Contacts of the helix formed by residues 109 - 120 (chain S) in PDB entry 5A0Q
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 VAL 109 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74S ILE* 3.8 20.4 - - + -
108S THR* 1.4 71.7 - - - +
110S GLU* 1.4 60.3 + - - +
112S VAL* 3.7 0.8 - - - +
113S THR* 2.8 43.1 + - - +
143S PHE* 3.9 19.5 - - + -
145S GLY* 3.3 45.1 - - - +
147S ASP* 3.9 7.7 + - + -
152S GLN* 3.5 16.4 - - + +
154S PHE* 3.9 21.8 - - + +
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Residues in contact with GLU 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108S THR* 3.3 7.9 + - - +
109S VAL* 1.4 76.9 - - - +
111S SER* 1.3 71.6 + - - +
113S THR* 4.1 2.4 - - - -
114S GLN* 3.2 40.1 + - - +
152S GLN* 4.4 8.1 + - - +
154S PHE* 3.8 34.7 - - + -
162S PHE* 3.4 20.9 - - + -
78a SER 4.2 1.6 - - - +
79a ASN 4.0 14.9 - - - +
80a ASN* 5.1 5.9 + - - -
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Residues in contact with SER 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107S MET* 3.9 26.4 - - - +
108S THR* 3.2 13.3 + - - -
110S GLU* 1.3 82.3 + - - +
112S VAL* 1.3 60.7 + - - +
113S THR 3.2 1.3 - - - -
114S GLN* 3.6 9.9 + - - +
115S ALA* 3.0 30.0 + - - +
78a SER* 3.1 26.6 + - - -
79a ASN* 3.9 14.6 + - - -
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Residues in contact with VAL 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70S ILE* 4.7 7.4 - - + -
74S ILE* 3.5 16.6 - - + -
92S ALA* 4.9 4.3 - - + +
95S GLU* 6.3 0.7 - - - -
96S THR* 3.5 30.7 - - + -
107S MET* 3.4 28.0 - - - +
108S THR 3.1 16.7 + - - +
109S VAL* 3.7 5.4 - - - +
111S SER* 1.3 76.1 - - - +
113S THR* 1.3 61.0 + - - +
115S ALA* 3.9 3.7 + - - +
116S VAL* 3.3 22.2 + - - +
143S PHE* 3.8 27.3 - - + -
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Residues in contact with THR 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109S VAL* 2.8 18.0 + - - +
110S GLU 4.1 3.6 - - - -
112S VAL* 1.3 73.1 - - - +
114S GLN* 1.3 60.4 + - - +
116S VAL* 3.3 4.9 + - - +
117S SER* 3.0 25.6 + - - -
143S PHE* 3.5 35.3 - - + -
154S PHE* 3.5 20.6 - - + +
155S HIS 4.5 0.2 - - - +
156S MET* 3.8 17.4 - - + +
162S PHE* 3.4 28.5 - - + -
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Residues in contact with GLN 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110S GLU* 3.2 38.7 + - - +
111S SER* 3.3 8.9 + - - +
113S THR* 1.3 76.8 - - - +
115S ALA* 1.3 60.9 + - - +
117S SER* 3.1 4.0 + - - -
118S ASN* 2.9 38.6 + - - +
162S PHE* 4.1 24.4 - - + -
82T ARG* 4.1 5.6 + - - +
89T ARG* 5.6 5.8 + - - +
77a HIS 5.5 1.4 + - - -
78a SER* 3.8 32.1 + - - +
80a ASN* 5.8 2.0 - - - +
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Residues in contact with ALA 115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95S GLU* 4.1 34.9 - - + +
107S MET* 5.2 4.9 - - + -
111S SER 3.0 16.8 + - - +
112S VAL* 4.1 6.5 - - - +
113S THR 3.3 0.2 - - - -
114S GLN* 1.3 77.5 - - - +
116S VAL* 1.3 61.1 + - + +
118S ASN* 3.4 23.4 - - - +
119S LEU* 3.6 16.5 - - - +
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Residues in contact with VAL 116 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88S LEU* 4.2 25.5 - - + +
92S ALA* 3.8 28.9 - - + -
112S VAL 3.3 16.4 - - - +
113S THR 3.3 8.2 + - - +
114S GLN 3.2 0.4 - - - -
115S ALA* 1.3 74.9 - - + +
117S SER* 1.3 63.7 + - - +
118S ASN 3.2 0.4 - - - -
119S LEU* 3.3 20.6 + - + +
120S ALA* 3.5 10.7 + - - +
141S LEU* 3.8 19.5 - - + -
143S PHE* 4.0 8.7 - - + -
156S MET* 3.6 19.9 - - + +
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Residues in contact with SER 117 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113S THR 3.0 13.9 + - - -
114S GLN 3.1 9.8 + - - -
116S VAL* 1.3 73.4 - - - +
118S ASN* 1.4 62.4 + - - +
119S LEU 3.2 0.2 - - - -
120S ALA* 3.2 20.1 + - - +
121S LEU 4.5 0.9 + - - -
156S MET* 3.5 23.0 - - - +
160S GLY 3.7 12.8 + - - -
162S PHE* 3.5 22.5 + - - +
82T ARG* 2.9 29.1 + - - -
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Residues in contact with ASN 118 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114S GLN* 2.9 35.3 + - - +
115S ALA* 3.4 17.5 - - - +
116S VAL 3.2 0.4 - - - -
117S SER* 1.4 77.0 - - - +
119S LEU* 1.3 62.7 + - + +
120S ALA 3.5 0.2 + - - -
121S LEU 4.7 0.3 + - - -
122S GLN* 3.0 28.9 - - - +
82T ARG* 3.2 30.5 + - - +
83T LEU* 4.4 11.3 - - + +
86T ASN* 4.6 18.1 - - - +
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Residues in contact with LEU 119 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88S LEU* 4.1 22.7 - - + -
91S LYS* 4.2 28.0 - - + -
95S GLU* 6.1 4.5 - - + -
115S ALA 3.6 16.6 - - - +
116S VAL* 3.3 12.3 + - + +
117S SER 3.2 0.6 - - - -
118S ASN* 1.3 81.5 - - + +
120S ALA* 1.3 63.2 + - - +
121S LEU 3.5 1.9 + - - -
122S GLN* 3.8 20.5 + - + +
137S PHE* 3.6 13.8 - - + -
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Residues in contact with ALA 120 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88S LEU* 5.5 2.2 - - + -
116S VAL 3.5 6.8 + - - +
117S SER* 3.2 21.0 + - - +
119S LEU* 1.3 79.6 - - - +
121S LEU* 1.3 73.2 + - + +
122S GLN 3.9 0.3 + - - -
123S PHE* 4.6 0.7 - - - -
136S PRO* 4.5 3.1 - - - +
137S PHE* 3.6 28.0 + - + -
156S MET* 4.6 9.4 - - + -
158S PRO* 4.8 3.4 - - + +
160S GLY* 3.5 26.0 - - - +
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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