Contacts of the strand formed by residues 40 - 48 (chain C) in PDB entry 1AUT
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 LEU 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C VAL* 3.2 31.2 - - + -
33C LEU 3.7 4.5 - - - -
34C LEU* 3.8 6.2 - - + +
35C ASP* 5.4 1.3 - - - +
39C LYS* 1.3 76.2 - - - +
41C ALA* 1.3 61.4 + - - +
42C CYS 3.5 15.3 - - - +
43C GLY* 5.2 0.4 - - - -
73C LEU* 4.5 13.8 - - + +
141C TRP* 4.0 28.9 - - + +
142C GLY* 5.2 5.8 - - - +
193C GLY* 3.2 37.9 - - - +
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Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C 0G6 5.4 0.3 + - - -
33C LEU 2.8 13.4 + - - +
35C ASP* 4.8 6.3 - - + +
39C LYS 3.5 3.0 + - - +
40C LEU* 1.3 75.8 - - - +
42C CYS* 1.3 74.6 + - + +
60C GLU* 3.8 30.3 - - + -
61C SER* 4.5 3.6 - - - +
64C LEU* 3.7 24.7 - - + -
193C GLY* 4.1 11.1 + - - -
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Residues in contact with CYS 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C 0G6 4.7 4.9 - - - -
33C LEU* 3.0 29.8 + - + +
40C LEU* 3.5 13.3 - - - +
41C ALA* 1.3 89.5 - - + +
43C GLY* 1.3 67.0 - - - +
57C HIS* 5.0 0.7 - - - -
58C CYS* 2.0 57.4 - - + -
60C GLU* 4.8 5.8 - - - -
193C GLY 3.8 15.7 - - - -
195C SER* 3.3 13.0 - - - +
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Residues in contact with GLY 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLN* 4.5 9.2 - - - -
31C VAL 3.4 11.4 - - - -
32C VAL* 4.6 0.4 - - - -
33C LEU* 3.7 4.6 - - - +
40C LEU* 5.2 2.2 - - - -
42C CYS* 1.3 76.2 - - - +
44C ALA* 1.3 63.3 + - - +
54C THR* 2.9 20.4 + - - -
141C TRP* 5.5 1.3 - - - -
193C GLY 4.0 3.7 + - - -
194C ASP 4.7 2.0 - - - -
195C SER 2.8 18.3 + - - +
196C GLY* 3.9 2.8 - - - -
197C GLY* 4.3 4.7 - - - -
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLN* 3.8 1.6 - - - +
31C VAL* 2.8 46.1 + - + +
33C LEU* 4.3 7.2 - - + -
43C GLY* 1.3 77.3 - - - +
45C VAL* 1.3 65.0 + - - +
52C VAL* 3.5 12.1 - - + -
53C LEU 3.3 15.7 - - - +
54C THR* 4.1 5.2 - - - -
196C GLY 3.5 11.1 + - - -
197C GLY* 4.2 1.6 - - - +
198C PRO* 3.8 11.8 - - - +
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C TRP* 3.1 12.3 - - + +
31C VAL* 4.2 0.7 - - - -
44C ALA* 1.3 79.1 - - - +
46C LEU* 1.3 60.7 + - - +
47C ILE* 3.3 7.5 + - + +
52C VAL* 3.4 5.3 - - - -
53C LEU* 3.0 47.1 + - + +
121C ILE* 3.3 35.2 - - + -
196C GLY 4.5 0.2 - - - +
198C PRO* 3.8 21.3 - - + -
209C LEU* 4.3 10.3 - - + -
212C LEU* 3.7 22.0 - - + -
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PRO 4.7 2.2 - - - +
29C TRP* 2.7 21.1 + - - +
31C VAL* 3.9 9.2 - - + +
45C VAL* 1.3 68.5 - - - +
47C ILE* 1.3 59.0 + - - +
48C HIS 3.1 26.7 - - - +
49C PRO 4.4 3.1 - - - +
51C TRP 4.1 1.6 - - - -
52C VAL* 4.0 19.3 - - + -
68C LEU* 4.1 17.3 - - + -
108C LEU* 4.4 7.9 - - + -
112C ALA* 5.0 0.2 - - + -
114C LEU* 4.6 6.3 - - + -
118C ILE* 3.7 30.1 - - + -
119C VAL 4.1 8.3 - - - +
120C PRO* 3.1 22.8 - - + +
121C ILE* 2.9 26.2 + - - +
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL* 3.3 10.9 + - + +
46C LEU* 1.3 73.9 - - - +
48C HIS* 1.3 63.5 + - + +
51C TRP* 3.3 19.9 + - + +
53C LEU* 3.9 30.3 - - + -
105C LEU* 4.1 6.1 - - + -
120C PRO* 4.0 6.9 - - - +
121C ILE* 3.6 32.4 - - + +
123C LEU* 4.0 22.2 - - + +
209C LEU* 3.9 19.7 - - + -
238C ILE* 3.9 26.5 - - + -
242C ILE* 4.4 7.3 - - + +
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Residues in contact with HIS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 3.1 15.6 - - - +
47C ILE* 1.3 80.3 - - - +
49C PRO* 1.3 87.4 - - + +
50C SER* 2.9 27.0 + - - -
51C TRP* 3.1 54.4 + + + +
120C PRO* 4.0 4.4 - - - +
242C ILE* 4.3 22.8 - - + +
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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