Contacts of the strand formed by residues 73 - 80 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C ALA* 4.5 10.3 - - + -
71C LYS 3.1 6.2 + - - +
72C ASN* 1.3 78.2 - - - +
74C PRO* 1.3 67.6 - - + +
111C GLY 3.5 24.9 - - - +
113C ILE* 3.8 15.0 - - + +
163C GLU 3.1 9.8 + - - +
164C SER* 2.8 27.7 + - - -
165C ASN* 3.1 2.3 + - - -
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Residues in contact with PRO 74 (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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72C ASN 4.1 4.0 - - - +
73C ALA* 1.3 91.3 - - + +
75C ILE* 1.3 60.7 + - - +
110C GLY 5.6 1.1 - - - +
111C GLY 4.8 2.0 - - - +
112C TYR* 3.4 34.3 - - + -
113C ILE* 3.0 25.6 + - - +
165C ASN* 3.3 11.9 - - - +
167C LYS 3.7 4.0 - - - +
376C LEU* 3.4 43.5 - - + +
377C VAL* 4.1 13.9 - - + -
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Residues in contact with ILE 75 (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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74C PRO* 1.3 75.0 - - - +
76C VAL* 1.3 70.8 + - - +
77C LEU* 4.3 3.6 - - + +
113C ILE* 3.3 21.8 - - + +
115C VAL* 3.7 25.4 - - + -
157C LEU* 4.2 33.9 - - + +
158C VAL* 5.6 1.6 - - + -
161C VAL* 4.3 15.3 - - + -
164C SER* 3.4 30.3 - - - +
167C LYS 3.0 11.4 + - - +
168C VAL* 3.3 18.0 - - + -
169C GLY* 2.8 25.5 + - - +
376C LEU* 4.6 2.3 - - - +
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Residues in contact with VAL 76 (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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75C ILE* 1.3 75.0 - - - +
77C LEU* 1.3 60.9 + - - +
107C PHE* 3.9 16.6 - - + -
112C TYR* 3.4 31.4 - - + -
113C ILE 2.9 7.4 + - - +
114C ARG* 3.2 25.2 + - - +
115C VAL* 2.9 25.6 + - - +
169C GLY 3.3 4.5 - - - +
171C ILE* 3.5 30.7 - - + -
372C PHE* 3.8 26.5 - - + -
376C LEU* 4.7 0.4 - - + -
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Residues in contact with LEU 77 (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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75C ILE* 4.0 5.4 - - + -
76C VAL* 1.3 74.5 - - - +
78C THR* 1.3 78.2 + - - +
79C ARG* 4.4 10.5 - - + -
115C VAL* 3.4 29.6 - - + +
117C GLN* 4.7 4.9 - - + -
150C ALA 5.0 0.4 - - - +
153C THR* 4.1 20.9 - - + -
154C ILE* 3.8 28.0 - - + -
157C LEU* 4.3 9.4 - - + -
168C VAL* 4.2 8.1 - - + -
169C GLY 2.8 13.4 + - - +
170C MSE 3.3 29.5 - - + +
171C ILE 3.2 23.4 + - - +
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Residues in contact with THR 78 (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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77C LEU* 1.3 74.5 + - - +
79C ARG* 1.3 65.6 + - - +
80C THR 4.1 0.2 + - - -
114C ARG* 3.0 29.7 + - - -
115C VAL 2.9 6.1 + - - +
116C PHE* 3.3 23.0 - - + -
117C GLN 3.0 24.1 + - - -
170C MSE 5.3 1.3 - - - -
171C ILE* 2.5 26.0 + - - +
172C GLY* 4.3 1.1 - - - -
176C GLU* 3.4 39.9 - - + +
180C VAL* 6.1 0.4 - - - -
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Residues in contact with ARG 79 (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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60C LEU* 3.3 21.8 - - - +
77C LEU* 4.4 12.8 - - + -
78C THR* 1.3 74.9 - - - +
80C THR* 1.3 60.2 + - - +
117C GLN* 2.9 34.5 + - + +
119C VAL* 4.0 18.4 - - + +
120C ARG 4.6 0.4 - - - +
146C HIS* 3.2 36.2 + - - +
149C ASP* 3.5 18.7 + - - +
150C ALA* 3.8 22.6 - - - +
153C THR* 4.3 0.4 + - - -
170C MSE 3.6 28.6 - - + +
176C GLU* 3.6 10.2 - - - -
179C THR* 2.8 43.8 + - + +
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Residues in contact with THR 80 (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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78C THR* 4.6 1.3 - - - -
79C ARG* 1.3 75.8 - - - +
81C PRO* 1.3 66.2 - - - +
82C TYR* 2.9 21.6 + - - +
84C ALA* 4.1 22.4 - - - +
87C ARG* 4.4 4.0 - - + -
116C PHE* 4.2 17.7 - - + -
117C GLN 2.9 15.9 + - - +
118C ASP* 3.4 5.4 - - - +
119C VAL* 3.0 26.0 + - - +
122C LYS* 5.1 0.2 - - - +
176C GLU* 2.6 33.4 + - - +
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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