Contacts of the helix formed by residues 145 - 152 (chain V) in PDB entry 3IS7
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 GLY 145 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147Q GLU* 3.7 14.5 + - - -
141V ILE 3.0 17.4 + - - -
142V GLN 4.0 2.8 + - - -
143V LYS 3.5 2.2 - - - -
144V VAL* 1.3 83.0 - - - +
146V LEU* 1.3 66.3 - - - -
147V GLU 3.3 3.0 + - - -
148V ASN 3.4 0.8 + - - -
149V TYR* 3.0 19.2 + - - +
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Residues in contact with LEU 146 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E LYS 5.5 1.6 - - - +
83V THR* 5.4 0.9 - - - -
84V GLN* 4.6 20.0 - - + +
141V ILE* 3.6 39.1 + - + +
145V GLY* 1.3 70.7 - - - -
147V GLU* 1.3 66.7 + - + +
149V TYR* 3.1 2.7 + - - +
150V LEU* 2.9 56.5 + - + +
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Residues in contact with GLU 147 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E GLN 5.4 1.2 - - - +
143E LYS 4.0 15.4 - - - +
144E VAL* 3.0 31.4 - - - +
145E GLY* 3.8 14.9 + - - -
148E ASN* 3.6 10.3 + - - +
145V GLY 3.3 1.0 - - - -
146V LEU* 1.3 82.3 - - + +
148V ASN* 1.3 57.6 + - - +
150V LEU 3.5 0.3 + - - -
151V GLN* 2.9 28.6 + - - +
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Residues in contact with ASN 148 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E ASN* 3.0 21.1 + - - +
159E K 3.0 11.4 - - - -
147Q GLU* 3.6 22.1 + - - +
148Q ASN* 3.0 22.2 + - - +
151Q GLN* 2.8 38.7 + - - +
144V VAL* 3.1 32.7 + - + +
145V GLY 3.4 0.4 + - - -
146V LEU 3.3 0.2 - - - -
147V GLU* 1.3 76.8 - - - +
149V TYR* 1.3 64.8 + - - +
151V GLN 3.3 0.5 + - - -
152V SER* 3.0 11.8 + - - -
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Residues in contact with TYR 149 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154Q MET* 4.3 6.5 - - + -
40V LEU* 3.8 18.4 - - + +
83V THR* 4.3 14.8 - - + -
87V LEU* 4.2 2.8 - - + +
137V GLN* 2.5 58.3 + - + +
140V LEU* 4.0 21.1 - - + -
141V ILE* 3.6 33.0 - - + -
144V VAL* 3.7 10.5 - - + +
145V GLY 3.0 18.0 + - - +
146V LEU* 3.1 3.8 + - + +
148V ASN* 1.3 77.6 - - - +
150V LEU* 1.3 71.7 + - + +
152V SER* 3.3 5.8 + - - -
153V HIS* 2.8 51.7 + + - -
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Residues in contact with LEU 150 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E LYS* 3.7 35.4 - - + +
144E VAL* 3.8 14.6 - - + -
37V LEU* 3.5 24.4 - - + +
40V LEU* 4.7 2.2 - - + -
83V THR* 3.7 39.5 - - + +
146V LEU* 2.9 42.2 + - + +
147V GLU 3.9 0.2 - - - +
149V TYR* 1.3 79.8 - - + +
151V GLN* 1.3 57.9 + - - +
153V HIS* 2.7 24.8 + - - -
154V MET* 3.3 8.0 + - - +
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Residues in contact with GLN 151 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E VAL* 3.6 14.2 - - + +
148E ASN* 2.8 40.7 + - + +
151E GLN* 2.8 24.8 + - - +
152E SER* 2.9 25.9 + - - +
159E K 2.9 20.8 - - - -
151Q GLN* 2.9 15.1 + - - +
147V GLU 2.9 18.9 + - - +
148V ASN 3.3 2.7 + - - +
150V LEU* 1.3 76.8 - - - +
152V SER* 1.3 59.7 + - - +
153V HIS 3.0 1.6 + - - -
154V MET* 3.3 21.8 + - - +
155V HIS* 4.8 2.1 + - - -
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Residues in contact with SER 152 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151Q GLN* 2.7 38.9 + - - +
154Q MET* 4.2 11.4 - - - -
155Q HIS* 3.4 32.3 + - - -
39V ARG* 3.7 6.4 + - - -
148V ASN 3.0 9.9 + - - -
149V TYR 3.6 7.0 - - - -
150V LEU 3.1 0.4 - - - -
151V GLN* 1.3 74.7 - - - +
153V HIS* 1.3 65.1 + - - +
154V MET 3.5 0.7 - - - -
155V HIS 4.7 2.6 - - - +
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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