Contacts of the helix formed by residues 124 - 133 (chain A) in PDB entry 1UMK
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 GLY 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A TYR* 2.9 26.1 + - - +
123A GLY* 1.3 72.5 - - - -
125A LYS* 1.3 67.4 + - - +
128A GLN* 3.0 27.5 + - - +
1301A FAD 3.2 31.9 - - - -
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Residues in contact with LYS 125 (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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84A ILE* 3.6 29.4 - - + +
85A ASP* 4.5 16.8 - - - +
87A ASN* 6.0 4.7 - - - +
89A VAL* 3.9 28.3 - - + -
91A ARG* 4.2 9.8 - - - +
123A GLY 5.0 3.6 - - - +
124A GLY* 1.3 73.2 - - - +
126A MET* 1.3 65.2 + - - +
128A GLN* 4.0 1.4 - - - +
129A TYR* 3.1 17.2 + - - +
1301A FAD 3.0 23.4 + - - +
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Residues in contact with MET 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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80A LEU* 3.5 18.6 - - - +
81A SER* 3.8 2.0 - - - -
82A ALA* 3.8 15.0 - - + +
84A ILE* 3.8 11.0 - - + -
89A VAL* 3.4 35.9 - - + +
90A VAL* 4.6 1.1 - - - -
91A ARG* 3.6 10.1 - - + +
93A TYR* 3.2 32.5 - - + +
125A LYS* 1.3 75.3 - - - +
127A SER* 1.3 61.6 + - - +
129A TYR* 3.1 7.0 + - - +
130A LEU* 2.9 26.4 + - + +
139A ILE* 3.8 25.6 - - - -
1301A FAD 2.9 19.1 + - - +
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Residues in contact with SER 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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93A TYR* 4.4 1.0 + - - -
109A ILE* 4.4 4.9 - - - +
110A LYS 3.3 25.6 - - - -
111A VAL* 3.7 12.6 - - - +
112A TYR* 3.1 22.7 + - - +
124A GLY 3.8 5.0 + - - -
126A MET* 1.3 73.0 - - - +
128A GLN* 1.3 58.8 + - - +
130A LEU* 3.5 13.2 + - - +
131A GLU* 3.0 25.3 + - - +
1301A FAD 2.6 34.1 + - - -
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Residues in contact with GLN 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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111A VAL* 4.0 11.4 - - + -
112A TYR 3.3 20.6 + - - +
113A PHE* 3.7 5.5 - - + -
114A LYS* 2.9 35.0 + - - +
122A ALA 2.8 27.5 + - - -
123A GLY* 3.5 1.2 - - - -
124A GLY 3.0 28.4 + - - +
125A LYS* 4.0 1.5 - - - +
126A MET 3.2 0.4 - - - -
127A SER* 1.3 76.5 + - - +
129A TYR* 1.3 65.8 + - - +
131A GLU* 3.5 7.7 - - + +
132A SER* 3.1 24.3 + - - -
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Residues in contact with TYR 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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82A ALA* 3.6 24.6 - - + +
83A ARG 4.3 11.0 + - - -
84A ILE* 3.6 34.3 - - + -
125A LYS 3.1 5.5 + - - +
126A MET* 3.1 10.3 + - - +
128A GLN* 1.3 77.1 - - - +
130A LEU* 1.3 59.5 + - - +
132A SER* 3.0 24.7 + - - -
133A MET* 3.3 25.0 + - + +
138A THR 4.5 9.7 + - - -
139A ILE* 3.8 31.2 - - + -
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Residues in contact with LEU 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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46A LEU* 5.3 0.2 - - - +
59A PHE* 4.0 30.6 - - + -
61A PHE* 3.9 28.5 - - + -
80A LEU* 3.8 30.3 - - + -
93A TYR* 4.4 3.8 - - - +
107A LEU* 5.3 0.2 - - + -
109A ILE* 3.9 31.6 - - + -
126A MET* 2.9 25.5 + - + +
127A SER* 3.6 7.6 - - - +
129A TYR* 1.3 75.4 - - - +
131A GLU* 1.3 63.6 + - - +
133A MET* 3.1 34.8 + - - +
139A ILE* 4.1 9.0 - - + -
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Residues in contact with GLU 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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49A ARG* 2.9 49.9 + - - +
57A ARG* 2.7 41.2 + - - -
59A PHE* 4.1 2.7 - - - -
111A VAL* 3.6 9.5 - - + +
113A PHE* 3.9 22.8 - - + -
127A SER 3.0 17.5 + - - +
128A GLN* 3.5 12.3 - - + +
130A LEU* 1.3 77.3 - - - +
132A SER* 1.3 60.6 + - - +
133A MET 3.6 2.6 + - - +
134A GLN* 5.6 0.2 + - - -
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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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128A GLN 3.1 13.1 + - - -
129A TYR* 3.0 21.7 + - - -
131A GLU* 1.3 76.5 - - - +
133A MET* 1.3 64.6 + - - +
134A GLN* 3.1 20.1 + - - +
137A ASP* 4.6 0.9 - - - +
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Residues in contact with MET 133 (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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46A LEU* 3.8 20.5 - - + +
49A ARG* 5.2 7.8 + - - -
61A PHE* 4.1 13.0 - - + -
129A TYR* 3.3 24.8 + - + +
130A LEU* 3.1 39.6 + - - +
131A GLU 4.3 4.5 - - - +
132A SER* 1.3 79.0 - - - +
134A GLN* 1.3 64.4 + - - +
137A ASP* 3.3 43.5 - - + +
138A THR 3.7 18.6 - - - +
139A ILE* 3.9 17.5 - - + +
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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