Contacts of the strand formed by residues 113 - 118 (chain B) 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 ILE 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B ILE* 3.6 31.0 - - + -
65B VAL 3.5 7.9 - - - +
66B LEU* 3.9 24.0 - - + -
67B PRO* 4.3 9.9 - - + -
70B ALA* 4.6 1.3 - - + -
73B ALA* 3.8 33.2 - - + +
74B PRO 3.0 11.5 + - - +
75B ILE* 3.3 14.8 - - + +
76B VAL* 3.0 25.6 + - - +
112B TYR* 1.3 75.9 - - - +
114B ARG* 1.3 60.8 + - - +
115B VAL* 4.0 4.2 + - + -
161B VAL* 4.1 3.4 - - + -
163B GLU* 4.0 10.8 - - + +
164B SER* 4.0 16.6 - - - +
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL 3.8 0.9 - - - +
64B ILE* 3.6 1.4 - - - -
65B VAL* 2.8 44.7 + - + +
76B VAL* 3.2 40.9 + - - +
78B THR* 3.0 32.9 + - - +
87B ARG* 5.4 1.0 - - - +
88B THR* 5.4 0.4 - - + +
96B MSE 4.6 2.7 - - + -
100B LEU* 4.0 30.1 - - + -
104B ASP* 2.8 28.1 + - - +
107B PHE* 3.9 13.1 - - + -
112B TYR 3.8 2.3 + - - +
113B ILE* 1.3 72.1 - - - +
115B VAL* 1.3 74.6 + - - +
116B PHE* 3.4 31.8 - - + -
171B ILE* 3.7 12.1 - - - +
172B GLY* 5.9 0.4 - - - -
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B THR* 3.4 30.5 - - + -
63B VAL 3.3 5.8 - - - +
64B ILE* 4.0 26.0 - - + -
75B ILE* 3.6 25.1 - - + -
76B VAL 2.9 10.7 + - - +
77B LEU* 3.4 18.7 - - + -
78B THR 3.0 24.4 + - - -
113B ILE* 4.2 4.3 - - + -
114B ARG* 1.3 86.4 + - - +
116B PHE* 1.3 65.2 + - - +
157B LEU* 4.4 12.1 - - + -
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B THR* 3.6 1.2 - - - +
63B VAL 2.8 31.8 + - - +
78B THR* 3.3 30.1 - - + -
80B THR* 4.1 11.2 - - + -
84B ALA* 3.5 19.1 - - + +
87B ARG* 3.7 56.1 - - + -
88B THR* 3.6 27.4 - - + -
100B LEU* 5.8 0.7 - - + -
104B ASP* 3.8 14.4 - - - -
114B ARG* 3.4 39.9 - - + -
115B VAL* 1.3 79.4 - - - +
117B GLN* 1.3 59.8 + - - +
176B GLU* 4.0 0.7 - - - -
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Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ILE* 4.0 6.3 - - - +
60B LEU* 3.6 20.0 - - + +
61B HIS 3.5 5.4 - - - +
62B THR* 3.0 31.0 + - + +
77B LEU* 4.5 7.4 - - + -
78B THR 2.9 10.8 + - - +
79B ARG* 2.8 41.9 + - - +
80B THR* 2.9 27.5 + - - +
84B ALA* 4.0 3.8 - - - -
116B PHE* 1.3 77.7 - - - +
118B ASP* 1.3 71.4 - - - +
153B THR* 2.9 33.3 + - - +
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 3.9 3.6 - - - +
61B HIS* 2.8 38.6 + - - +
80B THR 3.4 5.1 - - - +
83B ASP* 3.6 11.1 + - - +
84B ALA* 2.8 29.0 + - - +
117B GLN* 1.3 82.1 - - - +
119B VAL* 1.3 60.1 + - - +
120B ARG 3.8 0.3 + - - -
122B LYS* 3.4 18.2 - - + +
123B TYR* 3.7 7.0 - - - +
124B GLY 3.2 13.2 + - - -
125B SER* 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