Contacts of the helix formed by residues 121 - 131 (chain A) in PDB entry 3QFC
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A SER 4.4 6.1 + - - +
72A PHE* 3.5 3.8 - - - -
120A TYR* 1.3 77.2 - - - +
122A LEU* 1.3 61.0 + - - +
123A ALA* 3.0 31.4 + - - +
124A ASP* 3.0 36.3 + - - +
158A TRP* 5.0 4.7 - - - -
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Residues in contact with LEU 122 (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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72A PHE* 4.2 2.9 - - + -
86A PHE* 3.8 35.0 - - + -
117A PRO* 3.8 37.0 - - + +
120A TYR* 4.2 1.5 + - + +
121A ASP* 1.3 73.7 + - - +
123A ALA* 1.3 60.5 + - - +
124A ASP 2.9 6.1 - - - -
125A LEU* 3.0 48.4 + - + +
138A PHE* 4.1 8.1 - - + -
155A PHE* 3.4 44.9 - - + -
158A TRP* 3.8 12.3 - - + -
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Residues in contact with ALA 123 (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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121A ASP* 3.0 21.2 + - - +
122A LEU* 1.3 77.9 - - - +
124A ASP* 1.3 59.8 + - - +
125A LEU* 3.0 5.4 + - - +
126A SER* 3.4 19.4 + - - -
158A TRP* 3.6 36.4 - - + +
164A VAL* 5.6 1.9 - - - +
166A LEU* 5.6 0.2 - - - +
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Residues in contact with ASP 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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70A SER 4.1 2.6 - - - +
71A SER* 3.6 36.4 - - - +
72A PHE* 3.6 15.8 + - + -
73A VAL* 3.4 16.1 - - + +
121A ASP* 3.0 32.0 + - - +
122A LEU 2.9 0.8 - - - -
123A ALA* 1.3 76.4 - - - +
125A LEU* 1.3 61.9 + - - +
126A SER* 3.1 4.5 - - - -
127A SER* 2.9 20.6 + - - +
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Residues in contact with LEU 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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72A PHE* 3.7 14.4 - - + -
122A LEU* 3.0 43.2 + - + +
123A ALA 3.0 0.8 - - - +
124A ASP* 1.3 78.4 - - - +
126A SER* 1.3 61.1 + - - +
127A SER 3.0 1.4 + - - -
128A LEU* 3.2 36.3 + - + +
136A VAL* 4.1 22.7 - - + -
138A PHE* 4.3 10.5 - - + -
155A PHE* 4.4 1.6 - - + -
158A TRP* 4.1 18.6 - - + -
166A LEU* 4.1 15.3 - - + -
169A VAL* 3.2 22.5 - - + +
195A LEU* 4.4 14.8 - - + -
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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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123A ALA 3.4 14.6 + - - -
124A ASP* 4.8 0.3 - - - -
125A LEU* 1.3 78.1 - - - +
127A SER* 1.3 60.9 + - - +
128A LEU 3.5 0.2 - - - -
129A PRO* 3.4 15.1 - - - +
164A VAL* 4.3 18.3 - - - +
165A ASP 4.4 7.0 - - - -
166A LEU* 3.9 19.6 - - - +
169A VAL* 4.6 3.6 - - - -
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Residues in contact with SER 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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71A SER* 5.8 0.7 - - - -
73A VAL* 3.8 19.8 - - - +
124A ASP* 2.9 18.3 + - - -
126A SER* 1.3 81.3 + - - +
128A LEU* 1.3 64.5 + - - +
129A PRO* 3.2 4.3 - - - -
130A GLU* 2.9 43.5 + - - +
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Residues in contact with LEU 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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72A PHE* 4.3 7.2 - - + -
73A VAL* 4.0 16.4 - - + +
76A MET* 3.9 30.7 - - + -
84A ILE* 4.8 2.7 - - + -
124A ASP 4.0 1.2 + - - -
125A LEU* 3.2 38.4 + - + +
127A SER* 1.3 76.8 - - - +
129A PRO* 1.3 62.7 - - + +
130A GLU 2.9 6.3 + - - -
131A ILE* 2.9 16.9 + - + +
134A ALA* 3.3 36.2 - - + +
135A LEU 5.2 2.2 - - - +
136A VAL* 3.9 24.2 - - + +
169A VAL* 4.2 13.2 - - + -
170A LYS 5.5 0.9 - - - +
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Residues in contact with PRO 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 LEU 4.1 1.6 - - - +
126A SER 3.4 17.3 - - - +
127A SER 3.2 4.5 - - - -
128A LEU* 1.3 93.3 - - + +
130A GLU* 1.3 59.0 + - + +
131A ILE 3.1 9.2 + - - +
132A ASP* 5.4 1.2 - - - +
134A ALA* 5.3 0.7 - - + -
167A SER 4.3 6.1 - - - +
168A GLY* 4.0 33.0 - - - +
169A VAL* 4.4 3.8 - - + +
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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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73A VAL* 4.6 0.9 - - + +
74A GLU* 4.2 4.0 - - - +
77A LYS* 2.6 44.9 + - - +
127A SER* 2.9 35.5 + - - +
128A LEU 2.9 1.4 + - - -
129A PRO* 1.3 78.6 - - + +
131A ILE* 1.3 60.6 + - - +
132A ASP* 4.1 2.1 + - - +
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Residues in contact with ILE 131 (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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73A VAL* 3.6 22.7 - - + +
76A MET* 3.5 42.0 - - + -
77A LYS* 3.7 24.7 - - + +
81A ARG 4.1 3.8 - - - +
82A ASN* 4.0 21.1 - - + -
128A LEU* 2.9 18.2 + - + +
129A PRO* 3.9 7.3 - - - +
130A GLU* 1.3 81.2 - - - +
132A ASP* 1.3 76.0 + - - +
133A ASN 3.4 0.3 + - - -
134A ALA* 3.3 15.2 + - + +
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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