Contacts of the helix formed by residues 127 - 141 (chain Q) in PDB entry 5A31
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 ASP 127 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q ARG* 5.1 0.9 - - - +
38Q GLU* 3.4 30.3 - - + +
41Q THR* 3.9 24.1 - - - +
89Q TYR* 4.4 1.3 - - - -
125Q LEU 3.5 4.5 + - - +
126Q TYR* 1.3 75.0 - - - +
128Q VAL* 1.3 66.2 + - - +
129Q ARG* 3.9 12.1 + - - +
130Q THR* 2.8 37.6 + - - -
131Q ILE* 3.1 27.9 + - - +
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Residues in contact with VAL 128 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q GLU* 2.9 27.0 + - + +
42Q LEU* 4.2 4.9 - - + -
52Q ALA* 4.1 6.7 - - + -
62Q TRP* 3.8 36.1 - - + -
83Q LEU* 4.2 10.1 - - + -
85Q PHE* 3.6 30.5 - - + -
127Q ASP* 1.3 73.6 - - - +
129Q ARG* 1.3 65.9 + - - +
131Q ILE* 3.0 11.5 + - + +
132Q LEU* 2.9 43.6 + - + +
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Residues in contact with ARG 129 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Q GLU 5.6 1.2 + - - +
41Q THR* 4.7 11.4 - - - -
42Q LEU* 3.8 29.2 - - + +
45Q SER* 3.4 21.1 + - - -
47Q ASP* 2.3 49.9 + - - +
50Q ILE* 4.2 1.7 - - + +
127Q ASP* 3.3 13.4 + - - +
128Q VAL* 1.3 79.3 - - - +
130Q THR* 1.3 61.1 + - - +
132Q LEU* 3.4 3.8 + - - +
133Q LEU* 2.9 51.4 + - + +
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Residues in contact with THR 130 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117Q ILE* 4.5 5.8 - - + -
126Q TYR* 3.9 32.6 - - + -
127Q ASP* 2.8 34.5 + - - -
129Q ARG* 1.3 81.5 + - - +
131Q ILE* 1.3 64.8 + - - +
133Q LEU* 3.4 8.0 + - - +
134Q SER* 2.9 36.8 + - - +
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Residues in contact with ILE 131 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Q LEU* 4.7 10.8 - - + -
85Q PHE* 5.4 0.9 - - + -
89Q TYR* 5.5 0.7 - - - +
94Q PRO* 3.5 31.4 - - + -
96Q VAL* 4.2 18.8 - - + -
115Q LEU* 4.9 0.4 - - + +
117Q ILE* 4.3 12.6 - - + -
118Q LEU* 4.3 14.4 - - + -
122Q TRP* 3.7 23.1 - - + -
126Q TYR* 5.2 0.9 - - + -
127Q ASP 3.1 16.7 + - - +
128Q VAL* 3.0 13.9 + - + +
130Q THR* 1.3 77.0 - - - +
132Q LEU* 1.3 59.6 + - + +
134Q SER* 3.2 3.1 + - - -
135Q ILE* 2.9 47.9 + - + +
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Residues in contact with LEU 132 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q LEU* 4.1 9.2 - - + -
50Q ILE* 3.9 20.8 - - + +
51Q SER 3.5 34.1 - - - +
52Q ALA* 3.8 13.7 - - + -
64Q GLY* 4.7 9.4 - - - -
66Q ILE* 3.6 26.8 - - + +
81Q LEU* 5.1 4.5 - - + -
83Q LEU* 4.6 16.6 - - + -
96Q VAL* 6.2 0.9 - - + -
128Q VAL* 2.9 26.6 + - + +
129Q ARG 3.8 3.4 - - - +
131Q ILE* 1.3 78.7 - - + +
133Q LEU* 1.3 62.3 + - - +
135Q ILE* 3.4 3.3 + - + -
136Q GLN* 2.9 25.5 + - - +
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Residues in contact with LEU 133 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Q ASP* 4.2 13.0 - - + +
48Q LYS 5.5 1.1 - - - +
50Q ILE* 3.7 21.3 - - + -
129Q ARG* 2.9 58.8 + - - +
130Q THR* 3.9 5.6 - - - +
132Q LEU* 1.3 76.9 - - - +
134Q SER* 1.3 59.9 + - - +
136Q GLN* 3.7 20.1 - - - +
137Q SER* 2.9 32.3 + - - +
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Residues in contact with SER 134 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115Q LEU* 3.9 14.0 - - - +
117Q ILE* 3.4 27.7 - - - +
130Q THR* 2.9 23.3 + - - +
131Q ILE 3.6 4.5 - - - -
133Q LEU* 1.3 77.9 - - - +
135Q ILE* 1.3 58.1 - - - +
137Q SER* 3.4 7.0 + - - -
138Q LEU* 2.9 27.4 + - - +
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Residues in contact with ILE 135 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q ILE* 3.7 20.2 - - + -
81Q LEU* 4.1 6.1 - - + -
96Q VAL* 3.8 18.8 - - + -
98Q PHE* 3.6 33.0 - - + -
113Q ILE* 3.7 25.4 - - + -
115Q LEU* 3.8 16.8 - - + -
118Q LEU* 4.7 2.9 - - + -
131Q ILE* 2.9 29.1 + - + +
132Q LEU* 5.1 2.2 - - + -
134Q SER* 1.3 72.5 - - - +
136Q GLN* 1.3 68.2 + - - +
138Q LEU* 3.1 13.6 + - + +
139Q LEU* 3.0 23.6 + - + +
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Residues in contact with GLN 136 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Q LYS 3.3 23.6 + - - +
49Q GLY* 3.4 11.7 + - - -
50Q ILE* 3.7 13.6 - - + +
66Q ILE* 3.9 16.7 - - + +
67Q HIS 3.0 27.9 + - - +
69Q ALA* 4.8 22.3 + - + +
132Q LEU 2.9 17.2 + - - +
133Q LEU* 3.7 16.3 - - - +
135Q ILE* 1.3 75.7 - - - +
137Q SER* 1.3 63.4 + - - +
139Q LEU* 3.2 20.7 + - + +
140Q GLY 3.8 2.6 + - - -
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Residues in contact with SER 137 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Q LEU* 2.9 19.8 + - - +
134Q SER* 3.5 7.9 - - - -
136Q GLN* 1.3 77.8 - - - +
138Q LEU* 1.3 61.4 + - - +
140Q GLY* 3.3 4.2 + - - -
141Q GLU* 3.1 25.2 + - - +
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Residues in contact with LEU 138 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104Q HIS* 2.8 25.3 + - + +
106Q ASN* 3.5 33.7 - - + +
107Q VAL* 5.3 2.9 - - + -
113Q ILE* 3.6 31.2 - - + -
114Q CYS 4.1 6.5 - - - +
115Q LEU* 4.2 21.8 - - + -
134Q SER 2.9 14.7 + - - +
135Q ILE* 3.1 14.3 + - + +
137Q SER* 1.3 75.3 - - - +
139Q LEU* 1.3 61.9 + - - +
141Q GLU 3.3 21.8 + - - +
142Q PRO* 3.3 7.3 - - + -
143Q ASN* 4.4 5.8 - - + +
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Residues in contact with LEU 139 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Q ILE* 4.0 26.2 - - + -
68Q GLY* 4.2 21.8 - - - +
69Q ALA 5.9 0.7 - - - +
72Q THR* 5.7 0.9 - - - +
74Q TYR* 3.2 43.6 - - + -
79Q TYR* 4.7 11.0 - - + -
98Q PHE* 4.5 12.6 - - + -
102Q CYS* 4.1 22.0 - - - -
104Q HIS* 3.5 24.7 + - + -
135Q ILE* 3.0 17.6 + - + +
136Q GLN* 3.4 10.8 - - - +
137Q SER 3.2 0.6 - - - -
138Q LEU* 1.3 77.7 - - - +
140Q GLY* 1.3 59.6 + - - +
142Q PRO* 4.1 0.2 - - - +
156Q TRP* 3.6 6.9 - - - -
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Residues in contact with GLY 140 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72Q THR* 4.0 30.1 - - - +
136Q GLN 3.8 2.8 + - - -
137Q SER 3.3 6.4 + - - -
139Q LEU* 1.3 79.8 - - - +
141Q GLU* 1.3 66.4 + - - +
142Q PRO* 3.6 1.6 - - - -
156Q TRP* 3.6 18.5 - - - -
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Residues in contact with GLU 141 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137Q SER 3.1 13.3 + - - +
138Q LEU* 3.3 17.0 + - - +
140Q GLY* 1.3 83.1 - - - +
142Q PRO* 1.3 69.6 - - - +
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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
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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