Contacts of the helix formed by residues 189 - 195 (chain I) in PDB entry 1SXG
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 189 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I TYR* 5.3 1.2 + - - -
100I GLN* 5.0 7.1 - - - +
124I SER 5.2 0.7 - - - +
125I GLY* 3.0 34.8 - - - +
126I ASN* 4.1 9.1 - - + +
186I THR* 3.3 26.0 + - - +
187I LEU 3.1 1.0 - - - -
188I GLU* 1.3 79.1 - - + +
190I PRO* 1.3 71.4 - - - +
191I ILE* 3.1 14.9 - - + +
192I ASN* 2.8 15.6 + - - +
193I HIS* 3.1 11.2 + - - -
221I TYR* 2.6 35.7 + - - -
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Residues in contact with PRO 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I GLY 3.8 5.4 - - - +
126I ASN* 3.5 34.3 - - - +
127I VAL 4.8 3.8 - - - +
148I ILE* 4.2 26.5 - - + +
149I GLU* 6.1 0.9 - - - -
150I SER* 5.4 9.0 - - - +
188I GLU 3.8 2.7 - - - +
189I GLU* 1.3 80.7 - - - +
191I ILE* 1.3 62.3 + - + +
193I HIS* 3.3 20.0 - - + +
194I ALA* 2.7 40.7 + - + +
195I LYS* 4.4 0.2 - - - +
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Residues in contact with ILE 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I GLY* 4.2 8.3 - - - +
147I SER* 6.4 0.7 - - - -
148I ILE* 3.8 18.5 - - + +
161I TYR* 3.2 54.5 - - + -
189I GLU* 3.5 30.3 - - + +
190I PRO* 1.3 80.3 - - + +
192I ASN* 1.3 66.4 + - - +
195I LYS* 3.3 6.6 + - + -
196I LYS* 2.9 45.3 + - - +
221I TYR* 4.6 0.9 - - - +
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Residues in contact with ASN 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I SER* 3.4 24.0 + - - +
185I GLY* 3.1 12.0 - - - +
186I THR 2.8 26.2 - - - +
187I LEU* 4.3 4.0 - - + -
189I GLU* 2.8 9.9 + - - +
191I ILE* 1.3 81.1 - - - +
193I HIS* 1.3 62.9 + - - +
196I LYS* 3.4 32.8 + - - +
197I VAL* 2.9 32.1 + - - +
221I TYR* 2.8 27.8 + - - -
246I GLY* 6.0 0.2 - - - -
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Residues in contact with HIS 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I LEU* 2.7 35.6 + - + +
188I GLU* 3.3 18.2 - - - -
189I GLU 3.1 9.1 + - - -
190I PRO* 3.3 27.2 - - + +
192I ASN* 1.3 79.1 - - - +
194I ALA* 1.3 78.0 + - + +
197I VAL* 3.0 23.3 - - + +
198I LYS* 3.2 16.6 - - - +
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Residues in contact with ALA 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I ILE* 5.4 0.7 - - + -
150I SER* 6.1 0.9 - - - +
162I GLU* 5.1 0.5 - - - +
190I PRO* 2.7 28.2 + - + +
193I HIS* 1.3 90.0 - - + +
195I LYS* 1.3 80.3 + - - +
198I LYS* 3.7 27.6 + - - +
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Residues in contact with LYS 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I ILE* 3.7 35.7 - - + +
150I SER* 6.2 1.8 - - - +
161I TYR* 4.0 10.8 - - + -
162I GLU* 3.4 41.2 - - + +
191I ILE* 3.3 12.3 + - + +
193I HIS 3.5 0.6 - - - -
194I ALA* 1.3 98.8 - - + +
196I LYS* 1.3 64.1 + - - +
197I VAL 3.6 0.7 - - - -
198I LYS* 3.5 1.2 + - - +
199I GLY 2.8 23.8 + - - -
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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