Contacts of the helix formed by residues 210 - 216 (chain 1) in PDB entry 3SDI
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 TRP 210 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1761 TYR* 5.8 6.3 - + - -
1771 TYR* 4.3 14.1 - + - -
2081 MET* 3.4 50.4 + - + +
2091 LYS* 1.3 73.0 - - - +
2111 ASP* 1.3 66.6 + - - +
2121 PHE* 3.3 7.6 - - - -
2131 ALA* 2.9 24.9 + - - +
19N ARG* 6.0 2.9 - - - -
29N ARG* 3.3 66.0 - - + -
30N VAL* 4.1 8.3 - - + -
171N GLY* 3.6 22.2 - - - -
172N VAL* 3.8 13.9 - - + -
187N TYR* 3.7 51.2 - + + +
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Residues in contact with ASP 211 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2091 LYS* 4.6 1.3 - - - +
2101 TRP* 1.3 78.0 - - - +
2121 PHE* 1.3 63.6 + - + +
2131 ALA 3.1 1.8 + - - -
2141 LYS* 3.0 48.6 + - - +
144H GLN* 4.3 11.5 + - - +
187N TYR* 3.8 24.5 - - - +
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Residues in contact with PHE 212 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2091 LYS* 3.4 31.9 - - + -
2101 TRP* 3.9 8.1 - - - -
2111 ASP* 1.3 77.6 + - - +
2131 ALA* 1.3 63.9 + - - +
2141 LYS 3.1 2.0 + - - -
2151 ASP* 3.1 27.6 + - - +
2161 ILE* 3.8 7.7 + - + +
123H TYR* 3.9 29.7 - + + -
124H TYR* 3.6 30.1 - + - -
142H TRP* 3.9 34.8 - + + -
144H GLN* 4.1 14.9 - - - +
29N ARG* 3.7 18.6 - - + -
30N VAL* 3.9 29.2 - - + -
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Residues in contact with ALA 213 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2101 TRP 2.9 17.8 + - - +
2121 PHE* 1.3 81.4 - - - +
2141 LYS* 1.3 56.0 + - - +
2161 ILE* 3.2 9.7 + - - +
30N VAL* 3.7 27.1 - - + -
172N VAL* 4.0 12.1 - - + -
174N ARG* 2.7 37.8 + - - +
187N ILE* 3.8 15.3 - - - -
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Residues in contact with LYS 214 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2111 ASP* 3.0 36.6 + - - +
2121 PHE 3.1 1.6 + - - -
2131 ALA* 1.3 78.2 - - - +
2151 ASP* 1.3 84.2 + - - +
2161 ILE 3.5 3.8 + - - +
2171 LYS* 5.1 4.0 - - - +
144H GLN* 4.5 5.1 + - - +
174N ARG* 4.4 1.9 + - - +
186N ARG* 5.6 5.7 - - - -
187N ILE* 3.7 42.9 - - + +
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Residues in contact with ASP 215 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2121 PHE* 3.1 12.0 + - - +
2141 LYS* 1.3 101.3 + - - +
2161 ILE* 1.3 59.8 + - - +
2171 LYS* 2.8 36.5 + - - +
123H TYR* 2.9 27.8 + - - +
144H GLN* 3.1 24.3 - - - +
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Residues in contact with ILE 216 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2121 PHE* 4.1 9.6 - - + +
2131 ALA 3.2 9.9 + - - +
2141 LYS 4.4 2.2 - - - +
2151 ASP* 1.3 76.9 - - - +
2171 LYS* 1.3 64.0 + - - +
2181 GLY 4.7 2.2 - - - +
121H VAL* 4.2 24.9 - - + +
122H GLY* 4.1 23.8 - - - -
123H TYR* 3.9 31.0 - - + +
28N ASN* 6.2 0.2 - - - +
30N VAL* 3.5 44.4 - - + +
31N THR* 5.4 0.2 - - - -
32N ASP* 4.2 6.9 - - - +
174N ARG* 3.4 23.3 + - - +
186N ARG* 5.3 2.1 - - - -
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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