Contacts of the helix formed by residues 140 - 152 (chain A) in PDB entry 3CUQ
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 SER 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A PRO* 4.3 23.1 - - - +
65A ARG* 5.3 0.2 - - - -
125A HIS* 4.0 6.5 - - - -
138A ASP 4.3 0.2 + - - -
139A VAL* 1.3 78.2 - - - +
141A GLN* 1.3 69.7 + - - +
142A ASP* 3.3 12.2 + - - +
143A ASP* 2.6 46.3 + - - +
144A LEU* 3.2 10.6 + - - +
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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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121A LEU* 3.8 32.1 - - + +
122A GLU* 5.8 3.3 - - - +
125A HIS* 3.7 34.5 + - + +
140A SER* 1.3 76.1 - - - +
142A ASP* 1.3 57.6 + - - +
144A LEU* 2.9 27.1 + - - +
145A ILE* 3.2 13.6 + - - +
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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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66A VAL* 3.5 22.2 - - + +
69A GLN* 5.2 1.4 + - - -
140A SER* 3.3 10.0 + - - +
141A GLN* 1.3 76.6 - - - +
143A ASP* 1.3 68.2 + - - +
145A ILE* 3.3 12.5 + - - +
146A ARG* 3.0 54.6 + - - +
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Residues in contact with ASP 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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65A ARG* 3.1 32.3 + - - +
96A PHE* 3.7 7.1 - - + -
97A TYR* 2.9 36.9 + - + -
100A LEU* 3.7 10.3 - - + +
139A VAL* 3.6 14.6 - - + -
140A SER* 2.6 39.5 + - - +
142A ASP* 1.3 77.8 - - - +
144A LEU* 1.3 64.5 + - - +
146A ARG* 3.1 3.7 - - - +
147A ALA* 3.1 20.6 + - - +
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Residues in contact with LEU 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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100A LEU* 3.9 27.4 - - + -
104A ILE* 4.0 19.1 - - + -
121A LEU* 3.9 22.4 - - + -
124A LEU* 4.3 9.2 - - + -
125A HIS* 3.6 47.8 - - + +
128A VAL* 4.2 11.4 - - + -
139A VAL* 3.9 10.1 - - + -
140A SER 3.2 8.9 + - - +
141A GLN* 2.9 11.0 + - - +
143A ASP* 1.3 75.5 - - - +
145A ILE* 1.3 58.1 + - - +
147A ALA* 3.0 6.4 + - - +
148A ILE* 3.0 31.9 + - - +
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Residues in contact with ILE 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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121A LEU* 3.5 36.8 - - + -
141A GLN* 3.2 6.9 + - + +
142A ASP* 3.9 14.1 - - - +
144A LEU* 1.3 75.8 - - - +
146A ARG* 1.3 68.3 + - - +
148A ILE* 3.4 7.3 + - + +
149A LYS* 3.1 38.8 + - + +
160A ILE* 4.2 21.6 - - + +
167A TYR* 4.0 30.7 - - + -
169A ILE* 5.4 3.1 - - + -
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Residues in contact with ARG 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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66A VAL* 4.5 15.4 - - - +
69A GLN* 2.7 52.1 + - - +
70A ASP* 3.9 15.8 + - - -
80A LEU* 4.4 9.3 - - + +
97A TYR* 3.4 21.1 - - + -
142A ASP* 3.0 44.2 + - - +
143A ASP 3.1 11.7 - - - +
145A ILE* 1.3 80.5 - - - +
147A ALA* 1.3 62.7 + - - +
149A LYS* 3.3 15.2 + - - +
150A LYS* 3.5 15.0 + - - +
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Residues in contact with ALA 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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80A LEU* 6.1 0.2 - - - -
97A TYR* 4.3 26.9 - - + +
100A LEU* 4.3 5.6 - - + -
101A GLY* 4.3 6.7 - - - +
104A ILE* 3.6 18.8 - - + -
143A ASP 3.1 6.7 + - - +
144A LEU 3.0 9.4 + - - +
146A ARG* 1.3 77.4 - - - +
148A ILE* 1.3 67.1 + - - +
150A LYS* 3.0 10.7 + - - +
151A LEU* 2.9 23.2 + - - +
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Residues in contact with ILE 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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104A ILE* 3.3 45.3 - - + -
124A LEU* 4.9 3.1 - - + -
144A LEU 3.0 15.2 + - - +
145A ILE* 3.4 8.5 + - + +
147A ALA* 1.3 74.5 - - - +
149A LYS* 1.3 57.2 + - - +
151A LEU* 2.6 29.8 + - + -
152A LYS* 3.1 13.2 + - + +
158A PHE* 3.8 35.9 - - + -
159A GLY 4.6 2.0 - - - +
160A ILE* 3.9 23.3 - - + -
169A ILE* 4.5 20.0 - - + -
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Residues in contact with LYS 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 ILE* 3.1 32.4 + - + +
146A ARG* 3.5 10.8 - - - +
148A ILE* 1.3 76.9 - - - +
150A LYS* 1.3 67.6 + - + +
152A LYS* 3.3 27.2 - - + +
153A ALA* 4.4 1.6 + - - +
160A ILE* 4.2 14.8 - - + -
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Residues in contact with LYS 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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78A ASP* 3.2 32.0 + - - -
80A LEU* 4.4 31.2 - - + +
97A TYR* 6.4 0.9 - - + -
98A TYR* 5.5 4.5 - - + -
146A ARG 3.5 11.1 + - - +
147A ALA* 3.0 11.4 + - - +
149A LYS* 1.3 83.2 + - + +
151A LEU* 1.3 66.9 + - + +
153A ALA* 3.1 14.8 + - - +
284B PRO* 3.3 33.8 - - + +
285B GLU* 3.5 26.3 + - - +
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Residues in contact with LEU 151 (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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101A GLY* 3.7 21.5 - - - +
104A ILE* 4.7 2.2 - - + -
105A ILE* 3.7 32.3 - - + -
147A ALA 2.9 15.2 + - - +
148A ILE* 2.6 35.0 + - + +
150A LYS* 1.3 74.6 - - - +
152A LYS* 1.3 49.8 + - - +
153A ALA 3.0 0.2 - - - -
154A LEU* 2.8 59.5 + - + +
155A GLY 4.4 2.1 + - - +
158A PHE* 4.6 21.4 + - + -
270B TYR* 4.1 13.2 - - + +
284B PRO* 4.2 7.9 - - + -
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Residues in contact with LYS 152 (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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148A ILE* 3.1 20.3 + - + +
149A LYS* 3.3 23.6 - - + +
150A LYS 3.1 0.2 - - - -
151A LEU* 1.3 74.4 - - - +
153A ALA* 1.3 59.3 + - - +
154A LEU 3.1 1.1 - - - -
155A GLY* 3.2 23.3 + - - +
158A PHE* 3.2 31.9 + - - +
159A GLY* 3.8 12.5 - - - -
160A ILE* 4.8 6.3 - - + +
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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