Contacts of the helix formed by residues 30 - 40 (chain F) in PDB entry 7CR3
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 THR 30 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29F THR* 1.3 72.4 - - - +
31F LYS* 1.3 83.1 + - + +
33F LEU* 3.3 13.3 + - - +
34F GLY 3.0 21.3 + - - -
46F GLU* 4.7 4.1 + - - +
49F LEU* 3.1 33.8 - - - +
50F GLN* 4.2 2.6 + - - +
53F ILE* 3.6 22.6 - - + +
62F GLY 4.3 8.4 + - - +
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Residues in contact with LYS 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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29F THR* 3.2 9.5 - - - +
30F THR* 1.3 93.2 - - + +
32F GLU* 1.3 60.1 - - + +
34F GLY* 3.1 2.6 + - - +
35F THR* 2.9 30.1 + - - +
46F GLU* 2.4 44.2 + - - -
49F LEU* 4.8 6.8 - - - +
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Residues in contact with GLU 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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20F PHE* 2.9 27.8 - - - +
21F ASP* 2.8 15.1 - - - +
22F LYS* 2.4 35.5 + - + -
23F ASP* 3.1 16.6 - - - +
27F THR 4.4 0.4 - - - -
28F ILE* 3.2 29.1 - - + +
29F THR* 3.4 23.2 + - - +
30F THR 3.3 0.2 - - - -
31F LYS* 1.3 77.7 - - + +
33F LEU* 1.3 61.5 + - - +
35F THR* 3.2 10.7 - - - +
36F VAL* 3.0 29.3 + - - +
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Residues in contact with LEU 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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546A MET* 4.5 5.4 - - - -
20F PHE* 3.7 19.7 - - + -
28F ILE* 3.6 25.1 - - + -
29F THR 3.3 9.4 - - - +
30F THR* 3.4 18.4 - - - +
32F GLU* 1.3 77.6 - - - +
34F GLY* 1.3 61.7 + - - +
36F VAL* 3.1 7.5 - - - +
37F MET* 3.0 26.3 + - - +
49F LEU* 3.8 35.2 - - + +
52F MET* 4.5 11.2 - - + -
53F ILE* 4.1 3.4 - - + -
64F ILE* 3.6 28.9 - - + -
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Residues in contact with GLY 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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30F THR 3.0 11.7 + - - -
31F LYS* 3.1 4.4 + - - -
33F LEU* 1.3 77.1 - - - +
35F THR* 1.3 55.5 + - - +
37F MET* 3.5 2.3 + - - +
38F ARG* 2.9 37.3 + - - +
44F PRO* 4.2 6.1 - - - +
49F LEU* 3.5 25.0 - - - +
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Residues in contact with THR 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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22F LYS* 3.3 31.4 + - + +
31F LYS 2.9 16.7 + - - +
32F GLU* 3.2 20.2 - - - +
34F GLY* 1.3 76.2 - - - +
36F VAL* 1.3 58.2 + - - +
38F ARG* 3.7 12.0 - - - +
39F SER* 2.9 25.0 + - - -
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Residues in contact with VAL 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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543A VAL* 5.3 9.4 - - + -
19F LEU* 4.3 11.0 - - + +
20F PHE* 4.6 29.2 - - + -
22F LYS* 3.9 27.6 - - - +
32F GLU 3.0 25.2 + - - +
33F LEU* 3.1 17.5 - - - +
35F THR* 1.3 73.7 - - - +
37F MET* 1.3 65.9 + - + +
38F ARG 3.3 0.2 - - - -
39F SER* 3.1 20.8 + - - -
40F LEU* 3.3 9.7 + - - +
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Residues in contact with MET 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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543A VAL* 4.1 24.5 - - + -
547A ARG* 4.2 27.4 - - - +
33F LEU 3.0 17.8 + - - +
34F GLY 3.8 0.2 - - - +
36F VAL* 1.3 77.4 - - - +
38F ARG* 1.3 61.7 + - - +
40F LEU* 3.2 44.2 + - + +
41F GLY 3.3 0.2 + - - -
42F GLN* 2.9 57.6 + - + +
44F PRO* 3.6 20.0 - - + -
49F LEU* 5.1 2.7 - - + -
52F MET* 5.5 4.3 - - - -
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Residues in contact with ARG 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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34F GLY 2.9 24.5 + - - +
35F THR* 3.7 11.0 - - - +
37F MET* 1.3 76.1 - - - +
39F SER* 1.3 56.5 - - - +
40F LEU 3.0 0.2 - - - -
41F GLY* 2.9 19.2 + - - -
42F GLN 3.2 14.6 - - - +
43F ASN* 4.1 30.1 - - - +
44F PRO* 4.2 10.8 + - + +
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Residues in contact with SER 39 (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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367A VAL* 5.2 6.4 - - - +
22F LYS* 6.1 1.1 - - - -
35F THR 2.9 17.2 + - - -
36F VAL* 3.1 18.7 + - - -
38F ARG* 1.3 75.6 - - - +
40F LEU* 1.3 57.1 + - - +
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Residues in contact with LEU 40 (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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363A TYR* 3.6 43.7 - - + +
366A THR* 2.7 31.5 - - - +
367A VAL* 3.4 15.4 - - + +
540A ILE* 3.8 31.4 - - + -
543A VAL* 5.4 3.1 - - + -
547A ARG* 5.2 4.9 - - - +
36F VAL 3.3 7.6 + - - +
37F MET* 3.2 33.9 + - + +
38F ARG 3.0 0.6 - - - -
39F SER* 1.3 77.4 - - - +
41F GLY* 1.3 51.8 + - - +
42F GLN* 3.7 3.5 + - + +
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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