Contacts of the helix formed by residues 125 - 132 (chain A) in PDB entry 1MVM
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 PRO 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A GLN* 1.3 95.2 - - + +
126A SER* 1.3 62.7 + - - +
128A TRP* 3.8 2.8 - - - +
129A GLN* 3.3 21.0 + - - +
463A TYR* 2.9 18.8 - - + +
564A TRP* 3.8 39.9 - - + +
577A LEU* 4.6 9.5 - - + +
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Residues in contact with SER 126 (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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124A GLN* 4.5 12.6 - - - -
125A PRO* 1.3 79.5 - - - +
127A ASP* 1.3 71.4 + - - +
129A GLN* 2.7 25.5 + - - +
130A TYR* 2.8 14.3 + - - +
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Residues in contact with ASP 127 (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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51A THR* 2.4 50.1 + - - +
53A TYR* 3.8 19.2 - - - +
123A LEU* 4.1 12.5 - - + +
124A GLN* 3.6 28.4 + - - +
126A SER* 1.3 79.6 + - - +
128A TRP* 1.3 52.0 + - - +
130A TYR* 2.8 10.2 + - - +
131A ILE* 2.6 40.1 + - - +
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Residues in contact with TRP 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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119A TRP* 3.6 31.6 - + - -
123A LEU* 3.4 21.3 - - + +
124A GLN 3.2 15.1 + - - +
125A PRO 3.8 4.0 - - - +
127A ASP* 1.3 78.2 - - - +
129A GLN* 1.3 58.2 + - - +
131A ILE* 2.9 12.2 + - + +
132A CYS* 2.6 56.4 + - + +
138A LEU* 5.6 3.4 - - + -
279A LEU* 5.5 1.1 - - + -
461A PRO* 4.0 24.0 - - + -
462A VAL 5.0 0.2 - - - -
463A TYR* 3.8 56.5 - + + +
549A VAL* 6.4 1.8 - - + -
577A LEU* 4.4 13.4 + - + -
578A ILE 4.0 8.0 + - - -
579A THR* 2.0 45.3 + - + -
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Residues in contact with GLN 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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125A PRO 3.3 13.2 + - - +
126A SER* 2.7 24.4 + - - +
128A TRP* 1.3 79.5 - - - +
130A TYR* 1.3 52.4 + - - +
132A CYS* 5.1 0.7 - - - -
133A ASN* 2.2 64.3 + - + +
549A VAL* 3.4 32.9 + - + -
550A SER* 4.2 9.7 + - - +
551A VAL* 4.6 14.0 - - - +
577A LEU* 6.1 1.3 - - + -
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Residues in contact with TYR 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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53A TYR* 4.0 34.3 - + - +
55A PHE* 2.9 36.3 - + - -
126A SER* 2.8 11.4 + - - +
127A ASP* 2.8 16.5 + - - +
129A GLN* 1.3 77.9 - - - +
131A ILE* 1.3 55.6 + - - +
133A ASN* 4.5 0.7 - - - -
134A THR* 2.3 54.9 + - + -
135A MET* 4.5 7.9 - - + +
537A LEU* 6.1 0.2 - - + -
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Residues in contact with ILE 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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53A TYR* 3.3 19.3 - - + +
63A ILE* 4.6 20.4 - - + -
123A LEU* 3.6 41.5 - - + -
127A ASP 2.6 22.2 + - - +
128A TRP* 2.9 9.8 + - + +
130A TYR* 1.3 69.9 - - - +
132A CYS* 1.3 72.2 + - - +
133A ASN 3.0 0.7 - - - -
134A THR 3.0 1.0 + - - -
135A MET* 2.8 47.0 + - + +
138A LEU* 5.0 14.6 - - + -
279A LEU* 4.3 15.0 - - + -
533A MET* 5.8 2.9 - - - -
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Residues in contact with CYS 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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128A TRP* 2.6 49.3 + - + +
129A GLN* 4.8 1.1 - - - +
131A ILE* 1.3 80.7 - - - +
133A ASN* 1.3 60.2 + - - +
134A THR 3.6 0.2 + - - -
135A MET 3.8 8.7 - - - +
279A LEU* 4.3 15.9 - - - +
549A VAL* 5.8 1.1 - - + -
578A ILE 4.4 3.4 - - - +
579A THR* 2.3 58.3 - - + +
580A ARG 4.7 0.2 - - - +
581A PRO* 4.5 10.6 - - + +
582A VAL* 5.2 5.7 - - - +
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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