Contacts of the strand formed by residues 127 - 132 (chain A) in PDB entry 1MU5
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 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PHE* 3.8 14.1 - - + -
116A VAL* 3.7 40.6 - - + -
119A SER* 4.4 9.0 - - - +
120A GLN* 4.5 4.0 - - - +
126A PRO* 1.3 75.5 - - - +
128A GLU* 1.3 59.3 + - - +
129A ILE* 3.8 14.8 - - + -
143A LYS* 3.2 5.4 - - - -
144A LEU* 2.6 79.8 + - + +
145A LYS* 5.8 0.4 - - - -
172A VAL* 5.5 0.7 - - + -
173A ALA 3.3 12.1 - - - +
174A ILE* 4.1 28.3 - - + +
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LYS* 2.7 39.5 + - - -
125A LYS* 5.4 7.6 - - - +
126A PRO* 4.0 11.8 - - + +
127A ILE* 1.3 76.5 - - - +
129A ILE* 1.3 64.2 + - - +
130A GLU* 5.9 0.2 - - - -
142A PHE 3.6 5.6 - - - +
143A LYS* 4.4 26.2 + - + +
171A SER* 3.7 1.4 + - - +
172A VAL* 3.4 4.2 - - - -
173A ALA* 2.7 48.0 + - + +
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 5.6 0.2 - - + -
86A VAL* 3.9 16.2 - - + -
90A PHE* 3.2 52.5 - - + -
127A ILE* 3.8 5.6 - - + -
128A GLU* 1.3 79.5 - - - +
130A GLU* 1.3 74.3 + - - +
131A THR* 4.5 6.1 - - - -
141A THR* 3.3 4.0 - - - -
142A PHE* 2.8 47.2 + - + +
144A LEU* 3.2 32.5 - - + -
170A THR* 4.4 8.7 - - + -
171A SER 3.3 6.5 - - - +
172A VAL* 4.4 7.0 - - + -
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ILE* 1.3 75.5 - - - +
131A THR* 1.3 62.3 + - - +
139A ILE* 4.3 12.5 - - + +
140A TYR 3.3 4.3 - - - +
141A THR* 3.5 27.8 - - + +
169A GLY 3.9 0.2 - - - +
170A THR* 3.2 2.9 - - - +
171A SER* 2.7 53.1 + - - +
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Residues in contact with THR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY* 3.4 0.2 - - - -
81A ILE* 2.9 40.1 + - + +
83A PRO 5.4 0.2 - - - -
86A VAL* 4.0 20.2 - - + -
129A ILE* 4.5 3.6 - - + -
130A GLU* 1.3 75.7 - - - +
132A SER* 1.3 62.5 + - - +
133A PRO* 4.9 0.7 - - + -
139A ILE* 4.2 3.3 - - - +
140A TYR* 2.8 56.2 + - + +
142A PHE* 4.7 1.3 - - + -
167A PHE* 5.7 0.4 - - - -
169A GLY 3.3 3.4 - - - -
170A THR* 2.9 27.7 + - - -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY* 3.9 4.8 - - - -
131A THR* 1.3 76.4 + - - +
133A PRO* 1.3 73.8 + - - +
136A SER* 3.9 0.7 - - - -
138A ARG 3.5 13.3 + - - -
139A ILE* 4.0 6.7 - - - -
163A ASN* 3.1 23.7 + - - -
167A PHE* 3.4 28.2 + - - -
168A HIS* 3.2 2.9 - - - +
169A GLY 2.9 29.8 + - - -
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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