Contacts of the helix formed by residues 123 - 130 (chain A) in PDB entry 4QMG
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ILE* 5.7 0.7 - - + -
51A LEU* 3.8 22.4 - - + -
86A LEU* 3.6 28.2 - - + +
89A LYS* 5.5 4.0 - - - -
90A LEU* 3.6 33.2 - - + -
112A ILE* 3.0 45.5 + - + +
113A TYR 4.7 0.2 - - - +
114A LEU* 4.1 20.0 - - + +
121A GLU* 4.3 9.0 - - + +
122A ASN* 1.3 71.0 + - - +
124A ALA* 1.3 63.4 + - - +
126A SER* 3.2 9.2 + - - +
127A LEU* 3.1 22.0 + - - +
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Residues in contact with ALA 124 (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 LEU* 4.5 10.8 - - + +
52A SER 4.4 9.0 - - - +
54A ILE* 3.8 35.8 - - + +
111A MSE 5.9 6.7 - - + -
112A ILE 4.8 1.7 + - - +
122A ASN* 3.1 10.2 + - - +
123A ILE* 1.3 78.1 - - - +
125A GLU* 1.3 63.0 + - - +
127A LEU* 3.4 3.2 + - - +
128A VAL* 3.2 29.3 + - - +
149A LEU* 4.0 8.1 - - + -
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Residues in contact with GLU 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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122A ASN* 3.1 37.1 + - - +
124A ALA* 1.3 74.0 - - - +
126A SER* 1.3 61.6 + - - +
128A VAL* 3.4 2.0 + - - +
129A ALA* 2.8 33.3 + - - +
145A GLU* 5.1 2.3 - - - +
148A ARG* 3.2 45.7 + - + +
149A LEU* 3.9 22.4 - - + -
152A CYS* 3.9 17.9 - - - -
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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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85A PHE* 4.0 19.5 - - - -
89A LYS* 5.0 1.3 - - - -
121A GLU* 2.7 34.0 + - - +
122A ASN 3.0 14.5 + - - -
123A ILE* 3.2 12.5 + - - -
125A GLU* 1.3 76.7 - - - +
127A LEU* 1.3 62.4 + - - +
129A ALA* 3.5 4.9 + - - +
130A GLU* 3.2 30.5 + - - +
184B ARG* 5.4 0.9 - - - -
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Residues in contact with LEU 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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31A CYS* 3.8 31.0 - - + -
51A LEU* 3.8 17.5 - - + -
54A ILE* 3.8 21.3 - - + -
56A ALA* 5.1 0.2 - - + -
82A ALA* 4.1 5.2 - - + +
85A PHE* 4.0 20.2 - - + -
86A LEU* 3.9 14.6 - - + -
123A ILE 3.1 12.5 + - - +
124A ALA 3.6 6.7 - - - +
126A SER* 1.3 76.8 - - - +
128A VAL* 1.3 61.2 + - - +
130A GLU* 3.2 7.4 + - - -
132A LEU* 3.0 50.1 + - + +
133A ALA* 3.8 15.0 - - + -
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Residues in contact with VAL 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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54A ILE* 3.7 24.5 - - + -
124A ALA 3.2 18.2 + - - +
125A GLU 3.9 2.9 - - - +
127A LEU* 1.3 74.2 - - - +
129A ALA* 1.3 62.0 + - - +
130A GLU 3.2 1.2 + - - -
131A GLY* 3.2 9.7 + - - -
133A ALA* 3.4 26.5 - - + +
134A THR 4.9 2.7 - - - -
135A ARG* 4.9 1.3 - - + +
149A LEU* 3.4 34.8 - - + +
152A CYS* 3.6 4.1 - - + +
153A GLU* 3.6 25.1 - - + +
156A ALA* 3.5 11.3 - - - +
164A TRP* 5.0 1.4 + - - +
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Residues in contact with ALA 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 GLU 2.8 20.0 + - - +
126A SER* 3.8 8.3 - - - +
127A LEU 3.2 0.4 - - - -
128A VAL* 1.3 77.2 - - - +
130A GLU* 1.3 69.1 + - - +
131A GLY 3.5 0.2 - - - -
152A CYS* 3.7 25.0 - - + +
155A GLN* 5.2 5.5 - - + +
156A ALA* 3.5 14.7 + - - +
161A LYS* 3.6 14.0 + - - +
188B ASP* 6.0 2.7 - - - +
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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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85A PHE* 3.9 17.8 - - + -
126A SER* 3.2 17.1 - - - +
127A LEU 3.2 4.4 + - - +
128A VAL 3.1 0.8 - - - -
129A ALA* 1.3 86.9 - - - +
131A GLY* 1.3 64.2 + - - +
132A LEU* 3.3 14.5 + - + -
161A LYS* 2.8 45.4 + - - +
162A GLY 3.9 0.5 + - - -
266B GLU 4.3 0.2 - - - +
267B SER* 3.0 26.5 + - - -
302B ALA* 3.5 18.2 - - + +
303B VAL* 3.3 24.7 - - + +
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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