Contacts of the helix formed by residues 139 - 150 (chain A) in PDB entry 3KQQ
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 CYS 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A CYS* 3.6 1.6 - - - -
137A GLY 3.6 2.8 + - - -
138A GLU* 1.3 80.7 - - - +
140A TRP* 1.3 68.1 + - + +
141A GLN* 3.5 5.8 - - - +
142A ASP* 3.1 38.6 + - - +
143A LYS 3.2 8.1 + - - -
47B LEU* 4.8 4.7 - - + +
48B CYS* 2.0 59.4 + - - +
129B HIS* 5.1 7.9 - - + +
132B LEU* 4.8 4.5 - - - -
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Residues in contact with TRP 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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124A SER* 3.7 25.1 - - - -
127A SER* 3.9 2.4 - - - -
128A GLN* 3.2 58.7 - - + +
131A CYS* 3.5 11.5 - - - +
138A GLU 3.9 0.2 + - - -
139A CYS* 1.3 74.3 - - + +
141A GLN* 1.3 86.0 + - + +
142A ASP 3.3 0.2 - - - -
143A LYS* 3.4 3.9 + - - +
144A GLU* 3.0 57.8 + - - +
125B MET* 3.4 35.8 - - + +
128B GLN* 3.9 18.6 + - + +
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Residues in contact with GLN 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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139A CYS* 3.5 2.9 - - - +
140A TRP* 1.3 111.9 + - + +
142A ASP* 1.3 65.1 + - - +
144A GLU* 4.0 4.9 - - - +
145A ARG* 3.0 44.0 + - - +
48B CYS* 3.4 22.8 - - - -
125B MET* 3.5 29.7 - - - -
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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 GLU* 3.7 16.5 - - + +
139A CYS* 3.1 28.3 + - - +
141A GLN* 1.3 77.1 - - - +
143A LYS* 1.3 64.3 + - - +
145A ARG* 2.8 31.2 + - - +
146A GLN* 3.0 25.5 + - - +
48B CYS* 3.7 14.9 - - - +
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Residues in contact with LYS 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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88A LEU* 3.2 44.5 + - + +
89A SER* 4.3 0.6 - - - +
91A CYS* 4.0 8.5 - - - -
92A SER* 4.9 7.1 + - - -
127A SER* 4.4 8.7 - - - +
130A ALA* 4.4 7.6 - - - -
131A CYS* 3.7 24.7 - - - -
134A GLU* 2.7 40.0 + - - -
138A GLU* 3.2 26.4 + - - +
139A CYS 3.2 1.2 + - - -
140A TRP 3.4 9.6 - - - +
141A GLN 3.2 0.2 - - - -
142A ASP* 1.3 80.7 - - - +
144A GLU* 1.3 62.8 + - - +
146A GLN* 3.4 6.3 + - - +
147A LEU* 3.1 19.9 + - - +
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Residues in contact with GLU 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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88A LEU* 5.3 1.1 - - + -
113A TRP* 3.6 26.0 + - + -
124A SER* 3.4 22.3 + - - -
127A SER* 2.7 30.8 + - - +
140A TRP* 3.0 35.1 + - - +
141A GLN* 4.1 5.0 - - - +
142A ASP 3.3 0.2 - - - -
143A LYS* 1.3 73.3 - - + +
145A ARG* 1.3 67.4 + - - +
147A LEU* 3.1 8.8 + - - +
148A ARG* 2.9 54.1 + - - +
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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 GLN* 3.0 37.1 + - - +
142A ASP* 2.8 34.2 + - - +
144A GLU* 1.3 77.2 - - - +
146A GLN* 1.3 63.5 + - - +
148A ARG* 3.4 9.3 + - - +
149A ALA* 3.0 24.5 + - + +
48B CYS* 4.4 5.5 - - - +
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Residues in contact with GLN 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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91A CYS* 3.6 23.5 - - - +
92A SER* 3.4 26.9 + - - +
138A GLU* 4.4 11.5 - - - +
142A ASP 3.0 15.7 + - - +
143A LYS* 3.8 4.5 + - - +
145A ARG* 1.3 76.4 - - - +
147A LEU* 1.3 58.1 + - - +
149A ALA* 3.0 6.9 + - - +
150A ARG* 2.8 69.8 + - + +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A VAL* 4.1 20.0 - - + +
87A LEU* 3.9 19.7 - - + -
88A LEU* 3.6 28.7 - - + -
91A CYS* 3.8 27.7 - - + -
97A ILE* 4.5 3.6 - - + -
99A MET* 5.8 0.4 - - - -
113A TRP* 3.9 24.2 - - + -
114A LEU* 5.5 0.7 - - + -
143A LYS 3.1 11.5 + - - +
144A GLU* 3.1 10.1 + - - +
146A GLN* 1.3 78.4 - - - +
148A ARG* 1.3 62.6 + - - +
150A ARG* 3.1 2.1 + - - -
151A VAL* 3.0 40.2 + - + +
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Residues in contact with ARG 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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113A TRP* 2.8 73.0 + - + +
114A LEU* 3.4 32.8 - - + +
116A GLU* 3.5 38.0 + - - +
144A GLU* 2.9 49.6 + - - +
145A ARG* 3.8 7.5 - - - +
147A LEU* 1.3 73.2 - - - +
149A ALA* 1.3 61.3 + - - +
151A VAL* 3.7 14.2 - - - +
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Residues in contact with ALA 149 (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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145A ARG* 3.0 18.0 + - + +
146A GLN* 3.4 8.5 - - - +
148A ARG* 1.3 80.0 - - - +
150A ARG* 1.3 63.4 + - + +
151A VAL 3.6 1.7 + - - +
152A LYS* 3.0 22.6 + - - +
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Residues in contact with ARG 150 (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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91A CYS 2.9 26.9 + - - +
92A SER 3.7 10.7 + - - -
93A HIS 4.3 1.0 - - - -
94A PHE 3.0 34.6 + - - +
95A GLU* 3.5 35.6 + - + +
97A ILE* 2.7 43.2 + - + -
146A GLN* 2.8 43.2 + - + +
147A LEU* 4.1 2.5 - - - +
149A ALA* 1.3 78.3 - - + +
151A VAL* 1.3 56.3 + - - +
152A LYS* 3.3 6.7 + - - +
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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