Contacts of the helix formed by residues 31 - 39 (chain A) in PDB entry 1SFU
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 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A TYR* 5.0 6.1 - - + -
30A THR* 1.3 84.6 + - - +
32A ALA* 1.3 65.0 + - - +
33A ILE* 2.9 29.0 - - + +
34A SER* 3.2 11.2 + - - -
35A LEU* 3.0 27.4 + - - +
66A PRO* 4.6 15.0 - - + -
67A PRO 3.9 18.8 - - - +
68A LYS* 4.7 10.5 - - + -
69A TRP* 4.2 5.2 - - - -
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 1.3 74.2 - - - +
33A ILE* 1.3 54.0 + - - +
35A LEU* 3.2 1.2 + - - +
36A SER* 2.7 37.1 + - - -
43A LYS* 3.8 20.6 - - + -
46A ILE* 3.9 14.5 - - + +
47A ASN* 3.4 28.3 - - - +
50A LEU* 4.1 9.6 - - + -
66A PRO* 6.0 0.4 - - - +
67A PRO 4.8 1.0 + - - -
69A TRP* 4.3 7.3 - - - +
3C C 5.9 0.4 - - - +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR* 2.9 29.4 - - + +
32A ALA* 1.3 80.3 - - - +
34A SER* 1.3 63.5 + - - +
36A SER* 3.6 7.1 - - - +
37A ASN* 3.0 25.5 + - + +
43A LYS* 4.0 21.1 - - + +
66A PRO* 5.1 9.9 - - + -
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Residues in contact with SER 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A THR* 3.7 16.1 + - - -
31A THR* 3.2 15.1 + - - -
33A ILE* 1.3 84.6 - - - +
35A LEU* 1.3 62.3 + - - +
37A ASN* 3.0 11.3 + - - +
38A ARG* 3.0 50.3 + - - +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 4.2 9.9 - - + -
20A GLU* 3.9 30.7 - - + +
21A VAL* 4.6 3.6 - - + -
30A THR* 3.9 28.5 - - + +
31A THR 3.0 20.8 + - - +
32A ALA 3.7 3.1 - - - +
34A SER* 1.3 75.3 - - - +
36A SER* 1.3 64.3 + - - +
38A ARG* 3.1 8.0 + - - +
39A LEU* 2.9 40.1 + - + +
46A ILE* 3.8 16.6 - - + -
50A LEU* 3.9 34.3 - - + -
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ALA 2.7 21.4 + - - -
33A ILE* 3.6 10.2 - - - +
35A LEU* 1.3 72.2 - - - +
37A ASN* 1.3 57.8 + - - +
40A LYS* 3.1 23.4 + - - -
41A ILE 2.4 35.7 + - - +
42A ASN* 4.2 0.2 - - - -
43A LYS* 3.5 27.2 + - - +
46A ILE* 3.7 9.5 - - - +
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Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 3.0 18.9 + - + +
34A SER* 3.0 15.2 + - - +
36A SER* 1.3 79.8 - - - +
38A ARG* 1.3 58.7 + - - +
40A LYS* 2.7 41.1 + - - +
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU* 4.1 17.9 + - - +
30A THR* 5.3 3.8 + - - -
34A SER* 3.0 37.8 + - - +
35A LEU* 3.1 6.3 + - - +
37A ASN* 1.3 82.5 - - + +
39A LEU* 1.3 71.6 + - + +
40A LYS* 3.0 21.2 + - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.6 46.2 - - + +
17A VAL* 4.0 8.5 - - + +
20A GLU* 3.8 22.9 - - + -
35A LEU* 2.9 29.2 + - + +
38A ARG* 1.3 83.6 - - + +
40A LYS* 1.3 69.6 + - - +
41A ILE* 3.0 27.2 - - + +
46A ILE* 4.1 17.5 - - + -
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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