Contacts of the helix formed by residues 110 - 121 (chain A) in PDB entry 1A16
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 PHE 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLU* 3.5 66.9 - - + +
60A ALA* 3.9 3.1 - - - -
61A VAL* 3.9 26.2 - - + -
77A PHE* 4.1 13.7 - - + -
78A ASN 3.0 18.5 + - - +
79A ARG* 4.2 5.3 - - + +
80A VAL 5.1 0.2 - - - +
108A LEU 3.5 1.2 + - - -
109A ALA* 1.3 71.9 - - - +
111A SER* 1.3 63.4 + - - +
113A ILE* 3.0 32.2 + - + +
136A TYR* 4.1 23.3 - + - -
140A ILE* 4.1 13.0 - - + -
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Residues in contact with SER 111 (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 VAL* 5.2 6.4 - - - +
109A ALA* 3.5 16.5 - - - +
110A PHE* 1.3 82.0 - - - +
112A GLU* 1.3 73.2 + - - +
113A ILE* 3.7 0.3 + - - +
114A ASN 5.0 1.0 + - - -
115A GLN* 3.6 8.7 - - - +
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Residues in contact with GLU 112 (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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77A PHE* 4.4 1.3 - - + -
108A LEU* 5.6 1.6 - - + -
109A ALA* 2.9 24.0 + - + +
111A SER* 1.3 95.3 + - - +
113A ILE* 1.3 62.8 + - - +
114A ASN 3.3 2.9 - - - -
115A GLN* 2.9 38.5 + - + +
116A GLN* 3.1 26.9 + - + +
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Residues in contact with ILE 113 (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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28A PHE* 5.0 0.2 - - + -
61A VAL* 3.5 40.2 - - + -
77A PHE* 3.8 30.7 - - + -
109A ALA 3.8 1.0 + - - -
110A PHE* 3.0 29.5 + - + +
111A SER 3.4 1.5 - - - +
112A GLU* 1.3 76.5 - - - +
114A ASN* 1.3 70.5 + - - +
117A LEU* 2.8 39.3 + - + +
140A ILE* 4.0 41.1 - - + -
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Residues in contact with ASN 114 (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 SER 5.0 1.0 + - - +
112A GLU 3.3 0.8 - - - -
113A ILE* 1.3 84.5 - - - +
115A GLN* 1.3 71.5 + - - +
116A GLN 3.4 0.2 - - - -
117A LEU* 4.6 2.3 + - - +
118A TYR* 3.6 10.0 + - - +
140A ILE* 4.1 39.6 + - - +
143A SER* 4.4 12.1 + - - -
147A LYS* 2.8 34.0 + - - +
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Residues in contact with GLN 115 (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 SER 3.6 7.1 - - - +
112A GLU* 2.9 40.9 + - - +
114A ASN* 1.3 90.7 + - - +
116A GLN* 1.3 60.9 + - - +
118A TYR* 3.2 13.7 - - - -
119A GLN* 2.5 34.2 + - - +
147A LYS* 4.8 4.7 - - - +
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Residues in contact with GLN 116 (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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77A PHE* 3.7 17.3 - - + -
106A ARG* 5.2 4.2 - - - +
108A LEU* 3.9 24.4 - - + +
112A GLU* 3.1 27.4 + - + +
115A GLN* 1.3 86.0 - - - +
117A LEU* 1.3 65.4 + - - +
118A TYR 3.4 2.2 - - - -
119A GLN* 3.1 37.7 + - - +
120A LEU* 3.1 21.8 + - + +
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Residues in contact with LEU 117 (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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26A LEU* 4.1 39.5 - - + -
28A PHE* 5.2 1.8 - - + -
61A VAL* 5.9 1.3 - - + -
63A VAL* 4.5 13.9 - - + -
77A PHE* 4.2 5.5 - - + -
113A ILE* 2.8 31.5 + - + +
114A ASN* 5.2 1.8 - - - +
116A GLN* 1.3 72.3 - - - +
118A TYR* 1.3 59.0 + - - +
120A LEU* 2.8 32.6 + - + +
121A LEU* 3.0 27.6 + - + +
140A ILE* 3.7 36.1 - - + +
141A VAL* 4.5 4.9 - - + +
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Residues in contact with TYR 118 (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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114A ASN 3.6 18.7 + - - +
115A GLN* 3.2 25.4 - - - -
117A LEU* 1.3 77.5 - - - +
119A GLN* 1.3 81.7 + - + +
121A LEU* 3.3 3.7 + - - +
122A ASN* 2.9 25.1 + - - +
143A SER 5.2 1.6 - - - +
145A LEU 5.0 6.5 - - - +
147A LYS* 3.9 33.7 - - + -
148A LEU* 3.4 40.7 - - + +
156A LEU* 4.0 26.5 - - + -
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Residues in contact with GLN 119 (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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115A GLN* 2.5 26.4 + - - +
116A GLN* 3.1 29.4 + - - +
118A TYR* 1.3 110.2 + - + +
120A LEU* 1.3 63.7 + - + +
121A LEU 3.6 0.2 + - - -
122A ASN* 3.6 17.4 + - - +
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Residues in contact with LEU 120 (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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24A ALA* 5.0 0.4 - - - +
63A VAL* 4.3 19.3 - - + -
65A ILE* 4.2 26.8 - - + +
73A HIS* 5.4 2.0 - - - +
75A VAL* 4.3 18.2 - - + -
77A PHE* 3.9 33.7 - - + -
106A ARG* 4.8 12.6 - - - +
108A LEU* 5.2 0.7 - - + -
116A GLN* 3.1 20.1 + - + +
117A LEU* 2.8 16.1 + - + +
119A GLN* 1.3 81.2 - - + +
121A LEU* 1.3 57.8 + - + +
122A ASN 3.4 1.6 + - - +
124A LEU* 3.4 19.1 - - - +
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Residues in contact with LEU 121 (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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24A ALA* 3.8 28.0 - - + -
26A LEU* 4.4 13.0 - - + -
63A VAL* 5.7 0.2 - - + -
117A LEU* 3.0 39.8 + - + +
118A TYR* 3.3 1.5 + - - -
120A LEU* 1.3 77.8 - - + +
122A ASN* 1.3 65.9 + - - +
123A GLY 3.3 1.2 + - - -
124A LEU* 3.2 20.0 + - + +
127A VAL* 4.1 24.5 - - + -
141A VAL* 5.4 2.5 - - + +
145A LEU* 4.1 27.6 - - + +
148A LEU* 3.7 15.9 - - + -
159A PRO* 3.4 18.4 - - + +
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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