Contacts of the helix formed by residues 38 - 50 (chain F) in PDB entry 3A13
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 38 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33F PRO* 4.3 1.6 - - - -
37F TYR* 1.3 78.3 - - - +
39F ILE* 1.3 60.1 + - - +
40F GLU* 3.6 17.3 + - - +
41F GLN* 2.7 44.9 + - - +
42F ALA* 3.0 26.3 + - - +
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Residues in contact with ILE 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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31F VAL* 3.8 35.9 - - + -
33F PRO* 4.0 10.5 - - + +
38F THR* 1.3 72.8 - - - +
40F GLU* 1.3 75.5 + - - +
42F ALA* 4.2 0.7 - - + -
43F ALA* 2.7 33.8 + - - +
77F PHE* 3.9 18.6 - - + -
85F TRP* 3.6 68.1 - - + +
87F VAL* 3.9 5.4 - - + -
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Residues in contact with GLU 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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9F TYR* 5.3 0.5 - - - +
13F VAL* 3.5 22.3 - - + +
15F LYS* 2.7 40.6 + - - +
38F THR* 3.2 17.2 - - - +
39F ILE* 1.3 94.4 - - - +
41F GLN* 1.3 56.7 + - + +
43F ALA* 4.5 0.2 - - - -
44F GLY* 2.9 24.6 + - - -
77F PHE* 4.2 13.8 - - + +
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Residues in contact with GLN 41 (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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9F TYR* 4.5 4.3 - - - -
36F GLY 4.3 1.6 - - - +
37F TYR* 3.3 26.4 - - + -
38F THR* 2.7 53.5 + - - +
40F GLU* 1.3 78.4 - - + +
42F ALA* 1.3 60.4 + - - +
44F GLY* 5.1 0.4 - - - -
45F ALA 3.3 12.6 + - - -
117F ARG* 3.1 34.9 + - - +
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Residues in contact with ALA 42 (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 VAL* 3.8 21.5 - - + -
33F PRO* 4.1 11.7 - - + -
37F TYR* 5.4 0.2 - - + -
38F THR 3.0 16.8 + - - +
39F ILE* 3.6 5.4 - - - +
41F GLN* 1.3 75.5 - - - +
43F ALA* 1.3 64.9 + - - +
45F ALA* 3.3 4.2 + - - +
46F VAL* 3.1 28.9 + - - +
117F ARG* 4.1 18.1 - - + +
118F VAL* 4.0 12.1 - - + +
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Residues in contact with ALA 43 (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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13F VAL* 4.9 0.4 - - + -
31F VAL* 5.1 3.6 - - - -
39F ILE* 2.7 21.3 + - - +
40F GLU 4.0 1.6 - - - +
42F ALA* 1.3 73.5 - - - +
44F GLY* 1.3 57.4 + - - +
46F VAL* 3.2 8.3 + - - +
47F ALA* 2.9 30.8 + - - +
74F ALA* 4.1 5.2 - - + -
77F PHE* 3.5 28.7 - - + -
87F VAL* 3.8 24.9 - - + -
89F ILE* 4.3 3.2 - - - +
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Residues in contact with GLY 44 (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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9F TYR* 3.9 25.7 - - - -
12F TYR* 3.9 9.9 - - - +
13F VAL* 3.9 8.0 - - - +
40F GLU 2.9 19.0 + - - -
41F GLN 4.1 0.9 - - - -
42F ALA 3.2 0.2 - - - -
43F ALA* 1.3 77.3 - - - +
45F ALA* 1.3 57.3 + - - +
47F ALA* 3.4 0.7 + - - -
48F ALA* 3.0 29.8 + - - +
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Residues in contact with ALA 45 (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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9F TYR* 3.9 28.1 - - + +
41F GLN 3.3 18.5 + - - +
42F ALA 3.3 4.5 + - - +
44F GLY* 1.3 75.2 - - - +
46F VAL* 1.3 62.7 + - - +
48F ALA* 3.4 0.5 + - - +
49F GLU* 3.0 29.6 + - - +
115F MET* 4.0 16.4 - - + -
117F ARG* 3.7 20.2 - - + +
118F VAL* 6.2 0.2 - - + -
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Residues in contact with VAL 46 (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 PHE* 4.1 13.5 - - + -
31F VAL* 5.0 4.3 - - + -
42F ALA 3.1 17.1 + - - +
43F ALA* 3.2 9.8 + - - +
45F ALA* 1.3 77.5 - - - +
47F ALA* 1.3 60.4 + - - +
50F SER* 2.8 27.9 + - - +
89F ILE* 3.9 18.2 - - + -
112F ILE* 3.5 25.3 - - + +
115F MET* 3.4 25.1 - - + -
118F VAL* 4.4 9.4 - - + -
121F LEU* 4.2 17.7 - - + -
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Residues in contact with ALA 47 (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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12F TYR* 3.8 29.6 - - + +
43F ALA 2.9 16.3 + - - +
46F VAL* 1.3 76.0 - - - +
48F ALA* 1.3 61.4 + - - +
50F SER* 3.1 15.1 + - - -
51F SER* 3.0 21.0 + - - -
72F ALA* 4.0 6.9 - - + +
74F ALA* 4.4 2.7 - - + +
89F ILE* 3.9 27.8 - - + -
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Residues in contact with ALA 48 (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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9F TYR* 3.6 23.3 - - + -
12F TYR* 3.5 36.3 - - + -
44F GLY 3.0 17.5 + - - +
45F ALA 3.8 0.7 - - - +
47F ALA* 1.3 77.4 - - - +
49F GLU* 1.3 62.7 + - + +
51F SER 3.2 9.7 + - - -
52F THR 3.4 0.5 + - - -
53F GLY* 3.0 28.8 + - - -
54F THR 4.9 0.2 - - - +
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Residues in contact with GLU 49 (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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9F TYR* 4.2 13.8 + - - +
45F ALA* 3.0 21.9 + - + +
48F ALA* 1.3 77.0 - - + +
50F SER* 1.3 57.8 + - - +
51F SER 3.3 2.3 + - - +
53F GLY 5.3 2.6 - - - +
54F THR* 4.2 22.7 + - - -
55F TRP* 4.4 4.0 + - - +
107F SER* 4.5 3.1 - - - +
111F ASN* 5.1 18.6 + - + +
112F ILE* 3.8 20.6 + - + +
115F MET* 3.6 19.1 - - + -
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Residues in contact with SER 50 (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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46F VAL 2.8 21.2 + - - -
47F ALA* 3.1 8.7 + - - -
49F GLU* 1.3 76.6 - - - +
51F SER* 1.3 60.0 + - - +
91F TYR* 2.7 37.8 + - - -
96F PHE* 5.1 1.0 - - - -
107F SER* 3.0 48.2 + - - +
108F ILE* 4.4 2.2 - - - -
112F ILE* 4.2 8.5 - - - -
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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