Contacts of the strand formed by residues 73 - 80 (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 ALA 73 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D ALA* 4.4 10.3 - - + -
71D LYS 3.1 5.6 - - - +
72D ASN* 1.3 76.8 - - - +
74D PRO* 1.3 68.1 - - + +
111D GLY 3.6 24.0 - - - +
113D ILE* 3.7 22.6 - - + +
163D GLU 3.1 6.5 + - - +
164D SER* 3.0 26.0 - - - -
165D ASN* 3.2 3.1 + - - +
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Residues in contact with PRO 74 (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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72D ASN 4.0 5.6 - - - +
73D ALA* 1.3 88.9 - - + +
75D ILE* 1.3 59.9 + - - +
110D GLY 5.6 1.3 - - - +
111D GLY 4.8 5.6 - - - +
112D TYR* 3.4 29.6 - - + -
113D ILE* 3.0 24.6 + - - +
165D ASN* 3.4 14.8 - - - +
167D LYS 3.7 3.4 - - - +
376D LEU* 3.5 37.5 - - + +
377D VAL* 4.0 17.9 - - + -
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Residues in contact with ILE 75 (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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74D PRO* 1.3 76.8 - - - +
76D VAL* 1.3 71.1 + - - +
77D LEU* 4.3 2.2 - - + +
112D TYR* 4.8 0.2 - - - -
113D ILE* 3.4 20.0 - - + +
115D VAL* 3.6 26.5 - - + -
157D LEU* 4.2 35.2 - - + +
158D VAL* 5.2 1.6 - - + +
161D VAL* 4.4 13.0 - - + -
164D SER* 3.7 31.4 - - - +
166D GLY 5.9 0.2 - - - +
167D LYS 3.1 11.8 + - - +
168D VAL* 3.3 16.3 - - + -
169D GLY* 2.9 26.0 + - - +
376D LEU* 4.6 2.4 - - - +
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Residues in contact with VAL 76 (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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75D ILE* 1.3 73.7 - - - +
77D LEU* 1.3 60.0 + - - +
107D PHE* 3.8 24.0 - - + -
112D TYR* 3.3 34.8 - - + -
113D ILE 3.0 6.4 + - - +
114D ARG* 3.2 26.2 + - - +
115D VAL* 2.9 24.8 + - - +
169D GLY 3.3 4.3 - - - +
171D ILE* 3.5 31.6 - - + -
372D PHE* 3.8 18.6 - - + -
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Residues in contact with LEU 77 (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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75D ILE* 4.0 5.8 - - + -
76D VAL* 1.3 75.1 - - - +
78D THR* 1.3 78.5 + - - +
79D ARG* 4.4 12.8 - - + -
115D VAL* 3.4 28.5 - - + +
117D GLN* 4.5 4.7 - - + -
150D ALA 5.0 0.4 - - - +
153D THR* 4.2 23.1 - - + -
154D ILE* 3.9 28.3 - - + -
157D LEU* 4.4 5.2 - - + -
168D VAL* 4.1 9.6 - - + -
169D GLY 2.8 14.0 + - - +
170D MSE 3.3 27.6 - - + +
171D ILE 3.2 24.4 + - - +
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Residues in contact with THR 78 (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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77D LEU* 1.3 74.5 + - - +
79D ARG* 1.3 66.8 + - - +
80D THR 4.1 0.2 + - - -
114D ARG* 3.1 28.7 + - - +
115D VAL 3.0 6.1 + - - +
116D PHE* 3.3 22.7 - - + -
117D GLN 2.9 23.7 + - - -
170D MSE 5.2 1.3 - - - -
171D ILE* 2.4 29.7 + - - +
172D GLY* 4.3 1.1 - - - -
176D GLU* 3.5 38.8 - - + +
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Residues in contact with ARG 79 (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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60D LEU* 3.4 20.6 - - - +
77D LEU* 4.4 13.0 - - + -
78D THR* 1.3 75.1 - - - +
80D THR* 1.3 61.1 + - - +
117D GLN* 2.8 34.9 + - + +
119D VAL* 4.0 19.0 - - + +
120D ARG 4.6 0.4 - - - +
146D HIS* 3.2 36.2 + - - -
149D ASP* 3.4 19.5 + - - +
150D ALA* 3.8 22.2 - - - +
153D THR* 4.4 0.8 + - - -
170D MSE 3.7 27.7 - - + +
176D GLU* 3.6 10.9 - - - -
179D THR* 2.8 42.3 + - + +
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Residues in contact with THR 80 (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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78D THR* 4.6 1.1 - - - -
79D ARG* 1.3 75.4 - - - +
81D PRO* 1.3 67.8 - - - +
82D TYR* 2.9 22.3 + - - +
84D ALA* 4.1 21.3 - - - +
87D ARG* 4.4 4.0 - - + -
116D PHE* 4.1 19.1 - - + -
117D GLN 2.9 15.8 + - - +
118D ASP* 3.4 5.4 - - - +
119D VAL* 3.0 25.8 + - - +
122D LYS* 5.0 0.2 - - - +
176D GLU* 2.6 31.9 + - - +
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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