - +
302E ARG* 2.7 37.9 + - - -
306E ARG* 5.5 0.3 + - - -
345E SER* 3.8 8.3 + - - +
32F VAL* 3.2 28.6 + - - +
33F PRO* 3.2 15.1 + - - +
35F SER* 1.3 80.0 + - - +
37F ILE* 1.3 64.7 + - + +
103F GLU* 5.2 4.0 - - - +
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Residues in contact with ILE 37 (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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299E SER* 6.0 0.9 - - - -
33F PRO* 3.4 16.1 + - + +
35F SER 3.1 0.2 - - - -
36F GLU* 1.3 90.3 - - + +
38F LEU* 1.3 58.6 + - - +
42F ASP* 4.0 2.1 - - - +
103F GLU* 3.6 47.1 - - + +
106F ALA* 3.8 33.2 - - + +
107F ARG* 4.1 18.2 - - + +
110F GLU* 3.5 35.3 - - + +
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Residues in contact with LEU 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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20F VAL* 4.6 9.2 - - + -
34F ALA 2.8 14.5 + - - +
35F SER* 3.2 25.1 - - - +
37F ILE* 1.3 79.9 - - - +
39F ILE* 1.3 68.0 - - - +
42F ASP* 3.2 17.7 - - + +
43F PHE* 3.7 30.7 - - + -
52F PHE* 3.7 11.5 - - + -
56F LEU* 5.3 0.9 - - - +
106F ALA* 3.3 39.3 - - + +
109F VAL* 3.9 15.0 - - + -
110F GLU* 3.5 22.9 - - + +
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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