Contacts of the strand formed by residues 59 - 67 (chain D) in PDB entry 1MPX
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 59 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D MSE 3.6 38.8 - - + +
52D ILE 3.3 6.1 - - - +
53D PRO* 4.0 24.7 - - + -
57D GLY 3.8 13.2 + - - +
58D VAL* 1.3 73.0 - - - +
60D LEU* 1.3 62.6 + - - +
126D GLU* 3.0 51.9 + - - +
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Residues in contact with LEU 60 (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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50D VAL 3.4 0.4 - - - +
51D MSE 4.4 2.0 - - - -
52D ILE* 3.0 25.2 + - - +
54D MSE 3.6 33.4 - - + -
58D VAL* 4.1 7.6 - - + -
59D LYS* 1.3 79.9 - - - +
61D HIS* 1.3 60.4 + - - +
62D THR* 3.0 17.0 + - - -
79D ARG* 3.4 29.4 - - - +
117D GLN* 3.6 18.4 - - - +
118D ASP 3.8 6.7 - - - +
120D ARG* 3.6 30.3 - - + +
125D SER* 3.3 13.0 - - - +
126D GLU 4.1 5.2 - - - +
149D ASP* 4.0 5.6 - - - +
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Residues in contact with HIS 61 (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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49D GLU* 2.6 37.4 + - + +
50D VAL 4.5 2.2 - - - -
51D MSE 3.6 19.7 - - + -
60D LEU* 1.3 68.1 - - - +
62D THR* 1.3 63.2 + - - +
63D VAL* 3.7 14.1 + - + +
83D ASP* 5.8 0.4 - - - -
84D ALA* 4.6 0.7 - - - +
85D SER* 3.2 28.0 - - - -
116D PHE 4.4 0.3 - - - +
117D GLN* 3.4 2.8 - - - +
118D ASP* 2.8 51.9 + - - +
124D GLY* 3.5 32.4 - - - +
125D SER* 3.0 8.5 + - - +
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Residues in contact with THR 62 (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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48D ARG 3.7 0.3 - - - +
49D GLU* 3.4 4.0 - - - +
50D VAL* 2.9 43.2 + - - +
52D ILE* 3.3 24.2 - - + +
60D LEU 3.0 13.9 + - - -
61D HIS* 1.3 73.1 - - - +
63D VAL* 1.3 61.4 + - - +
64D ILE* 4.5 6.1 - - + -
115D VAL* 3.4 31.4 - - + -
116D PHE 3.7 4.9 - - - +
117D GLN* 3.1 26.5 + - + +
153D THR* 5.0 1.8 - - + -
157D LEU* 4.9 1.6 - - + -
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Residues in contact with VAL 63 (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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47D LYS* 3.9 27.6 - - + -
48D ARG 3.6 4.0 - - - +
49D GLU* 4.2 7.0 - - + -
61D HIS* 3.7 30.7 - - + +
62D THR* 1.3 71.5 - - - +
64D ILE* 1.3 62.5 + - - +
65D VAL* 4.3 2.5 - - + -
84D ALA* 4.0 13.2 - - + +
85D SER* 4.0 13.5 - - - +
88D THR* 3.4 32.4 - - + +
114D ARG 3.7 1.6 - - - +
115D VAL* 3.3 5.4 - - - +
116D PHE 2.9 35.4 + - - +
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Residues in contact with ILE 64 (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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46D ILE 3.4 2.3 - - - +
47D LYS* 3.4 3.8 - - - +
48D ARG* 2.8 57.5 + - - +
50D VAL* 3.9 26.0 - - + -
62D THR* 4.5 4.3 - - + +
63D VAL* 1.3 76.3 - - - +
65D VAL* 1.3 63.3 + - - +
66D LEU* 3.8 18.5 - - + +
113D ILE* 3.5 26.5 - - + -
114D ARG 3.6 2.5 - - - -
115D VAL* 3.9 20.4 - - + -
156D TRP* 4.3 3.6 - - + -
157D LEU* 4.1 17.9 - - + -
161D VAL* 4.2 13.5 - - + -
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Residues in contact with VAL 65 (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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45D TYR* 4.2 14.1 - - + -
46D ILE 3.4 2.7 - - - -
47D LYS* 4.0 25.1 - - + -
63D VAL* 4.3 2.5 - - + -
64D ILE* 1.3 76.1 - - - +
66D LEU* 1.3 61.1 + - - +
88D THR* 4.2 11.9 - - + -
96D MSE 3.7 34.8 - - + +
99D LEU* 4.2 14.6 - - + -
100D LEU* 4.2 16.4 - - + -
113D ILE* 3.5 3.3 - - - -
114D ARG* 2.8 46.3 + - + +
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Residues in contact with LEU 66 (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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45D TYR* 3.2 5.1 - - - -
46D ILE* 2.8 56.1 + - + +
48D ARG* 3.7 25.1 - - + +
64D ILE* 3.8 17.9 - - + +
65D VAL* 1.3 75.8 - - - +
67D PRO* 1.3 75.5 - - + +
70D ALA* 4.5 2.0 - - + -
96D MSE 4.4 0.9 - - - -
113D ILE* 3.8 22.9 - - + -
161D VAL* 4.1 7.0 - - + -
163D GLU* 3.6 42.8 - - + +
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Residues in contact with PRO 67 (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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44D ASP 3.8 8.5 - - - +
46D ILE* 5.8 0.2 - - - -
65D VAL 4.2 0.9 - - - +
66D LEU* 1.3 90.1 - - + +
68D LYS* 1.3 69.0 + - - +
69D GLY 3.4 0.2 + - - -
70D ALA* 3.2 29.6 + - + +
96D MSE 3.9 18.4 - - - -
108D VAL 5.7 1.6 - - - +
111D GLY* 3.8 22.4 - - - +
112D TYR 3.5 28.7 - - - +
113D ILE* 4.2 2.2 - - + -
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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