Contacts of the helix formed by residues 141 - 152 (chain A) in PDB entry 4I7Z
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 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A TYR* 4.2 12.3 - - + -
136A TYR 4.6 1.7 - - - +
139A PRO* 3.1 18.8 - - + +
140A TRP* 1.3 80.5 - - - +
142A GLN* 1.3 65.3 + - - +
143A VAL* 3.8 20.0 + - - +
144A GLY* 3.0 19.8 + - - -
145A TYR* 3.0 23.2 + - - +
63B GLY* 3.9 21.7 + - - +
64B GLU 3.2 16.8 - - - +
65B PRO* 4.2 2.0 - - - -
66B ALA 3.8 6.3 - - - +
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Residues in contact with GLN 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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141A ASP* 1.3 72.2 - - - +
143A VAL* 1.3 61.4 + - + +
146A TRP* 2.9 47.4 + - - +
64B GLU* 2.9 38.4 + - + +
65B PRO 4.2 2.0 - - - -
66B ALA* 3.4 3.2 - - - +
67B ASP* 2.6 39.4 + - - +
70B ALA 2.9 24.7 + - - -
72B PRO* 3.4 23.7 - - + +
16C PRO 3.6 21.2 + - - -
17C THR* 5.1 0.2 - - - +
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Residues in contact with VAL 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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136A TYR* 3.4 35.7 - - + +
141A ASP* 3.4 14.9 - - - +
142A GLN* 1.3 79.8 - - + +
144A GLY* 1.3 56.8 + - - +
146A TRP* 4.3 2.2 - - - +
147A ALA* 2.8 33.9 + - + +
72B PRO* 5.7 3.4 - - + -
75B ILE* 5.0 8.1 - - + +
76B LEU 4.3 12.1 - - - +
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Residues in contact with GLY 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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136A TYR* 3.7 24.0 + - - -
137A SER* 3.6 17.2 - - - -
141A ASP* 3.0 18.6 + - - -
143A VAL* 1.3 76.8 - - - +
145A TYR* 1.3 57.0 + - - +
147A ALA* 3.3 4.2 + - - +
148A VAL* 2.9 31.9 + - - +
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Residues in contact with TYR 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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140A TRP* 3.4 45.4 - + + +
141A ASP 3.0 19.0 + - - +
142A GLN 3.8 2.0 - - - +
144A GLY* 1.3 77.4 - - - +
146A TRP* 1.3 77.6 + + + +
148A VAL* 3.3 7.1 + - - +
149A LYS* 2.9 61.6 + - + +
175A VAL* 3.6 29.9 + - + +
176A GLY* 5.3 0.2 - - - -
66B ALA* 3.7 17.7 - - + -
67B ASP 4.9 0.2 - - - -
68B PRO* 3.3 40.5 - - + +
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Residues in contact with TRP 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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142A GLN* 2.9 40.3 + - - +
143A VAL 4.3 0.2 - - - +
145A TYR* 1.3 84.7 - + - +
147A ALA* 1.3 60.6 + - - +
149A LYS* 3.7 34.9 - - + +
150A ILE* 3.2 32.6 + - + +
67B ASP 3.1 25.6 + - - -
68B PRO* 3.5 22.4 - - + -
69B PHE 5.2 0.2 - - - -
70B ALA 3.0 27.4 + - - -
71B THR* 3.4 29.2 - - + -
72B PRO* 3.3 19.5 - - + -
75B ILE* 3.4 23.1 - - + -
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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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136A TYR* 4.2 23.1 - - + -
137A SER* 6.0 0.4 - - - -
143A VAL* 2.8 20.3 + - + +
144A GLY 3.6 3.4 - - - +
146A TRP* 1.3 74.5 - - - +
148A VAL* 1.3 60.5 + - - +
150A ILE* 3.1 8.8 + - - +
151A VAL* 2.9 38.1 + - + +
75B ILE* 4.2 4.8 - - + +
76B LEU 5.4 4.7 - - - +
77B PRO* 5.8 4.9 - - + -
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Residues in contact with VAL 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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133A VAL* 5.6 1.3 - - + +
137A SER* 3.7 16.8 - - - +
140A TRP* 4.8 5.4 - - + -
144A GLY 2.9 14.9 + - - +
145A TYR* 3.5 9.9 - - - +
147A ALA* 1.3 74.5 - - - +
149A LYS* 1.3 61.3 + - - +
151A VAL* 3.4 6.2 - - + +
152A SER* 2.9 35.7 + - - -
175A VAL* 3.5 31.9 - - + -
179A THR* 4.2 7.4 - - + -
183A TYR* 3.1 48.0 - - + +
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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 TYR* 2.9 50.0 + - + +
146A TRP* 3.7 39.0 - - + +
147A ALA 3.2 0.4 - - - -
148A VAL* 1.3 79.3 - - - +
150A ILE* 1.3 61.3 + - + +
152A SER* 3.3 13.9 + - - -
153A GLY* 4.0 5.2 + - - -
174A SER* 6.5 0.4 - - - -
175A VAL* 3.9 17.0 - - + +
68B PRO* 4.1 8.9 + - - +
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Residues in contact with ILE 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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146A TRP* 3.2 20.5 + - + +
147A ALA* 3.1 8.9 + - - +
148A VAL 3.1 0.6 - - - -
149A LYS* 1.3 78.4 - - + +
151A VAL* 1.3 71.9 + - + +
152A SER 3.3 0.2 - - - -
153A GLY* 3.3 11.4 + - - -
154A VAL* 3.6 14.2 + - + +
75B ILE* 3.5 29.4 - - + +
85B PHE* 5.3 19.1 - - + -
88B LEU* 5.5 9.2 - - + -
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Residues in contact with VAL 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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133A VAL* 4.3 27.4 - - + -
147A ALA* 2.9 25.6 + - + +
148A VAL* 3.4 12.8 - - - +
150A ILE* 1.3 81.1 - - + +
152A SER* 1.3 65.2 + - - +
153A GLY 3.2 1.0 + - - -
154A VAL* 3.3 22.7 + - + +
155A PRO* 3.6 8.1 - - - +
169A LEU* 5.1 1.7 - - - +
183A TYR* 3.9 13.5 - - - +
77B PRO* 6.4 2.0 - - + -
81B LEU* 5.8 5.4 - - + -
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Residues in contact with SER 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 VAL* 2.9 24.1 + - - -
149A LYS 3.3 10.0 + - - -
151A VAL* 1.3 79.3 - - - +
153A GLY* 1.3 60.0 + - - +
155A PRO* 3.6 6.2 - - - +
166A SER* 3.2 27.5 + - - -
169A LEU* 4.5 12.4 - - - +
170A ARG* 4.0 26.8 + - - -
175A VAL* 3.7 14.9 - - - +
179A THR* 5.7 0.2 - - - -
183A TYR* 4.4 12.1 - - - -
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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