Contacts of the strand formed by residues 18 - 25 (chain C) 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 PHE 18 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C THR* 1.3 77.6 - - - +
19C LEU* 1.3 63.2 + - - +
20C HIS* 3.5 13.6 + + + -
35C GLU* 3.2 37.0 - - + -
36C ALA 3.5 12.6 - - - -
37C TYR* 4.8 4.9 - - + -
42C LEU* 3.9 26.9 - - + -
43C PHE* 6.2 0.4 - + - -
9D SER 3.8 0.3 - - - +
10D THR* 3.3 5.0 - - - -
11D CYS* 2.9 46.8 + - + +
13D LEU* 5.8 1.6 - - + -
82D HIS* 3.7 24.7 - + - -
83D THR* 4.3 16.8 - - + -
86D PHE* 4.1 11.9 - + - -
87D TRP* 4.9 13.5 - + + -
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Residues in contact with LEU 19 (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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17C THR* 4.0 7.6 - - + +
18C PHE* 1.3 74.2 - - - +
20C HIS* 1.3 58.0 + - - +
21C THR* 3.2 21.1 - - - +
34C SER 3.5 1.9 - - - +
35C GLU* 3.2 8.7 - - - +
36C ALA* 3.0 41.4 + - + +
152C ALA* 3.8 31.2 - - + +
153C VAL* 4.1 14.4 - - - -
154C ASP* 4.3 12.6 - - + +
8D GLU* 3.4 21.5 - - + +
9D SER 4.1 0.9 - - - -
10D THR* 3.5 24.5 - - + -
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Residues in contact with HIS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PHE* 3.5 12.5 + + + -
19C LEU* 1.3 72.7 - - - +
21C THR* 1.3 59.8 + - - +
22C VAL* 4.0 12.8 + - + +
33C LEU* 3.3 34.5 - - + +
34C SER 4.0 0.4 - - - -
35C GLU* 3.0 37.5 + - + -
52C ARG* 4.4 3.8 + - - -
68C ASP* 4.5 8.5 + - - -
71C ALA* 6.0 2.0 - - + -
72C ILE* 4.2 16.2 - - + +
75C ASP* 4.8 8.2 + - - -
7D VAL 4.0 0.7 + - - +
8D GLU* 3.5 1.7 - - - +
9D SER* 2.7 62.8 + - - +
71D ARG* 6.1 0.4 + - - -
82D HIS* 5.9 0.4 - + - -
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Residues in contact with THR 21 (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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19C LEU* 3.2 19.6 - - - +
20C HIS* 1.3 72.4 - - - +
22C VAL* 1.3 62.9 + - - +
23C TYR* 3.5 11.0 - - + -
33C LEU* 3.2 9.2 - - - +
34C SER 2.9 38.5 + - - -
152C ALA* 3.8 21.3 - - + -
6D HIS* 4.1 22.0 - - + +
7D VAL 4.2 1.8 - - - -
8D GLU* 2.8 32.1 + - + +
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Residues in contact with VAL 22 (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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20C HIS* 4.1 14.1 - - + +
21C THR* 1.3 76.9 - - - +
23C TYR* 1.3 66.3 + - - +
31C VAL* 4.9 3.6 - - + -
32C GLY 3.5 9.2 - - - +
33C LEU* 3.9 23.6 - - + +
47C PHE* 5.1 2.2 - - + -
72C ILE* 5.4 2.0 - - - +
75C ASP* 3.8 21.8 - - + +
76C LYS* 3.8 32.1 - - + +
79C CYS* 4.5 6.1 - - + -
6D HIS* 3.5 1.9 - - - -
7D VAL* 2.7 47.6 + - + +
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Residues in contact with TYR 23 (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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21C THR* 3.5 18.2 - - + -
22C VAL* 1.3 75.3 - - - +
24C CYS* 1.3 69.0 + - - +
25C GLN* 4.9 7.9 - - - -
29C PRO* 5.5 5.0 - - + +
31C VAL* 3.3 6.7 - - - +
32C GLY* 2.8 72.5 + - - +
33C LEU* 3.8 4.9 + - - -
34C SER* 4.2 13.4 - - - -
79C CYS* 3.8 1.6 - - - -
129C PRO* 4.0 16.8 - - + +
150C VAL* 4.8 14.6 + - - +
151C SER* 6.1 0.7 - - - -
158C PHE* 3.8 42.6 - + + -
4D VAL* 4.7 3.4 - - + -
5D ALA 3.2 13.5 - - - +
6D HIS* 4.3 9.0 - - + +
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Residues in contact with CYS 24 (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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23C TYR* 1.3 80.0 - - - +
25C GLN* 1.3 63.9 + - - +
30C SER 3.2 14.8 - - - +
31C VAL* 4.0 15.7 - - + +
79C CYS* 2.0 65.5 - - - -
80C GLU* 3.4 10.1 - - + -
83C ILE* 3.7 11.6 - - + +
4D VAL* 3.3 6.3 - - - +
5D ALA 2.9 28.9 + - - +
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Residues in contact with GLN 25 (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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23C TYR* 4.9 6.3 - - + -
24C CYS* 1.3 78.8 - - - +
26C ASP* 1.3 64.9 + - - +
27C GLY 3.6 11.0 + - - +
29C PRO* 2.9 32.0 + - - +
30C SER* 2.9 20.7 + - - +
83C ILE* 3.7 15.5 - - - +
128C PRO* 3.5 25.7 - - + +
129C PRO* 3.2 35.2 + - - +
130C MET* 3.5 21.3 - - - +
3D PHE 3.2 15.0 - - - +
4D VAL* 4.0 6.5 - - + -
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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