Contacts of the strand formed by residues 41 - 49 (chain X) in PDB entry 2AT8
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 CYS 41 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40X TYR* 1.4 80.0 - - - +
42X ALA* 1.3 63.3 + - - +
58X TYR* 4.9 2.9 - - + -
59X HIS 3.7 0.2 - - - -
60X TYR* 2.9 62.7 + - + +
62X PRO* 4.2 5.4 - - - -
166X THR* 4.9 2.7 - - - -
169X ASN* 4.0 9.9 - - - -
171X CYS* 2.0 57.7 - - + -
173X TYR* 4.7 4.9 - - + -
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Residues in contact with ALA 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X VAL* 3.0 46.8 + - + +
40X TYR* 4.5 2.0 - - + -
41X CYS* 1.3 75.5 - - - +
43X ALA* 1.3 63.1 + - - +
58X TYR* 3.2 14.6 - - - +
59X HIS* 4.7 3.6 - - + +
166X THR* 5.3 1.2 - - - +
173X TYR* 3.9 11.6 + - - -
185X FDD 4.2 31.0 - - + -
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Residues in contact with ALA 43 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22X VAL* 4.5 0.4 - - + -
23X TRP 3.3 13.9 - - - +
24X TYR* 3.9 11.4 - - + +
25X VAL* 4.4 4.2 - - - +
42X ALA* 1.3 77.2 - - - +
44X LEU* 1.3 66.6 + - - +
57X LEU* 3.6 1.7 - - - +
58X TYR* 2.9 33.2 + - + +
173X TYR* 3.8 23.3 - - + -
178X LEU* 3.9 17.5 - - + -
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Residues in contact with LEU 44 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X TYR* 4.1 7.6 - - - +
22X VAL* 3.4 1.6 - - - +
23X TRP* 2.7 66.6 + - + +
25X VAL* 5.7 1.3 - - + -
43X ALA* 1.3 78.5 - - - +
45X ALA* 1.3 71.4 + - - +
46X ALA* 4.1 8.3 - - + -
55X GLU* 4.4 6.5 - - - +
56X ALA 3.0 13.7 - - - +
57X LEU* 3.7 15.9 - - + -
107X PHE* 4.2 18.4 - - + -
137X LEU* 4.6 12.3 - - + -
178X LEU* 4.4 7.2 - - - -
185X FDD 4.2 25.4 - - + -
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Residues in contact with ALA 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X GLY 4.5 0.2 - - - +
21X ASP 3.3 13.7 - - - +
22X VAL* 4.3 6.5 - - + -
44X LEU* 1.3 76.6 - - - +
46X ALA* 1.3 62.2 + - - +
55X GLU* 3.2 6.2 - - - +
56X ALA 2.8 32.1 + - - +
178X LEU* 3.5 37.5 - - + +
179X LYS* 4.3 1.6 - - - +
182X LEU* 3.8 16.6 - - + -
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Residues in contact with ALA 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X TYR* 3.9 28.3 - - + +
18X PHE* 3.5 24.2 - - + -
19X ASN 3.4 5.2 + - - -
20X GLY* 2.8 23.3 + - - -
21X ASP 3.3 6.0 + - - +
23X TRP* 4.5 2.7 - - + -
44X LEU* 4.1 10.3 - - + -
45X ALA* 1.3 77.7 - - - +
47X GLY* 1.3 58.0 + - - +
54X LYS 3.4 6.1 - - - -
55X GLU* 4.1 3.8 - - + -
182X LEU* 4.2 1.3 - - - -
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Residues in contact with GLY 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X PHE* 3.5 20.2 - - - -
20X GLY* 3.6 11.9 - - - -
46X ALA* 1.3 75.5 - - - +
48X THR* 1.3 63.2 + - - -
53X LEU* 3.8 1.6 - - - +
54X LYS* 2.8 37.8 + - - +
182X LEU* 3.9 9.3 - - - +
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Residues in contact with THR 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X PHE* 3.9 10.4 + - - +
19X ASN 5.6 0.4 - - - -
47X GLY* 1.3 71.0 - - - -
49X ALA* 1.3 62.2 + - - +
50X SER 4.3 0.7 + - - +
51X GLY* 3.6 35.9 - - - +
52X LYS 3.2 5.8 + - - +
53X LEU* 3.7 18.5 - - - +
182X LEU* 6.1 0.4 - - - -
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Residues in contact with ALA 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X GLY 4.0 0.4 + - - -
48X THR* 1.3 73.0 - - - +
50X SER* 1.3 73.9 + - - +
51X GLY 3.2 0.2 - - - -
52X LYS* 2.8 26.9 + - - +
54X LYS* 4.1 7.9 - - + +
182X LEU* 3.4 33.9 - - + +
183X THR* 4.1 15.3 - - + -
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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