Contacts of the strand formed by residues 4 - 11 (chain D) in PDB entry 4FQX
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 VAL 4 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C TYR* 4.7 6.1 - - + -
24C CYS 3.3 7.9 - - - +
25C GLN* 4.0 9.9 - - + -
83C ILE* 4.1 1.6 - - - -
127C PHE* 3.7 24.4 - - + -
128C PRO* 3.7 30.5 - - + -
129C PRO* 4.2 6.5 - - + -
158C PHE* 4.5 7.4 - - + -
3D PHE* 1.3 80.9 - - - +
5D ALA* 1.3 66.2 + - - +
6D HIS* 3.3 35.1 - - + +
28D PHE* 3.7 1.7 - - - -
29D ASN* 2.9 29.0 + - - +
30D LYS 4.2 0.2 + - - -
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Residues in contact with ALA 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 3.2 8.8 - - - +
24C CYS 2.9 27.6 + - - -
79C CYS* 3.6 18.6 - - - -
82C MET* 3.9 25.4 - - + -
83C ILE* 3.4 21.3 - - + +
4D VAL* 1.3 75.2 - - - +
6D HIS* 1.3 62.0 + - - +
27D SER 3.6 6.3 - - - +
28D PHE* 4.1 5.6 - - + +
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Residues in contact with HIS 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C THR* 4.1 18.5 - - + +
22C VAL 3.5 2.9 - - - +
23C TYR* 4.3 3.4 - - + +
82C MET* 4.0 0.3 - - - +
127C PHE* 3.8 15.8 - + - -
156C LEU* 3.2 46.4 + - + +
157C SER 5.7 0.4 - - - -
158C PHE* 3.7 27.1 - + - -
4D VAL* 3.3 35.4 - - + +
5D ALA* 1.3 73.9 - - - +
7D VAL* 1.3 65.7 + - - +
8D GLU* 3.9 5.6 - - + +
26D ILE* 3.3 7.4 - - - +
27D SER* 2.9 43.4 + - - +
30D LYS 5.0 3.4 - - - -
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Residues in contact with VAL 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C HIS* 4.0 1.7 + - - +
22C VAL* 2.7 45.1 + - + +
75C ASP* 3.2 40.4 - - + +
78C PHE* 4.0 10.1 - - + -
79C CYS* 3.7 18.4 - - + -
82C MET* 3.6 23.1 - - + -
5D ALA 4.3 0.2 - - - -
6D HIS* 1.3 74.4 - - - +
8D GLU* 1.3 59.6 + - - +
9D SER 4.1 0.3 + - - -
24D TYR* 3.5 20.6 - - + +
25D CYS 3.7 2.7 - - - +
26D ILE* 4.4 6.7 - - + -
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Residues in contact with GLU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 3.4 24.0 - - + +
20C HIS 3.5 4.3 - - - +
21C THR* 2.8 36.7 + - + +
152C ALA* 5.4 0.3 - - - +
153C VAL 4.9 5.2 - - - +
154C ASP* 5.1 6.8 - - - +
155C GLY 5.4 0.6 + - - -
156C LEU* 3.8 32.5 + - + +
6D HIS* 5.0 2.2 - - + -
7D VAL* 1.3 74.7 - - - +
9D SER* 1.3 61.1 + - - +
10D THR* 4.2 9.3 + - + +
23D THR* 4.6 1.0 + - - -
24D TYR* 3.4 3.4 + - - -
25D CYS* 2.7 49.7 + - + +
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Residues in contact with SER 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C PHE 3.8 0.3 - - - +
20C HIS* 2.7 63.7 + - - +
75C ASP* 5.2 3.1 + - - -
7D VAL 4.1 0.8 + - - -
8D GLU* 1.3 74.1 - - - +
10D THR* 1.3 63.2 + - - +
22D PHE* 4.7 9.4 - - - -
23D THR 3.4 13.2 - - - -
24D TYR* 3.9 20.0 - - - -
71D ARG* 5.3 3.1 + - - -
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Residues in contact with THR 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C THR* 4.5 15.3 - - + +
18C PHE 3.3 8.5 - - - -
19C LEU* 3.5 28.3 - - + -
154C ASP* 6.1 0.7 - - - +
8D GLU* 4.2 11.9 - - + +
9D SER* 1.3 78.1 - - - +
11D CYS* 1.3 62.2 + - - +
12D LEU* 5.2 0.9 + - - +
22D PHE* 3.6 6.4 - - - -
23D THR* 2.7 50.7 + - - +
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Residues in contact with CYS 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C THR* 3.8 1.7 - - - -
18C PHE* 2.9 47.7 + - + +
10D THR* 1.3 75.4 - - - +
12D LEU* 1.3 61.2 + - - +
13D LEU* 3.4 21.2 + - + +
19D PRO* 4.1 4.9 - - - -
21D ASP 3.8 11.9 - - - -
22D PHE* 4.4 1.6 - - + -
79D CYS* 2.0 56.1 - - + -
83D THR* 6.1 0.9 - - + -
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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