Contacts of the helix formed by residues 145 - 152 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141R ILE 2.9 16.6 + - - -
142R GLN 4.2 1.5 + - - -
143R LYS 3.6 1.4 - - - -
144R VAL* 1.3 82.7 - - - +
146R LEU* 1.3 66.8 + - - -
147R GLU 3.3 2.6 + - - -
148R ASN 3.4 1.0 + - - -
149R TYR* 3.1 21.5 + - - +
147T GLU* 3.8 14.8 + - - -
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Residues in contact with LEU 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143P LYS 5.4 1.1 - - - +
83R THR* 5.4 1.1 - - - -
84R GLN* 3.8 46.4 - - + +
141R ILE* 3.6 27.7 + - + +
145R GLY* 1.3 72.1 - - - -
147R GLU* 1.3 70.0 + - + +
149R TYR* 3.0 4.2 + - + -
150R LEU* 3.0 47.6 + - + +
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Residues in contact with GLU 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142P GLN 4.6 3.8 - - - +
143P LYS 3.5 23.2 - - - +
144P VAL* 3.5 24.0 - - - +
145P GLY* 3.6 20.1 + - - -
148P ASN* 3.7 8.8 + - - +
145R GLY 3.3 0.6 - - - -
146R LEU* 1.3 83.3 - - + +
148R ASN* 1.3 59.1 + - - +
150R LEU* 3.5 1.1 + - - +
151R GLN* 3.0 27.5 + - - +
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Residues in contact with ASN 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N K 3.0 18.4 - - - -
148P ASN* 3.1 14.2 + - - +
144R VAL* 3.2 30.9 + - + +
145R GLY 3.4 1.0 + - - +
146R LEU 3.3 0.4 - - - -
147R GLU* 1.3 76.4 - - - +
149R TYR* 1.3 59.1 + - - +
151R GLN* 3.2 0.7 + - - +
152R SER* 2.9 18.4 + - - -
147T GLU* 3.5 23.2 + - - +
148T ASN* 3.1 20.7 + - - +
151T GLN* 2.8 35.6 + - - +
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Residues in contact with TYR 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R LEU* 3.9 16.1 - - + +
83R THR* 4.3 15.3 - - + -
87R LEU* 4.2 1.6 - - + +
137R GLN* 2.6 61.6 + - + +
140R LEU* 4.0 21.8 - - + -
141R ILE* 3.6 31.6 - - + -
144R VAL* 4.0 8.7 - - + -
145R GLY 3.1 16.8 + - - +
146R LEU* 3.0 6.1 + - + +
148R ASN* 1.3 76.2 - - - +
150R LEU* 1.3 74.1 + - + +
152R SER* 3.2 8.5 + - - -
153R HIS* 2.8 51.1 + + - -
154T MET* 4.4 6.1 - - + -
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Residues in contact with LEU 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143P LYS* 3.8 37.7 - - + +
144P VAL* 3.9 9.9 - - + -
37R LEU* 3.4 30.2 - - + +
40R LEU* 4.6 2.2 - - + -
83R THR* 3.3 39.3 - - + +
84R GLN* 5.8 0.7 - - - +
146R LEU* 3.0 37.9 + - + +
147R GLU 3.9 2.7 - - - +
149R TYR* 1.3 80.2 - - + +
151R GLN* 1.3 66.8 + - - +
153R HIS* 2.9 12.5 + - - +
154R MET* 3.2 9.4 + - - +
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Residues in contact with GLN 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N K 2.9 15.1 - - - -
144P VAL* 3.8 10.9 - - + +
148P ASN* 3.0 38.8 + - + +
151P GLN* 2.6 29.2 + - - +
152P SER* 3.1 23.4 + - - +
147R GLU 3.0 15.5 + - - +
148R ASN 3.2 6.5 + - - +
150R LEU* 1.3 78.1 - - - +
152R SER* 1.3 60.7 + - - +
153R HIS 3.1 1.2 + - - -
154R MET* 3.2 21.5 + - - +
155R HIS* 4.8 2.6 + - - -
151T GLN* 2.8 24.7 + - - +
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Residues in contact with SER 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39R ARG* 3.4 9.9 + - - -
148R ASN 2.9 7.9 + - - -
149R TYR 3.5 9.6 - - - -
150R LEU 3.2 0.2 - - - -
151R GLN* 1.3 75.4 - - - +
153R HIS* 1.3 58.2 + - - +
154R MET 3.6 0.4 - - - -
155R HIS 4.5 2.2 + - - +
151T GLN* 3.0 36.8 + - - +
154T MET* 3.8 24.6 - - - +
155T HIS* 3.3 26.6 - - - -
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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