Contacts of the strand formed by residues 123 - 130 (chain D) in PDB entry 3MX4
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 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D SER* 4.3 3.3 - - - -
37D LEU* 3.7 30.6 + - + -
51D LEU* 4.7 4.9 - - + -
52D TYR 3.1 16.6 - - - -
53D TYR* 3.3 36.1 - + + -
75D ILE* 4.2 11.0 - - + -
112D ILE* 3.6 39.0 - - + -
118D LEU* 4.0 15.5 - - + -
119D ASP 3.4 17.3 - - - -
120D LEU* 3.2 15.2 + - - +
121D CYS 4.5 3.6 - - - +
122D ASP* 1.3 80.1 - - - +
124D SER* 1.3 68.3 + - - +
153D TRP* 3.9 31.9 - + - -
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Residues in contact with SER 124 (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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34D VAL* 3.9 7.0 - - - -
35D HIS 3.1 15.0 - - - -
37D LEU* 4.4 6.1 - - - -
51D LEU* 3.1 9.9 - - - +
52D TYR* 2.7 34.7 + - - -
54D THR* 5.2 3.1 + - - +
71D TYR* 3.6 33.8 + - - -
122D ASP 5.0 1.2 + - - -
123D PHE* 1.3 80.4 + - - +
125D CYS* 1.3 63.7 + - - +
2F HIS 3.9 6.8 + - - -
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Residues in contact with CYS 125 (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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34D VAL* 3.5 5.5 - - - +
35D HIS* 2.8 38.2 + - - +
36D SER 3.4 21.1 - - - -
37D LEU* 4.3 4.3 - - + -
39D PRO* 3.9 23.6 - - - -
49D TYR* 5.4 1.1 - - + -
50D ALA 3.0 12.1 - - - +
51D LEU* 3.8 15.3 - - + -
52D TYR* 4.2 4.0 - - - -
105D ILE* 4.4 10.3 - - + -
124D SER* 1.3 77.1 - - - +
126D ARG* 1.3 66.0 + - - +
127D PHE* 4.6 9.5 - - - -
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Residues in contact with ARG 126 (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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29D PHE* 3.7 25.1 - - + -
30D SER* 3.4 24.0 + - - +
31D GLY* 5.2 0.8 - - - -
32D THR* 2.9 31.1 + - - +
33D PRO 3.8 15.7 - - - +
34D VAL* 3.4 22.8 - - + +
49D TYR* 3.2 2.8 - - - +
50D ALA 3.0 28.7 + - - -
52D TYR* 3.0 29.6 + - + -
71D TYR* 2.9 36.6 + - - +
125D CYS* 1.3 78.4 - - - +
127D PHE* 1.3 67.4 + - - +
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Residues in contact with PHE 127 (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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29D PHE* 4.2 1.8 - - - -
32D THR* 4.2 3.6 + - - -
35D HIS* 4.4 10.8 - - - -
39D PRO* 4.3 14.6 - - + -
43D PHE* 3.6 47.6 - + - -
48D VAL 3.4 11.2 - - - +
49D TYR* 3.9 0.9 - - + +
101D LEU* 4.2 8.1 - - + -
105D ILE* 3.9 22.4 - - + -
125D CYS* 4.6 5.4 - - - -
126D ARG* 1.3 81.9 - - - +
128D VAL* 1.3 69.2 + - - +
129D ILE* 4.1 8.1 - - + -
6F PHE* 4.1 13.5 - + - -
8F ARG* 5.4 0.7 - - + -
11F HIS* 3.1 71.3 + + + +
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Residues in contact with VAL 128 (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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25D ALA 5.3 1.3 - - - +
28D PHE* 4.3 4.9 - - + -
29D PHE* 3.2 43.9 - - + -
32D THR* 3.9 12.8 - - + -
47D GLY* 3.1 7.3 - - - -
48D VAL* 2.9 34.8 + - + +
101D LEU* 3.3 5.8 - - - +
127D PHE* 1.3 79.0 - - - +
129D ILE* 1.3 70.6 + - - +
130D PHE* 3.7 18.5 - - + -
141D VAL* 6.4 0.4 - - + -
11F HIS 3.3 10.3 - - - +
13F TYR* 3.7 20.2 - - + -
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Residues in contact with ILE 129 (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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43D PHE* 3.8 13.0 - - + -
44D GLN 3.8 6.1 - - - +
45D GLY* 4.3 9.6 - - - -
46D ALA 3.2 9.2 - - - +
101D LEU* 4.0 15.5 - - + -
127D PHE* 4.1 11.2 - - + -
128D VAL* 1.3 76.6 - - - +
130D PHE* 1.3 66.8 + - - +
131D GLU* 3.8 23.1 - - - +
8F ARG* 3.6 53.6 - - + +
11F HIS* 2.9 9.6 + - + +
12F VAL* 3.4 12.2 - - + +
13F TYR* 2.9 26.9 + - - -
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Residues in contact with PHE 130 (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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25D ALA* 5.0 2.7 - - + -
46D ALA* 2.9 19.4 + - - +
47D GLY* 3.8 2.5 - - - -
48D VAL* 4.1 19.7 - - + -
128D VAL* 3.7 28.7 - - + -
129D ILE* 1.3 81.5 - - - +
131D GLU* 1.3 62.7 + - - +
132D ALA 3.9 0.7 + - - -
134D GLY* 3.6 29.4 - - - +
135D SER* 4.3 5.9 + - - +
137D MET* 4.1 13.7 - - + -
138D ILE* 3.8 24.7 - - + -
141D VAL* 3.6 37.2 - - + -
13F TYR* 3.8 32.8 - + - -
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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