Contacts of the helix formed by residues 129 - 148 (chain A) in PDB entry 3QZS
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 LYS 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A VAL 4.4 14.4 - - - +
66A LEU* 2.7 50.6 + - + +
67A THR 4.5 6.1 - - - +
68A PRO* 4.6 6.8 - - + +
69A LEU* 3.7 12.6 - - - +
127A TYR* 4.3 1.6 - - - +
128A GLU* 1.3 102.2 + - + +
130A LEU* 1.3 67.9 + - - +
131A THR* 3.8 17.5 - - - +
132A GLU* 3.0 33.5 + - + +
133A PHE 3.6 3.1 + - - -
88B LYS* 6.3 3.1 - - - -
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Residues in contact with LEU 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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65A VAL 5.6 0.4 + - - -
67A THR 5.0 3.0 + - - -
69A LEU* 3.8 20.7 - - + +
77A LEU* 3.8 28.7 - - + -
129A LYS* 1.3 72.9 - - - +
131A THR* 1.3 64.5 + - + +
133A PHE* 3.1 8.8 + - + +
134A VAL* 2.9 27.7 + - + +
169A LEU* 4.0 16.8 - - + -
172A PHE* 3.9 16.8 - - + -
173A LYS* 3.8 40.2 - - + +
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Residues in contact with THR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 4.5 21.6 + - + +
129A LYS* 3.8 19.6 - - - +
130A LEU* 1.3 79.6 - - + +
132A GLU* 1.3 60.0 + - - +
134A VAL* 3.4 8.4 + - - +
135A ALA* 2.9 28.3 + - - +
85B GLN 5.2 9.0 - - - +
86B ALA* 5.7 2.5 - - - -
94B LEU* 3.8 28.9 - - + -
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Residues in contact with GLU 132 (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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126A TYR* 4.3 5.8 - - + +
127A TYR* 3.5 22.5 - - + -
128A GLU* 2.7 44.6 + - - +
129A LYS* 3.0 23.6 + - + +
131A THR* 1.3 78.8 - - - +
133A PHE* 1.3 64.6 + - - +
135A ALA* 3.4 7.8 + - - +
136A ASP* 3.2 20.1 + - - +
86B ALA 6.1 1.3 - - - +
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Residues in contact with PHE 133 (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 LEU* 3.6 57.0 - - + -
80A VAL* 4.6 7.2 - - + -
81A LEU* 4.5 8.3 - - + -
118A MET* 3.5 28.8 - - + +
122A VAL* 3.9 19.1 - - + -
127A TYR* 3.4 30.7 - + + -
129A LYS 3.6 2.1 + - - +
130A LEU* 3.1 17.4 + - + +
132A GLU* 1.3 73.8 - - - +
134A VAL* 1.3 73.2 + - + +
136A ASP 3.3 1.4 + - - -
137A MET* 3.0 31.5 + - + +
165A PHE* 3.9 24.0 - + - -
169A LEU* 5.5 1.3 - - + -
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Residues in contact with VAL 134 (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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130A LEU* 2.9 25.9 + - + +
131A THR* 3.7 10.5 - - - +
133A PHE* 1.3 80.4 - - + +
135A ALA* 1.3 56.1 + - - +
137A MET* 3.3 4.7 + - - +
138A THR* 2.9 51.2 + - + +
165A PHE* 4.1 12.8 - - + -
169A LEU* 3.6 39.7 - - + -
173A LYS* 5.6 1.8 - - - +
82B ARG* 6.0 1.1 - - - +
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Residues in contact with ALA 135 (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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131A THR 2.9 17.9 + - - +
132A GLU* 3.7 9.0 - - - +
133A PHE 3.2 0.4 - - - -
134A VAL* 1.3 77.3 - - - +
136A ASP* 1.3 63.3 + - - +
138A THR* 3.2 17.3 + - - -
139A ALA* 3.2 14.0 + - - +
82B ARG 5.7 0.2 - - - +
85B GLN 5.9 0.4 - - - -
86B ALA* 3.8 29.8 - - + -
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Residues in contact with ASP 136 (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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113A MET* 3.5 25.8 - - + +
118A MET* 3.7 14.4 - - + -
121A ARG* 2.7 32.0 + - - -
126A TYR* 5.1 1.1 + - - -
127A TYR* 2.6 39.7 + - - +
132A GLU 3.2 9.7 + - - +
133A PHE 3.3 2.7 + - - +
135A ALA* 1.3 73.8 - - - +
137A MET* 1.3 68.6 + - - +
139A ALA* 3.2 12.2 + - - +
140A ILE* 3.3 7.8 + - - +
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Residues in contact with MET 137 (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* 5.4 0.2 - - + -
81A LEU* 4.1 14.6 - - + -
84A LEU* 3.6 31.6 - - + -
115A LEU* 3.8 19.5 - - + -
118A MET* 3.6 25.0 - - + +
133A PHE* 3.0 29.4 + - + +
134A VAL 3.7 3.8 - - - +
136A ASP* 1.3 77.1 - - - +
138A THR* 1.3 62.8 + - - +
140A ILE* 3.0 25.1 + - - +
141A PHE* 3.5 16.0 + - + -
165A PHE* 3.6 40.8 - - + -
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Residues in contact with THR 138 (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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134A VAL* 2.9 41.2 + - + +
135A ALA* 3.2 13.3 + - - -
137A MET* 1.3 71.4 - - - +
139A ALA* 1.3 56.5 + - - +
141A PHE* 3.2 11.7 + - + +
142A ASP* 2.9 33.4 + - - +
162A GLU* 5.6 3.6 - - + +
165A PHE* 4.5 11.7 - - + -
82B ARG* 3.6 46.6 + - - +
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Residues in contact with ALA 139 (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 GLU* 4.9 4.9 - - + +
113A MET* 4.5 7.6 - - + -
135A ALA 3.2 17.1 + - - +
136A ASP* 3.6 8.7 - - - +
137A MET 3.1 0.8 - - - -
138A THR* 1.3 75.6 + - - +
140A ILE* 1.3 64.9 + - - +
142A ASP* 4.2 6.7 - - - +
143A ASN* 2.9 43.3 + - - +
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Residues in contact with ILE 140 (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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93A PHE* 3.6 36.7 - - + -
113A MET* 3.6 38.3 - - + +
114A ASP 3.6 24.7 - - - -
115A LEU* 3.6 23.1 - - + +
118A MET* 3.7 17.5 - - - -
136A ASP 3.3 2.2 + - - +
137A MET* 3.0 13.0 + - - +
139A ALA* 1.3 77.6 - - - +
141A PHE* 1.3 73.4 + - + +
143A ASN* 4.1 3.0 - - - +
144A CYS* 3.4 20.4 + - - +
16C ALY 5.9 0.3 - - - +
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Residues in contact with PHE 141 (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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84A LEU* 4.1 11.0 - - + -
93A PHE* 4.3 4.5 - + - -
115A LEU* 5.7 0.4 - - + -
137A MET* 3.5 36.8 + - + -
138A THR* 3.2 10.9 + - + +
139A ALA 3.2 0.2 - - - -
140A ILE* 1.3 90.9 - - + +
142A ASP* 1.3 66.0 + - - +
144A CYS* 3.3 3.1 + - - +
145A ARG* 3.2 42.0 + - - +
158A ALA* 4.1 22.7 - - + +
161A LEU* 3.5 46.7 - - + -
162A GLU* 3.8 33.7 - - + -
165A PHE* 4.2 8.7 - + + -
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Residues in contact with ASP 142 (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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138A THR* 2.9 20.8 + - - +
139A ALA* 4.3 5.4 + - - +
141A PHE* 1.3 74.1 - - - +
143A ASN* 1.3 69.3 + - - +
145A ARG* 3.0 29.0 + - - +
146A TYR* 2.9 24.6 + - - +
75B GLU* 4.4 4.4 - - - +
78B LYS* 3.3 31.4 + - + +
79B ARG* 5.8 4.0 - - - +
82B ARG* 2.8 36.7 + - + +
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Residues in contact with ASN 143 (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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105A TYR* 3.8 16.0 + - - +
109A ILE* 3.5 25.7 - - + +
111A GLU* 2.9 29.7 + - - +
112A PRO* 3.7 6.9 - - - +
113A MET 3.8 7.3 + - - +
139A ALA* 2.9 28.2 + - - +
140A ILE* 4.1 4.4 - - - +
142A ASP* 1.3 79.7 - - - +
144A CYS* 1.3 62.7 + - - +
146A TYR* 3.3 7.6 + - - +
147A TYR* 2.9 26.7 + - - +
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Residues in contact with CYS 144 (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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93A PHE* 3.7 25.4 - - + -
105A TYR* 5.3 0.4 - - - -
140A ILE 3.4 15.1 + - - +
141A PHE 3.3 5.6 + - - +
142A ASP 3.2 1.0 - - - -
143A ASN* 1.3 79.4 - - - +
145A ARG* 1.3 58.7 + - - +
147A TYR* 4.7 0.2 - - - -
148A ASN* 2.9 52.7 + - - +
154A PHE* 3.2 34.8 - - - -
155A TYR 4.1 0.7 - - - -
158A ALA* 3.8 6.7 - - + -
16C ALY 3.9 11.4 - - + +
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Residues in contact with ARG 145 (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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141A PHE* 3.2 25.2 + - - +
142A ASP* 3.0 29.4 + - - +
144A CYS* 1.3 74.9 - - - +
146A TYR* 1.3 58.3 + - - +
148A ASN 3.4 3.3 - - - +
155A TYR* 3.5 38.8 - - + -
158A ALA* 4.1 13.1 + - + -
159A GLU* 2.4 46.7 + - - +
162A GLU* 2.7 35.7 + - - -
75B GLU* 3.6 20.5 + - - +
78B LYS* 4.5 6.9 - - - +
19C ARG* 2.7 32.1 + - - -
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Residues in contact with TYR 146 (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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108A VAL* 3.9 26.0 - - + -
109A ILE* 3.7 17.3 - - + -
142A ASP 2.9 16.9 + - - +
143A ASN* 3.3 9.4 + - - +
145A ARG* 1.3 75.8 - - - +
147A TYR* 1.3 63.7 + - - +
72B LYS* 5.1 13.8 - - + +
75B GLU* 3.7 32.0 + - + +
76B GLY* 4.1 9.0 - - - -
79B ARG* 4.0 35.4 + - + -
18C HIS* 3.6 13.0 - + - -
19C ARG* 3.3 14.2 - - - +
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Residues in contact with TYR 147 (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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102A ALA* 4.1 10.9 - - - +
104A ASP* 2.4 29.6 + - - -
105A TYR* 3.7 42.8 + + + -
108A VAL* 3.8 20.0 - - + -
109A ILE* 4.2 3.4 - - + -
143A ASN 2.9 17.2 + - - +
144A CYS* 4.7 0.2 - - - -
146A TYR* 1.3 78.9 - - - +
148A ASN* 1.3 77.5 + - - +
16C ALY 3.4 25.4 + - + -
17C ARG* 3.6 18.2 - - - -
18C HIS* 2.9 40.4 + - + -
19C ARG* 2.8 31.8 + - - +
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Residues in contact with ASN 148 (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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144A CYS* 2.9 30.8 + - - +
145A ARG 3.4 9.0 - - - +
147A TYR* 1.3 101.1 - - - +
149A PRO* 1.3 72.2 - - + +
152A SER* 3.4 17.2 - - - +
154A PHE* 3.7 21.0 - - + +
155A TYR* 3.5 7.1 - - + +
16C ALY 2.9 41.1 + - - +
17C ARG 4.4 3.5 + - - +
19C ARG* 3.0 16.3 + - - -
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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