Contacts of the strand formed by residues 29 - 34 (chain C) in PDB entry 1MOX
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 LYS 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.3 15.3 - - + -
89A TYR* 4.5 8.6 + - - +
90A GLU* 3.8 32.1 + - - +
23C PHE* 3.4 11.2 - - - -
24C LEU* 3.0 30.0 + - + +
27C GLU* 3.5 37.4 + - + +
28C ASP* 1.3 75.7 - - - +
30C PRO* 1.3 80.1 - - + +
31C ALA* 6.1 0.2 - - + -
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Residues in contact with PRO 30 (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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357A PHE* 5.6 5.8 - - + -
8C CYS* 4.2 3.4 - - - -
15C PHE* 3.5 35.8 - - + -
21C CYS* 3.6 23.3 - - - -
22C ARG 3.4 6.5 - - - +
23C PHE* 3.7 18.6 - - + -
29C LYS* 1.3 98.1 - - + +
31C ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 31 (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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14A LEU* 3.7 35.2 - - + +
15A THR* 4.7 1.6 - - - -
45A TYR* 4.8 1.6 - - - +
15C PHE* 4.6 2.7 - - - -
16C CYS* 3.7 1.7 - - - -
21C CYS* 3.4 7.1 - - - -
22C ARG* 2.9 39.4 + - + +
24C LEU* 4.2 14.4 - - + -
29C LYS* 3.9 0.4 + - + -
30C PRO* 1.3 73.9 - - - +
32C CYS* 1.3 68.7 + - - +
41C ALA 5.4 1.3 - - - -
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Residues in contact with CYS 32 (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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14A LEU 4.4 0.7 - - - +
15A THR* 3.3 14.9 + - - +
16A GLN* 2.8 27.9 + - - +
15C PHE* 4.3 7.4 - - - -
16C CYS* 2.0 48.7 - - + -
20C THR 3.5 3.8 - - - -
22C ARG* 4.4 4.0 + - - -
31C ALA* 1.3 77.2 - - - +
33C VAL* 1.3 65.0 + - - +
41C ALA 3.7 15.9 - - - -
42C ARG* 3.9 8.1 - - - -
43C CYS* 3.3 19.7 - - - -
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Residues in contact with VAL 33 (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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16A GLN* 3.2 12.6 - - + +
18A GLY* 4.2 21.3 - - - +
19C GLY* 3.2 2.0 - - - -
20C THR* 3.1 37.4 + - + +
22C ARG* 3.5 41.7 - - - +
32C CYS* 1.3 80.3 - - - +
34C CYS* 1.3 67.4 + - - +
35C HIS* 4.9 1.2 - - - -
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Residues in contact with CYS 34 (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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15A THR* 3.6 16.4 - - - -
16A GLN 2.9 9.7 + - - +
17A LEU* 3.7 17.3 - - + -
18A GLY* 3.4 19.6 + - - -
18C HIS 3.1 10.5 - - - +
19C GLY* 3.6 0.4 - - - -
33C VAL* 1.3 79.0 - - - +
35C HIS* 1.3 65.3 + - - +
36C SER 3.7 0.3 + - - -
38C TYR* 3.6 20.9 - - + +
39C VAL* 4.4 0.2 - - - -
40C GLY 4.1 2.0 - - - -
43C CYS* 2.0 50.9 - - + -
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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