Contacts of the helix formed by residues 140 - 150 (chain A) in PDB entry 5ITY
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 GLU 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ARG* 2.9 27.3 + - - -
135A PRO* 3.3 12.8 - - + +
136A CYS* 2.8 38.8 + - + +
139A GLN* 1.3 84.0 - - - +
141A TYR* 1.3 64.6 + - - +
142A GLN 3.3 2.5 - - - -
143A GLN* 3.1 35.8 + - - +
144A PHE* 2.8 20.3 + - - +
139B GLN* 5.7 1.9 + - - -
234B LYS* 5.1 1.3 - - - +
501B GOL 3.7 26.4 + - - +
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Residues in contact with TYR 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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136A CYS 3.7 2.6 + - - -
137A VAL 4.3 2.0 + - - -
139A GLN 3.7 2.4 + - - -
140A GLU* 1.3 74.6 - - - +
142A GLN* 1.3 85.1 + - + +
144A PHE* 3.1 20.3 + + - +
145A ARG* 2.7 66.5 + - + +
226A LEU 3.4 22.7 - - - -
227A GLU* 3.6 20.8 + - + +
230A HIS* 3.6 46.0 - + + +
234B LYS* 5.0 7.2 - - - +
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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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140A GLU 3.3 0.6 - - - -
141A TYR* 1.3 99.6 - - + +
143A GLN* 1.3 59.9 + - + +
145A ARG* 3.2 18.9 + - - +
146A GLU* 2.8 54.3 + - - +
234B LYS* 6.0 2.6 - - - +
238B GLN* 3.4 46.4 - - + +
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Residues in contact with GLN 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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135A PRO* 3.6 17.6 - - + +
140A GLU* 3.1 41.9 + - - +
142A GLN* 1.3 79.5 - - + +
144A PHE* 1.3 56.5 + - - +
146A GLU* 3.7 6.0 - - - +
147A ASN* 2.8 33.8 + - - +
150A ARG* 4.0 4.5 + - - +
8B HIS* 6.5 1.6 - - - -
139B GLN* 5.2 10.8 + - - +
501B GOL 5.6 0.3 + - - -
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Residues in contact with PHE 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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135A PRO* 3.6 27.0 - - + +
136A CYS 4.1 5.4 - - - +
137A VAL* 3.6 26.9 - - + -
140A GLU 2.8 13.2 + - - +
141A TYR* 3.3 23.8 - + - +
143A GLN* 1.3 78.3 - - - +
145A ARG* 1.3 70.7 + - - +
147A ASN* 3.4 2.1 + - - +
148A VAL* 3.1 26.7 + - + +
170A PHE 3.1 28.4 - - - +
171A PHE* 3.7 11.7 - + - -
226A LEU* 3.6 43.5 - - + -
229A CYS* 3.6 25.1 - - + -
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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 TYR* 2.7 63.4 + - + +
142A GLN* 3.6 20.4 - - - +
144A PHE* 1.3 77.1 - - + +
146A GLU* 1.3 63.7 + - + +
148A VAL* 3.1 5.1 + - - +
149A LEU* 3.0 38.1 + - + +
201A LEU* 3.7 21.2 + - - +
202A GLN 5.4 1.4 - - - -
224A ASP* 2.5 43.8 + - - -
226A LEU* 3.5 25.6 - - + +
227A GLU* 3.6 2.4 + - - +
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Residues in contact with GLU 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* 2.8 47.0 + - - +
143A GLN* 3.8 5.8 - - - +
145A ARG* 1.3 71.6 - - + +
147A ASN* 1.3 62.8 + - - +
149A LEU* 3.0 6.4 + - - -
150A ARG* 2.8 46.2 + - + +
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Residues in contact with ASN 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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134A GLY* 4.4 0.6 - - - -
135A PRO* 4.0 19.8 - - + +
143A GLN 2.8 21.7 + - - +
144A PHE 3.8 4.0 - - - +
146A GLU* 1.3 73.6 - - - +
148A VAL* 1.3 62.1 + - - +
150A ARG* 3.1 31.9 - - - +
151A ASN* 2.9 33.7 + - - +
169A ARG 3.5 20.6 - - - +
170A PHE* 3.6 15.8 - - - +
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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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144A PHE* 3.1 24.8 + - + +
145A ARG 3.1 7.2 + - - +
146A GLU 3.1 0.8 - - - -
147A ASN* 1.3 77.0 - - - +
149A LEU* 1.3 60.7 + - + +
151A ASN* 2.9 19.8 + - - +
152A LEU* 3.6 21.7 + - + +
157A PHE* 4.0 20.9 - - + -
170A PHE* 3.6 36.3 - - + +
171A PHE* 4.2 9.4 - - + -
198A LEU* 4.6 5.4 - - + -
226A LEU* 4.3 22.4 - - + -
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Residues in contact with LEU 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 45.6 + - + +
146A GLU* 3.9 4.7 - - - +
148A VAL* 1.3 78.4 - - + +
150A ARG* 1.3 59.0 + - - +
151A ASN 3.1 1.4 + - - -
152A LEU* 3.9 18.0 + - + +
198A LEU* 4.1 20.4 - - + +
201A LEU* 4.5 5.4 - - + -
202A GLN* 4.2 46.2 + - + +
226A LEU* 3.9 18.4 - - + -
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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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135A PRO* 5.9 0.4 - - - +
143A GLN* 4.0 5.3 + - - +
146A GLU* 2.8 32.6 + - + +
147A ASN* 3.1 51.8 - - - +
149A LEU* 1.3 70.5 - - - +
151A ASN* 1.3 78.1 + - - +
152A LEU 3.8 0.7 - - - -
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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