Contacts of the strand formed by residues 113 - 117 (chain 1) in PDB entry 5NER
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 THR 113 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781 VAL 3.5 1.6 - - - +
791 ALA* 3.4 0.9 - - - -
801 VAL* 2.9 27.4 + - - +
821 HIS* 3.5 23.5 + - - -
861 LEU* 5.2 0.7 - - - -
1061 ALA* 3.9 19.7 - - + -
1071 TYR 4.5 3.6 + - - +
1091 LYS* 4.0 13.9 + - - +
1121 LEU* 1.3 84.9 + - - +
1141 ARG* 1.3 63.5 + - - +
1151 LEU* 3.6 25.9 - - + +
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Residues in contact with ARG 114 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 PHE* 3.8 14.6 - - + -
771 GLU* 2.1 33.4 + - + +
781 VAL 2.9 10.3 - - - +
791 ALA* 4.3 11.0 - - + -
1121 LEU* 4.5 7.3 - - + +
1131 THR* 1.3 76.5 - - - +
1151 LEU* 1.3 63.8 + - - +
1791 ARG* 4.6 0.8 - - - +
143 LEU* 3.4 30.6 - - - +
183 ASP* 3.5 21.8 + - - -
203 LYS* 3.2 29.3 + - - +
213 THR 4.7 2.0 - - - -
223 ALA* 3.8 22.9 - - + +
233 ASP* 4.2 8.1 + - - +
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Residues in contact with LEU 115 (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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771 GLU* 3.3 4.3 - - - +
781 VAL* 2.8 46.4 + - + +
801 VAL* 5.5 1.1 - - + -
861 LEU* 4.2 20.6 - - + +
881 TRP* 5.0 11.9 - - + -
1041 PRO* 5.6 5.6 - - + +
1051 THR 6.3 0.2 - - - -
1061 ALA* 4.6 13.2 - - + +
1131 THR* 3.6 35.4 - - + +
1141 ARG* 1.3 75.6 - - - +
1161 ALA* 1.3 60.5 + - - +
1171 LEU* 3.8 24.4 + - + +
223 ALA* 3.6 4.7 - - - -
233 ASP 4.0 5.6 - - - +
253 ALA* 4.4 18.2 - - + -
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Residues in contact with ALA 116 (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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761 LEU 3.8 4.3 - - - +
771 GLU* 4.4 4.5 - - + +
1151 LEU* 1.3 71.0 - - - +
1171 LEU* 1.3 65.8 + - - +
1181 PRO* 4.2 4.0 - - - +
1811 LYS* 6.1 1.1 - - - +
223 ALA* 3.6 10.0 - - + +
233 ASP 3.1 22.3 + - - +
243 PRO* 4.2 4.2 - - + +
253 ALA* 3.9 17.3 + - - +
263 TYR* 5.2 0.9 + - - +
314 GLN* 3.9 33.5 - - - +
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Residues in contact with LEU 117 (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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511 LEU* 3.6 22.9 - - + -
751 ASP* 3.8 4.2 - - - +
761 LEU* 2.6 52.2 + - + +
781 VAL* 3.5 30.5 - - + -
881 TRP* 3.7 43.7 - - + +
1151 LEU* 4.3 26.0 - - + +
1161 ALA* 1.3 80.1 - - - +
1181 PRO* 1.3 70.2 - - + +
1651 TYR* 6.2 2.2 - - + -
1681 ILE* 5.4 1.3 - - + -
253 ALA* 5.1 4.7 - - + -
263 TYR* 6.0 0.4 - - + -
314 GLN 5.8 2.2 - - - -
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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