Contacts of the strand formed by residues 184 - 192 (chain H) 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 ALA 184 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLY* 2.9 38.8 - - + +
39H PRO 3.5 24.5 - - - +
40H LYS* 4.3 7.3 - - + +
42H TRP* 3.9 9.9 - - - +
104H VAL* 6.5 0.2 - - - -
176H CYS* 4.5 2.5 - - - -
177H VAL 3.4 5.8 - - - +
178H MET* 3.9 27.6 - - + +
182H LYS 3.9 0.8 + - - -
183H ASP* 1.3 72.2 - - - +
185H GLU* 1.3 60.1 + - - +
186H TYR 4.0 0.2 - - - -
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Residues in contact with GLU 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A THR* 3.5 16.9 - - - +
148H LYS* 3.2 31.2 + - - -
175H VAL 4.1 0.2 - - - +
176H CYS* 3.3 4.3 - - - -
177H VAL* 2.7 56.8 + - + +
182H LYS* 5.0 7.2 + - - -
183H ASP 3.6 4.9 + - - +
184H ALA* 1.3 72.8 - - - +
186H TYR* 1.3 62.5 + - - +
187H LEU* 3.6 26.5 + - + +
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Residues in contact with TYR 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A THR* 3.0 76.2 - + + +
32H ALA* 3.5 20.6 - - - +
34H LEU* 3.9 30.6 + - + -
42H TRP* 3.5 36.1 - + + -
174H ASP* 4.3 3.2 + - + -
175H VAL 3.8 7.4 - - - -
176H CYS* 4.1 7.4 - - + -
184H ALA 4.0 0.8 + - - -
185H GLU* 1.3 70.9 - - - +
187H LEU* 1.3 66.5 + - - +
189H ARG* 3.4 44.2 + - + -
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Residues in contact with LEU 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H ILE* 4.7 7.6 - - + -
174H ASP* 3.6 0.7 - - - -
175H VAL* 2.7 42.3 + - + +
177H VAL* 4.1 24.7 - - + -
185H GLU* 4.0 27.1 - - + +
186H TYR* 1.3 79.8 - - - +
189H ARG* 1.3 65.9 + - - +
191H TYR* 3.6 39.7 + - + -
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Residues in contact with ARG 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLY 5.5 4.2 + - - +
30H ASN* 2.6 44.5 + - - +
31H CYS* 3.0 20.2 + - - +
32H ALA* 3.3 14.1 - - - +
174H ASP* 2.8 33.8 + - - -
186H TYR* 3.4 38.1 + - + -
187H LEU* 1.3 69.9 - - - +
190H ASN* 1.3 85.3 + - + +
191H TYR* 3.2 1.4 + - - -
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Residues in contact with ASN 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ASN* 2.8 41.1 + - - -
172H ASN* 3.9 12.0 + - - +
173H VAL 3.5 4.0 - - - -
174H ASP* 2.9 27.8 + - - +
189H ARG* 1.3 85.0 + - + +
191H TYR* 1.3 63.6 + - - +
192H LEU 3.2 5.1 + - - -
193H THR* 3.6 22.9 - - + +
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Residues in contact with TYR 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152H ILE* 3.5 31.7 - - + +
153H LYS* 5.4 1.6 + - - -
156H SER* 4.0 21.8 - - - -
173H VAL* 2.9 12.7 + - + +
175H VAL* 3.9 19.1 - - + -
187H LEU* 3.6 40.1 + - + +
189H ARG 3.2 4.0 - - - -
190H ASN* 1.3 75.7 - - - +
192H LEU* 1.3 72.4 + - + +
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Residues in contact with LEU 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H SER* 3.4 25.4 - - - +
160H GLN* 3.5 28.3 - - - +
172H ASN* 3.3 4.0 - - - +
173H VAL* 3.1 42.0 + - + +
190H ASN 4.1 0.3 - - - -
191H TYR* 1.3 90.2 - - + +
193H THR* 1.3 72.3 + - - +
194H PRO* 3.8 11.0 - - + -
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Residues in contact with THR 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H ASN* 3.2 23.1 - - - +
190H ASN* 3.6 32.1 + - + +
192H LEU* 1.3 81.7 - - - +
194H PRO* 1.3 63.6 - - - +
195H ASN 3.4 3.3 + - - -
196H VAL* 4.0 17.6 - - - +
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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