Contacts of the helix formed by residues 124 - 140 (chain B) in PDB entry 1MF8
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 LYS 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B ASN* 5.7 1.6 - - - +
123B LEU* 1.3 75.8 - - - +
125B ASP* 1.3 66.5 + - - +
126B THR* 3.1 10.8 - - - +
127B GLN* 3.1 44.8 + - + +
128B LEU* 3.1 8.7 + - - +
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 3.5 28.6 - - + -
116B LYS* 2.8 29.0 + - - +
121B ASN* 4.6 2.3 + - - -
123B LEU 4.4 0.4 - - - -
124B LYS* 1.3 74.5 - - - +
126B THR* 1.3 55.9 + - - +
128B LEU* 4.5 2.7 - - - -
129B GLN* 2.8 33.3 + - - +
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Residues in contact with THR 126 (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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21A VAL* 4.1 25.3 - - + +
22A PRO* 6.5 0.2 - - + -
124B LYS* 4.2 9.6 - - - +
125B ASP* 1.3 79.6 - - - +
127B GLN* 1.3 58.2 + - + +
129B GLN* 3.5 1.9 + - - +
130B GLN* 2.8 57.1 + - - +
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 3.5 44.7 - - + +
122B ASN 4.4 2.3 - - - +
123B LEU* 3.4 26.0 - - + +
124B LYS* 3.1 55.2 + - + +
126B THR* 1.3 75.7 - - + +
128B LEU* 1.3 66.9 + - - +
130B GLN* 3.2 13.9 + - - +
131B ILE* 3.2 13.3 + - - +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A TRP* 5.2 3.6 - - + -
112B PHE* 3.1 62.4 - - + +
115B LEU* 3.9 16.6 - - + -
116B LYS* 4.0 6.1 - - + +
119B VAL* 3.2 37.0 - - + -
123B LEU* 3.7 16.5 - - + +
124B LYS 3.1 9.5 + - - +
125B ASP* 3.8 6.5 - - - +
127B GLN* 1.3 79.0 - - - +
129B GLN* 1.3 62.5 + - - +
131B ILE* 3.1 12.5 - - + +
132B VAL* 2.9 31.7 + - + +
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.1 23.6 - - + -
108B ASN* 3.0 29.1 + - - +
112B PHE* 3.3 27.5 - - + +
125B ASP 2.8 19.3 + - - +
126B THR 3.7 4.0 - - - +
128B LEU* 1.3 77.2 - - - +
130B GLN* 1.3 53.4 + - - +
132B VAL* 3.1 6.6 + - - +
133B ASP* 2.3 64.1 + - - +
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Residues in contact with GLN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 3.9 17.8 - - + +
22A PRO* 5.7 0.6 - - - +
53A GLU* 5.5 0.2 - - - -
339A HIS 5.1 1.0 + - - -
340A PRO* 2.9 22.8 - - - +
341A TYR* 2.4 42.1 + - + +
126B THR* 2.8 43.5 + - - +
127B GLN* 3.2 5.7 + - - +
129B GLN* 1.3 75.4 - - - +
131B ILE* 1.3 53.1 + - - +
133B ASP* 2.9 13.5 + - - +
134B LYS* 2.8 44.6 + - - +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 3.4 44.0 - - + +
342A TRP* 4.0 7.6 - - + +
343A LEU* 3.7 33.4 - - + +
347A MET 5.7 2.0 - - - +
349A VAL* 3.5 24.1 - - + +
352A TRP* 4.2 13.0 - - + -
123B LEU* 4.6 5.2 - - + -
127B GLN 3.2 4.4 + - - +
128B LEU* 3.1 24.0 - - + +
130B GLN* 1.3 71.7 - - - +
132B VAL* 1.3 56.5 + - + +
134B LYS* 4.3 7.8 - - - +
135B THR* 2.5 37.8 + - - -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A VAL* 4.5 2.0 - - + -
108B ASN* 3.8 33.9 - - - +
111B LEU* 3.5 22.7 - - + -
112B PHE* 4.1 13.2 - - - +
115B LEU* 3.5 29.4 - - + -
128B LEU* 2.9 29.4 + - + +
129B GLN* 3.1 11.2 + - - +
131B ILE* 1.3 75.2 - - - +
133B ASP* 1.3 71.6 + - - +
135B THR* 3.2 3.6 + - - -
136B ILE* 3.0 20.9 + - + +
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.7 5.8 - - - +
22A PRO 5.8 0.4 - - - -
23A PHE* 2.5 43.7 - - + -
24A PRO* 5.1 5.2 - - + -
108B ASN* 3.7 10.3 + - - +
129B GLN* 2.3 58.0 + - - +
130B GLN* 3.0 10.6 + - - +
132B VAL* 1.3 75.0 - - - +
134B LYS* 1.3 55.8 + - + +
135B THR 2.8 0.9 + - - -
136B ILE* 2.7 30.4 + - - +
137B ILE* 3.0 18.2 + - + +
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Residues in contact with LYS 134 (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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24A PRO* 4.7 14.6 - - + -
53A GLU* 2.6 43.6 + - - -
340A PRO* 3.9 4.4 - - - +
341A TYR 3.0 24.7 + - - +
342A TRP* 3.3 49.9 - - + +
130B GLN* 2.8 30.6 + - - +
131B ILE* 4.3 6.1 - - - +
133B ASP* 1.3 72.5 - - + +
135B THR* 1.3 57.9 + - - +
137B ILE* 3.9 11.7 - - + +
138B ASN* 2.9 33.7 + - - +
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A MET 4.8 1.0 + - - -
348A ASP* 3.6 17.6 - - + +
349A VAL* 3.0 49.1 + - + +
350A PHE* 4.0 24.5 - - + -
111B LEU* 4.3 3.4 - - + -
131B ILE 2.5 23.4 + - - -
132B VAL 3.4 4.3 - - - -
133B ASP 2.8 0.8 + - - -
134B LYS* 1.3 78.7 - - - +
136B ILE* 1.3 61.8 + - - +
138B ASN* 4.4 2.7 - - - +
139B ALA* 3.3 22.8 + - + +
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Residues in contact with ILE 136 (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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23A PHE* 6.1 2.9 - - + -
106B ILE 4.5 7.4 - - - +
107B SER 4.0 6.7 - - - +
108B ASN* 3.6 42.0 - - + +
111B LEU* 4.3 15.0 - - + -
132B VAL* 3.0 13.2 + - + +
133B ASP* 2.7 16.4 + - - +
135B THR* 1.3 73.2 - - + +
137B ILE* 1.3 60.3 + - + +
138B ASN 3.4 0.2 - - - -
139B ALA 3.8 0.2 - - - -
140B ASP* 2.8 46.4 + - + +
145B GLY* 4.2 21.8 - - - +
146B ARG* 4.6 1.1 - - - +
147B ILE* 4.2 19.7 - - + -
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Residues in contact with ILE 137 (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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23A PHE* 3.4 40.6 - - + -
24A PRO* 4.4 21.5 - - + +
55A ARG* 5.9 4.7 - - - +
133B ASP 3.0 18.3 + - - +
134B LYS* 4.0 10.5 - - + +
135B THR 3.3 0.2 - - - -
136B ILE* 1.3 80.8 - - + +
138B ASN* 1.3 74.2 + - - +
139B ALA 3.5 0.2 + - - -
140B ASP* 3.8 11.3 + - - +
141B LYS* 5.6 0.2 + - - -
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Residues in contact with ASN 138 (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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55A ARG* 4.9 15.4 + - - -
168A ILE* 5.0 18.3 - - - +
342A TRP* 5.2 8.5 - - - -
134B LYS* 2.9 28.0 + - - +
135B THR* 4.6 2.2 - - - +
137B ILE* 1.3 85.5 - - - +
139B ALA* 1.3 58.7 + - + +
140B ASP 3.6 0.2 - - - -
141B LYS* 3.0 33.6 + - - +
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Residues in contact with ALA 139 (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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350A PHE* 5.1 5.6 - - + -
135B THR* 3.3 19.4 + - + +
137B ILE 3.2 0.4 - - - -
138B ASN* 1.3 78.8 - - - +
140B ASP* 1.3 57.5 + - - +
141B LYS* 3.0 14.9 + - - +
147B ILE* 3.6 17.7 - - + -
151B GLU* 3.4 23.5 - - - +
155B VAL* 3.8 28.3 - - + -
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Residues in contact with ASP 140 (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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136B ILE* 2.8 27.6 + - + +
137B ILE* 3.8 9.4 + - - +
138B ASN 3.6 1.2 - - - -
139B ALA* 1.3 73.5 - - - +
141B LYS* 1.3 57.3 + - - +
142B ASP* 2.6 15.2 + - - +
143B GLY* 2.7 29.0 + - - -
144B ASP* 2.8 7.6 + - - +
145B GLY* 3.4 14.9 + - - -
146B ARG 3.6 0.4 - - - +
147B ILE* 4.2 4.9 - - + -
151B GLU* 4.2 0.2 - - - -
404B CA 2.4 34.6 - - - -
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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
------------------------------------------------------------
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