Contacts of the helix formed by residues 140 - 150 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C ARG* 6.0 1.6 - - - +
135C PRO* 3.6 21.9 - - + +
136C CYS* 2.5 21.4 + - + +
139C GLN* 1.3 77.1 - - + +
141C TYR* 1.3 58.3 + - - +
142C GLN 3.6 1.1 - - - -
143C GLN* 4.0 20.2 - - + +
144C PHE* 2.8 29.0 + - - +
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Residues in contact with TYR 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C CYS 3.8 0.6 + - - -
137C VAL 4.1 8.5 - - - +
138C LEU 3.9 4.9 + - - +
139C GLN 3.6 4.0 + - - -
140C GLU* 1.3 71.4 - - - +
142C GLN* 1.3 85.4 + - - +
143C GLN* 4.4 0.4 + - - -
144C PHE* 2.7 24.7 + + - -
145C ARG* 2.2 92.9 + - + +
226C LEU 3.2 22.9 - - - -
227C GLU* 3.7 10.8 + - + +
230C HIS* 3.4 33.7 - + + -
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Residues in contact with GLN 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C GLU 3.6 0.4 - - - -
141C TYR* 1.3 98.1 - - - +
143C GLN* 1.3 75.4 + - - +
145C ARG* 2.9 17.8 + - + +
146C GLU* 2.9 27.8 + - + +
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Residues in contact with GLN 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PRO* 3.9 16.8 - - + -
140C GLU* 3.8 23.3 - - + +
141C TYR 4.4 0.2 + - - -
142C GLN* 1.3 89.7 + - - +
144C PHE* 1.3 52.2 + - - +
146C GLU* 3.8 3.2 - - - +
147C ASN* 2.8 34.0 + - - +
150C ARG* 5.0 1.4 + - - +
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Residues in contact with PHE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PRO* 3.4 26.6 - - + +
137C VAL* 3.5 29.6 - - + -
140C GLU 2.8 20.6 + - - +
141C TYR* 2.7 31.0 + + - -
143C GLN* 1.3 71.5 - - - +
145C ARG* 1.3 72.2 + - - +
147C ASN* 3.3 2.4 - - - +
148C VAL* 3.3 25.4 + - + +
170C PHE 3.3 23.6 - - - -
171C PHE* 4.0 15.3 - + - -
226C LEU* 3.7 34.8 - - + -
229C CYS* 3.5 25.4 - - + -
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Residues in contact with ARG 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C TYR* 2.2 74.6 + - + +
142C GLN* 3.3 21.1 - - + +
144C PHE* 1.3 82.0 - - - +
146C GLU* 1.3 61.5 + - - +
148C VAL* 3.4 2.6 + - - +
149C LEU* 3.1 40.4 + - + +
200C ALA 5.9 1.8 + - - -
224C ASP* 3.0 28.0 + - - -
226C LEU* 3.6 25.0 - - + +
227C GLU* 3.5 19.5 - - - +
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Residues in contact with GLU 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C GLN* 2.9 19.6 + - + +
143C GLN* 4.0 2.7 - - - +
145C ARG* 1.3 72.3 - - - +
147C ASN* 1.3 68.8 + - - +
148C VAL 3.0 0.2 + - - -
149C LEU* 4.3 6.5 - - + +
150C ARG* 2.9 66.3 + - + +
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Residues in contact with ASN 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C GLY* 3.6 10.2 - - - -
135C PRO* 3.0 25.9 - - + +
143C GLN 2.8 18.7 + - - +
144C PHE* 3.3 10.5 - - - +
146C GLU* 1.3 78.2 - - - +
148C VAL* 1.3 60.4 + - - +
150C ARG* 3.7 14.8 + - - +
151C ASN* 2.9 33.8 + - - +
169C ARG 3.9 2.7 + - - +
170C PHE* 3.7 17.4 - - - -
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Residues in contact with VAL 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 3.3 30.9 + - + +
145C ARG 3.8 5.6 - - - +
146C GLU 3.1 0.4 - - - -
147C ASN* 1.3 77.0 - - + +
149C LEU* 1.3 67.2 + - + +
151C ASN* 3.1 14.7 + - - +
152C LEU* 3.3 10.3 - - + +
157C PHE* 3.9 23.0 - - + -
170C PHE* 3.4 36.1 - - + -
171C PHE* 4.4 7.2 - - + -
198C LEU* 4.3 14.1 - - + -
226C LEU* 4.3 16.6 - - + -
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Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ARG* 3.1 36.6 + - + +
146C GLU* 3.1 8.6 + - + +
148C VAL* 1.3 77.0 - - + +
150C ARG* 1.3 59.1 + - + +
151C ASN 3.2 3.8 + - - -
152C LEU* 3.4 34.2 + - + +
198C LEU* 4.5 18.4 - - + +
200C ALA 5.5 8.7 - - - +
226C LEU* 3.5 28.9 - - + -
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Residues in contact with ARG 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C GLN 5.0 1.2 + - - -
146C GLU* 2.9 50.2 + - + +
147C ASN* 3.7 26.2 + - - +
149C LEU* 1.3 75.9 - - + +
151C ASN* 1.3 72.6 + - - +
152C LEU 3.8 1.3 - - - -
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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